Monthly Archives: June 2022

An evolutionary tree, or phylogenetic tree, is a branching diagram showing the evolutionary relationships among various biological species based upon similarities and differences in their characteristics. Historically, this was done using their physical characteristics the similarities and differences in various species anatomies.

However, advances in genetic technology now enable biologists to use genetic data to decipher evolutionary relationships. According to a new study, scientists are finding that the molecular data is leading to much different results, sometimes overturning centuries of scientific work in classifying species by physical traits.

It means that convergent evolution has been fooling us even the cleverest evolutionary biologists and anatomists for over 100 years! Matthew Wills

Since Darwin and his contemporaries in the 19th Century, biologists have been trying to reconstruct the family trees of animals by carefully examining differences in their anatomy and structure (morphology).

However, with the development of rapid genetic sequencing techniques, biologists are now able to use genetic (molecular) data to help piece together evolutionary relationships for species very quickly and cheaply, often proving that organisms we once thought were closely related actually belong in completely different branches of the tree.

For the first time, scientists at Bath compared evolutionary trees based on morphology with those based on molecular data, and mapped them according to geographical location.

They found that the animals grouped together by molecular trees lived more closely together geographically than the animals grouped using the morphological trees.

Matthew Wills, Professor of Evolutionary Paleobiology at the Milner Center for Evolution at the University of Bath, said: It turns out that weve got lots of our evolutionary trees wrong.

For over a hundred years, weve been classifying organisms according to how they look and are put together anatomically, but molecular data often tells us a rather different story.

Our study proves statistically that if you build an evolutionary tree of animals based on their molecular data, it often fits much better with their geographical distribution.

Where things live their biogeography is an important source of evolutionary evidence that was familiar to Darwin and his contemporaries.

For example, tiny elephant shrews, aardvarks, elephants, golden moles, and swimming manatees have all come from the same big branch of mammal evolution despite the fact that they look completely different from one another (and live in very different ways).

Molecular trees have put them all together in a group called Afrotheria, so-called because they all come from the African continent, so the group matches the biogeography.

Molecular evolutionary trees show that elephant shrews are more closely related to elephants, than they are to shrews. Credit: Danny Ye

The study found that convergent evolution when a characteristic evolves separately in two genetically unrelated groups of organisms is much more common than biologists previously thought.

Professor Wills said: We already have lots of famous examples of convergent evolution, such as flight evolving separately in birds, bats, and insects, or complex camera eyes evolving separately in squid and humans.

But now with molecular data, we can see that convergent evolution happens all the time things we thought were closely related often turn out to be far apart on the tree of life.

People who make a living as lookalikes arent usually related to the celebrity theyre impersonating, and individuals within a family dont always look similar its the same with evolutionary trees too.

It proves that evolution just keeps on re-inventing things, coming up with a similar solution each time the problem is encountered in a different branch of the evolutionary tree.

It means that convergent evolution has been fooling us even the cleverest evolutionary biologists and anatomists for over 100 years!

Dr. Jack Oyston, Research Associate and first author of the paper, said: The idea that biogeography can reflect evolutionary history was a large part of what prompted Darwin to develop his theory of evolution through natural selection, so its pretty surprising that it hadnt really been considered directly as a way of testing the accuracy of evolutionary trees in this way before now.

Whats most exciting is that we find strong statistical proof of molecular trees fitting better not just in groups like Afrotheria, but across the tree of life in birds, reptiles, insects, and plants too.

It being such a widespread pattern makes it much more potentially useful as a general test of different evolutionary trees, but it also shows just how pervasive convergent evolution has been when it comes to misleading us.

Reference: Molecular phylogenies map to biogeography better than morphological ones by Jack W. Oyston, Mark Wilkinson, Marcello Ruta and Matthew A. Wills, 31 May 2022, Communications Biology.DOI: 10.1038/s42003-022-03482-x

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Convergent Evolution Has Been Fooling Us: Most of Our Evolutionary Trees Could Be Wrong - SciTechDaily

IBM CEO Arvind Krishna says that technology can help mitigate inflation. He sees the development of hybrid cloud and artificial intelligence (AI) at the nexus of the next wave of technology productivity and development.

We have inflation, we have demographic shifts because we dont have enough people. We have geopolitical instability, you sort of put all these together, Krishna said at TheSix Five Summit, a virtual event presented by Futurum Research and Moor Insights & Strategy.

Krishna, a self-professed engineering nerd, drew on the very history of the semiconductor industry itself as a point of perspective.

If you draw a graph of semiconductor productivity so think of that as how many transistors a dollar buys you and you draw global GDP [Gross Domestic Product], the curves look almost identical.

Krishna claims that the causal inference is undeniable: productivity is driven by technology. Human capital isnt scalable at the same rate the cloud is, he said.

To overcome this limitation, Krishna believes strongly that the next wave of tech-driven productivity is based around two emergent technologies: the hybrid cloud, and AI.

As a practical example, Krishna points to AIs role in cybersecurity. He recounted IBMs recent experience providing the technology for the Masters Tournament golf championship.

A four-day sporting event, 40 million attacks happened in those four days. IBM used a fraction of the security analysts they would have needed previously, thanks to AI, he said. Technology is getting rid of the inflation, just to make a simple point.

Seamless, instant, zero-touch network automation is held as the key to the ultimate success of any solution dependent on navigating the increasingly complicated hybrid cloud landscape. Here Krishna says AI will play a vital role.

Everyone wants to use multiple public clouds, said Krishna. People are still going to use on-premise. People are going to worry about [data] sovereignty. People want flexibility of deployment, and they want speed, and they want value.

To process all of that, AI is necessary, he said.

We generate two and a half quintillion bytes of data every day, he said. Thats two and a half with 18 zeroes after it. We know of no other technology that can digest and process that much data but AI.

In February, IBM announced ahybrid cloud partnershipwith enterprise software firm SAP. The businesses want to help enterprise customers move their enterprise resource planning (ERP) operations to the cloud. SAP has designated IBM a premium supplier of its RISE with SAP service.

IBMs hybrid cloud strategy has been foundational to the companys business efforts ever since its 2018 acquisition of Red Hat. In 2021, IBM spun off its GTS managed services business to become Kyndryl.

In 2020 IBM announced IBM Cloud for Telecommunications, a hybrid cloud service built on an open architecture. IBM Cloud for Telecommunications incorporates IBM Cloud Satellite and Red Hat OpenShift for flexible cloud-based service delivery, and integrates IBMs Edge Application Manager and Telco Network Cloud Manager.

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Hybrid cloud and AI will drive tech's evolution IBM CEO - RCR Wireless News

Identifying sex-linked regions in schistosomes and nematodes

To systematically identify the sex-linked regions in each ofthese two deeply diverged phyla, we compiled sexual system information as well as publishedgenomic (references shown inSupplementary Data1) and transcriptomic (Supplementary Data2) data from sexed individuals (when available) for 13 platyhelminths and 41 nematodesspecies (Fig.1a). Genome sequencing quality varied markedly among these published datasets (Supplementary Data1, with references of all used data included). For 11 nematodes and 3 platyhelminth species, chromosome-level genome assemblies are available, and 4 nematode chromosomal genome assemblies (from Trichuris muris in clade I, Brugia malayi in clade III, Strongyloides ratti in clade IV and C. elegans in clade V) were used as references to create chromosome assemblies from scaffold-level draft genomes of 19 other related species (Supplementary Data3; and between 60% and 99% of the sequences can be incorporated into the assemblies). Previous cytogenetic studies suggested a ZZ/ZW sex system in the ancestor of schistosomes41, and an XX/XO system in the ancestor of nematodes42,43. If extensive Y or W-linked regions of species in either phylum have become highly degenerated due to lack of recombination27,28, the X or Z-linked regions can be identified from low genomic read coverage in the heterogametic sex (females in schistosomes, and males in nematodes). Such low coverage results from substitutions accumulated in Y- or W-linked sequences, together with Y- or W-specific transposable element insertions, both of which hinder mapping of sequencing reads to their counterpart X- or Z-linked regions, plus the direct effect on coverage of large deletions28. Coverage analysis, without linkage map data for the sex chromosomes, can thus detect highly divergent sex-linked regions44, and is widely used, including in birds23, teleosts22, reptiles and theLepidoptera45. It has also previously been used to detect sex-linked regions in schistosomes20, and to identify the X-linked regions in several nematode species34,46. Our analysis looked for bimodal distributions of male or female read coverage, with separate peaks corresponding to autosomal and sex-linked regions. For all 8 species whose sex chromosomes have previously been identified, our coverage pipeline yielded results in agreement with the published ones33,34,46,47,48,49,50,51, confirming that this approach is reliable (Supplementary Data1). Physically small or non-differentiated sex-linked regions, however, may not be detectable by our approach.

Among all the platyhelminthspecies studied, only the schistosome genome sequences exhibited the signature indicating presence of sex chromosomes, and (as expected since males are ZZ) it was not seen when only male reads were available (Fig.1b; Supplementary Data4). Hermaphroditic trematodes and cestodes also exhibited similar coverage for all chromosomes or a unimodal coverage distribution, again as expected. By comparing the previously identified oldest evolutionary stratum (stratum 0 or S0) of Schistosoma japonicum52 to the sex-linked region of the distantly related S. haematobium (Supplementary Fig.1), we confirmed the previous conclusion that they share the same S0 region. Therefore, recombination was first suppressed between the Z and W chromosomes in the ancestor of all schistosomes20, estimated to be about 21 MYA53, and the younger strata evolved subsequently. Our results also support previous data5,20 suggesting that gonochorism and the presence of sex-linked degenerated regions have originated only once in flatworms, with only a single ancestral linkage group having evolved to become a sex chromosome pair.

In the nematodes, different chromosomes became sex-linked in different clades. Our analyses newly identified the sex-linked regions and/or allowed the annotation of their corresponding Nigon elements in 17 species (indicated by red arrowheads in Fig.1c). This was possible for almost all of the species with the expected bimodal read coverage distributions in males (Fig.1b, Supplementary Figs.24), whereas most parthenogenetic species did not show bimodal read coverage(see below), or species with reads available only in females, or with both sexes pooled (Fig.1b, c). In addition to identifying sex-linked sequences in the homogametic sex of the species studied, we also sought to identify Y- or W-linked genes. As such genes may not be well assembled, due to the presence of repetitive sequences or very long introns, we further identified genes whose de novo assembled transcriptome sequences showed sex differences in genomic read coverage values from sexed animals (Supplementary Fig.5). Combined with genes directly assembled from genomic reads, we annotated between 6 and 219 Y-linked genes in 17 individual nematode species studied, and 48 W-linked genes for S. mansoni (Fig.1c, Supplementary Data4).

Previous studies reported translocations between sex chromosomes and autosomes in some nematode species34,36,38. Our findings confirm these results, but also identify new translocations, and we now characterise the order and timing of these rearrangements in relation to the phylogenetic relationships, demonstrating independent events over a broad evolutionary time scale (Fig.2).

a Whole-genome alignments of sex chromosome sequences between six nematode species with chromosome-level genome sequence assemblies. The X chromosome of each species is indicated by a red bar, and blue bars represent the autosome numbers shown after the species names. The abbreviations are as follows: Srat: S. ratti, Tmur: T. muris, Bmal: B. malayi, Ovol: O. volvulus, Hcon: H. contortus. Each line represents an orthologous gene pair, with red lines indicating NX element genes and blue lines NN ones. b Venn diagrams118 showing the numbers of shared sex-linked genes belonging to the same Nigon element in different species, with the same abbreviations as in (a). c Summary of the sex chromosome constitutions and turnovers among six nematode species with chromosome-level genome assemblies, other than C. elegans, organised according to the phylogeny. Nodes inferred to have had XY systems (which we infer to be the ancestral state, see the section of Evolution of sex-linked gene transcription in the main text) are indicated with dark blue dots, and nodes with XO systems with light brown dots. The estimated divergence times54 are also shown at the nodes. The X chromosomes of different species are indicated in red at the edge of each circos plot119, and different colours indicate each Nigon element that contributes part of each species X (these are also indicated by the distinct colours of the branches of the phylogeny). d Homologous Nigon elements detected in the sex chromosomes of all studied nematode species (except those shown in gray, where the contributions could not be determined); contributions are indicated by squares with the same colours as in part c. These results allowed us to infer the nodes at which different Nigon elements became part of the sex chromosome. The parentheses under the element names at the top indicate the number of times each Nigon element became part of a sex chromosome. Rhabditophanes sp.KR3021 (yellow squares) has no sex chromosomes. The dotted blocks represent reversion of sex chromosomes back to autosomes in Dracunculus medinensis.

We first focused on seven representative species with chromosome-level genome assemblies available (six from the orderRhabditida, i.e., clade III, cladeIVand clade V species, one from clade I species) (Supplementary Data1), and compared their X-linked gene contents and genome sequences. The autosomes of C. elegans (clade V species) correspond to Nigon elements NA to NE, and its X chromosome corresponds to two elements, NX and NN (X+N)36. The X+N composition is based on alignments of C. elegans X-linked genes to those in the genomes of five other Rhabditida nematodes: 103 C. elegans genes orthologs are also located on the X chromosomes of all five species, and are classified as NX-derived genes (Fig.2a, b; Supplementary Fig.6). The orthologs of the other 417 genes are classified as the NN-derived genes. These orthologs are either autosomal (in another clade V species- Pristionchus pacificus, in clade IV species- Strongyloides ratti, and clade III species- O. volvulus; Fig.2a; Supplementary Fig.7), or are found on the X chromosome, but in a distinct region from that occupied by the NX-derived ones (in the clade V species- Haemonchus contortus, and the clade III species- B. malayi). These findings suggest that the NX element was already a sex chromosome in the ancestor of rhabditid species 241 MYA (http://www.timetree.org/) or even earlier (see Fig.2c below), and that sex chromosome-autosome fusions or translocations added the NN element independently in some clade III and clade IV species (Fig.2a). The sex chromosomesof the Rhabditida thus originated much earlier than the origin of the oldest sex-linked region in extant schistosomes.

The only non-rhabditid species in Fig.2, Trichuris muris from clade I, has a sex chromosome composition of NA and NB elements (A+B), and lacks genes derived from the NX element. The divergence between clade I and the Rhabditida is dated at 400 million years ago54. During this time, either separate sex chromosomes originated independently in clade I and the ancestorof theRhabditida, or an ancestral NX element was replaced in a turnover event in clade I, with either the NA or NB element subsequently becoming the sex chromosome, followed by a fusion with the other element, creating a neo-sex chromosome (see below).

Based on seven species with chromosomal genome assemblies shown in Fig.2, we infer that, in the non-clade I or rhabditid species, the NX element has undergone independent translocations involving other elements, repeatedly forming neo-sex chromosomes. In clade V species, the NN element has translocated to the NX element, forming an X+N sex chromosome in C. elegans and H. contortus, but not in the P. pacificus lineage. In clade III, the NE and ND elements have translocated to the NX in O. volvulus (X+E+D)33, and the NN and ND elements have translocated to the NX in B. malayi (X+N+D)34 (Fig.2c). As the X+D translocation was found in species within clade III and clade IV, but not in the clade V species studied, it could have occurred either in the common ancestor of the Rhabditida, or independently in the ancestors of the respective clades. The former scenario seems unlikely, as it requires an X+D translocation followed by a complete fission and reversion of the ND element to a separate autosome in the ancestor of clade V. By further examining the orthologous genes shared by the autosomal ND element of C. elegans (clade V species) and clade III and cladeIV species, all with the X+D translocation, we estimated that only ~60% of the S. ratti (clade IV) ND-derived genes orthologs are also X-linked in O. volvulus or B. malayi (clade III), much less than the proportion of at least 85% (and up to 98%) of the NX-derived genes found among X-linked genes in pairwise comparisons among all ofthe Rhabditida species studied (Fig.2b). This supports independent X+D translocations in the ancestors of the clade III or cladeIV species. Similarly, the NB element corresponds to part of the X chromosomes of both T. muris (clade I) and S. ratti (clade IV), but fewer than half of the NB-derived orthologs are shared between these two species (Fig.2b), also suggesting its independent translocation.

The Nigon element compositions of the X chromosomes of nematode species, in addition to the seven species studied above, suggest even more translocations (Fig.2d, Supplementary Figs.810, Supplementary Data5). As only scaffold-level draft genome assemblies are available for these species, we estimated the coverage of their orthologous genes on different Nigon elements in male or pooled-sex genomic sequences, to identify patterns that indicate sex-linked regions (see above).

Among clade I species, in addition to T. muris, the inferred X-linked genes of two other Trichuris species (T. trichiura and T. suis) also include orthologs in C. elegans on both the NA and NB elements. X-linked genes of Romanomermis culicivorax, an outgroup to the Trichuris species, had orthologs only on the NA element (Fig.2d, Supplementary Figs.8b, 10). Most likely, therefore, the NA element was a sex chromosome pair in the ancestor of clade I nematodes and a translocation created the A+B state in the ancestor of Trichuris. If the NX element was the sex chromosome in the ancestor of all nematodes, a turnover event must have occurred, and resulted in the NA element becoming a sex chromosome in clade I.

Among the clade III species, we inferred that, after the ancestral X+D translocation in a clade III ancestor, the NA and NB elements were translocated to the X chromosome in the ancestor of the infraorder Ascaridomorpha (creating an X+D+A+B chromosome that is found in species including Anisakis simplex and Ascaris suum). An independent translocation of the NE element (X+D+E) also occurred in the ancestor of Onchocerca species including O. volvulus, and a translocation of the NN element (X+D+N) in the ancestor of both B. malayi and Wuchereria bancrofti. Other lineage-specific changes include translocations in Thelazia callipaeda (X+D+B) and Dirofilaria immitis (X+D+N). Interestingly, the X+D ancestral sex chromosome configuration has been replaced by the NE element in Dracunculus medinensis in a turnover event which occurred long enough ago to be detected by our coverage analysis (Fig.2d, Supplementary Figs.8a10).

Among the clade IV species, we note that Strongyloides species are parasites, and have environmental sex determination in which XX females reproduce parthenogenetically in the parasitic stage, but can produce XO males in response to the host immune response. The mechanism involves loss of one copy of the X-linked sequences during oocyte mitosis46,55, suggesting that this is a derived state in these species, and that the X is ancestral. Our inference of sex chromosomes in clade IV (Fig.2d), including these species, suggested that, following the X+D translocation in the ancestor of clade IV species (Fig.2c), a second translocation involving the NB element created the (X+B+D) sex chromosomes in both the free-living Parastrongyloides trichosuri and all Strongyloides species studied here, as the sex chromosome of their outgroup species P. redivivus does not include NB element genes. It follows that these translocations occurred in a common ancestor of P. trichosuri and Strongyloides, consistent with the transition to parasitism, and environmental sex determination, in the latter being more recent.

We identified translocations only when the Nigon elements involved exhibited reduced male read coverage. Our analyses therefore inferred only regions that have been non-recombining for such a long evolutionary time that either Y-linked genes have been lost or have undergone so much sequence evolution that they do not map to their X-linked alleles. Importantly, however, the results suggest that (barring the unlikely possibility of insertion of large autosomal regions into a non-recombining part of the X) each of the translocation events led to a formerly autosomal region becoming completely sex-linked.

Despite the large number of rearrangements involving sex chromosomes that we identified, it is therefore currently not possible to ask whether sex chromosomes are more often involved in translocations than autosomes, because coverage analysis does not detect events involving only autosomes.

The time since a translocated Nigon element became non-recombining can be inferred if it still carries enough Y-linked sequences to estimate the divergence level from their X-linked counterparts. If recombination becomes completely suppressed in a formerly recombining region, the region will start to diverge in sequence (as explained above)56. Events causing loss of recombination at different times are detectable from different levels of divergence (termed evolutionary strata) between sequences on the two sex chromosomes. Strata may either occur through successive chromosome inversions (e.g., some strata in mammals24, birds23 and sticklebacks21), or by other mechanisms affecting local crossover rates56. Strata could also arise on neo-sex chromosomes either (i) over time after their translocation (as in mammals), or (ii) immediately, as a direct consequence of the fusion in a species without crossing over in the heterogametic sex (as in Drosophila, see above). Unlike Drosophila, nematode males undergo crossovers. In both sexes, C. elegans chromosomes exhibit distinct recombination domains: a low recombination central region, flanked by high recombination arms, and very low recombination at the tips and other nematodes show similar patterns57,58 (though exceptions are reported, including in H. contortus59). In P. pacificus, strong localisation of crossovers to one chromosomeend specifically in males was observed for elements NC and ND, though not for the three other autosomes60. If such a sex difference exists, it could prevent recombination across most of the genome in males, similar to the proposed situation in the guppy61. In species with a recombination landscape similar to that of C. elegans, an X-autosome fusion creates males heterozygous for the fused chromosome and the free autosome, and the protein machinery that ensures crossover localisation may re-position crossovers away from the fused chromosome end of the former autosome. Such a change was reported for an X-IV fusion in C. elegans62, which has a decreased recombination rate in the fusion-proximal former chromosome arm region, but an increased rate in the distal region. To discover whether, and how, the fusions affected recombination on the neo-X chromosomes, and whether the cessation of recombination occurred in a single or multiple steps, we examined the translocated Nigon elements in different nematode lineages.

In extant clade IV and cladeV species with XX/XO sex systems (Fig.2c), the homologous chromosome (the neo-Y chromosome) is no longer present, and only the translocated X-linked Nigon element (the neo-X) remains. In such systems, the only approach available to detect multiple recombination suppression events is to test for accumulation of repetitive sequences in the neo-X. Regions in which recombination was suppressed longest ago are likely to have higher accumulated repetitive content. However, deletions can occur in degenerated regions, and accumulation differences may be obscured by intrachromosomal rearrangements, so repeat distribution is unlikely to reliably reflect the pattern of distinct evolutionary strata. Not surprisingly, no clear evidence of evolutionary strata was found (e.g., in H. contortus, Fig.3, Supplementary Fig.4). The absence of neo-Y-linked genes shows only that these elements have completely stopped recombining, followed by genetic degeneration involving complete loss of genes, consistent with these neo-sex chromosomes having evolved long ago (Fig.2d).

For the X of each species, the component Nigon elements correspond to strata inferred based on the presence of mappable Y-linked sequences, male vs. female ratios of mapped read coverage and SNP densities, and repeat densities. All metrics were estimated for 50-kb long, 10-kb overlapping windows. For Brugia malayi and Onchocerca volvulus, the orthologous genes (vertical lines) are colour-coded according to their different Nigon elements. For Trichuris muris, B. malayi and O. volvulus, the Y-linked sequences that could be assembled along the X are colour-coded according to their pairwise sequence divergence between the X/Y, and the log2 male vs. female SNP density ratios and the repeat density on the X are indicated by colour-codes. Strata are labeled S0 for the oldest stratum, followed by S1, S2, etc.). PAR stands for the pseudoautosomal region.

Three other clade I andclade III species have XX/XY sex systems with retained neo-Y chromosome sequences, and we expect to find neighboring regions belonging to different strata, reflecting their different Nigon elements, and different times during which these have been sex-linked. First, recently translocated Nigon element(s) are expected to be either pseudoautosomal regions (PARs), where recombination still occurs, or young strata. PAR boundaries with the adjacent fully sex-linked regions should be revealed by sharply increased male read coverage to levels similar to that of autosomal sequences. Second, strata that evolved at different time points, via translocations or inversions, will have different Y-X sequence divergence levels (or, with less clarity, sex differences in SNP density), or, even less clearly, in the lengths of contiguously assembled Y-linked fragments. Repeat densities may also show increases at strata boundaries within fully sex-linked regions, particularly in the Y-linked haplotype (but also potentially in the X-linked one), as repeat elements are expected to accumulate rapidly after recombination stops63. We defined statistically significant transitions, and inferred strata boundaries, using change-point analyses (see Methods, Supplementary Fig.11).

Across almost all X chromosomes of the two clade III species, B. malayi and O. volvulus, read coverage in females is nearly uniformly twice that in males, except at the end of the neo-X chromosome, where the lack of any coverage difference identifies a single probable PAR (or a very young stratum) in both species (6.3% of the total assembly length in B. malayi, and 12.9% in O. volvulus). Nearly half of the X chromosome length consists of intermingled ND- and NX-element derived genes (Fig.3), indicating massive intrachromosomal rearrangements after the translocation of ND element genes to the NX element in the clade III ancestor (Fig.2d). Similarly, the X chromosomes of C. elegans and S. ratti are also derived from two Nigon elements, and genes from the two elements are also intermingled (Fig.2). The translocation boundary between the ND and NX elements in B. malayi or O. volvulus cannot be determined precisely due to the rearrangements, but we inferred in the previous section that the NX element must have been a sex chromosome for longer than the ND element. Therefore, each element should represent at least one stratum (labeled together as S0+S1 in Fig.3). S0 and S1 are shared by all clade III species, and S1 probably stopped recombining in males before the species divergence (estimated to be less than 50 MYA64; Fig.2d).

The other X-linked genes are almost entirely derived from the NN element in B. malayi, and from the NE element in O. volvulus, neither of which is intermingled with ND or NX element sequences, consistent with more recent translocations compared with the ND element that formed the S1 stratum (Fig.3, Supplementary Fig.12). Parts of the ND, NE or NN elements may have continued recombining with their autosomal homologs after the translocation, as discussed above. However, their lower coverage in males than autosomes indicates that the translocated regions have now completely lost recombination and become degenerated Y-linked regions.

Nematode chromosome end regions often have high repeat content, probably indicating that the terminal regions recombine very rarely57,58,60. Interestingly, in both B. malayi and O. volvulus, the translocation breakpoint between the S0+S1 region (ND+NX element) and the NE or NN element has a higher repeat content than other X-linked regions (P<2.21016, Chi-squared test), as do both ends of the fused chromosome (Fig.3). It is not clear whether this reflects accumulation of repeats after recombination was reduced by a translocation in a formerly recombining chromosome end region, similar to the case of X+IV fusion in C. elegans mentioned above62, or is simply a feature retained from the pre-translocation ancestral chromosome. If less distantly related species pairs differing by fusions can be found, it might be possible to distinguish between these possibilities.

Although few X-Y gametolog pairs were retained in either of B. malayi or O. volvulus (Supplementary Data6), and Y-X divergence cannot be reliably estimated, there are some signs that recombination might not have been suppressed directly by the fusions (as explained above, recombination suppression is not expected, in contrast to the effect of X-A fusions in Drosophila). Evolutionary strata may therefore have evolved since the fusions occurred. As expected if strata younger than S0+S1 subsequently evolved, the NE or NN elements have more assembled Y-linked sequences (indicating less degeneration) than the ND+NX element region (P<2.21016, Chi-squared test). Moreover, the NN element in B. malayi can be divided into a stratum S2 region next to S0+S1, based on genomic coverage indicating male hemizygosity (and pronounced gene loss from the Y), and a region with similar coverage in both sexes at the end of the chromosome (Fig.3). The latter can be further divided into an S3 region, with a significantly higher SNP density in males than females (P<0.001, Wilcoxon test, Supplementary Fig.11), suggesting some divergence between the X- and Y-linked sequences without pronounced Y gene loss (Fig.3), and a PAR with no SNP density difference between the sexes. Overall, we conclude that the B. malayi sex chromosomes could have at least four evolutionary strata and a PAR. A similar approach suggests five evolutionary strata and a PAR in O. volvulus (Fig.3, Supplementary Fig.11). Only 1% of O. volvulus X-linked S2 (element NE) sequences have corresponding Y-linked sequences, whereas the S3 carries 12% of the genes found in the counterpart X-linked region, suggesting that it formed more recently.

Analysis of the lengths of contiguously assembled Y-linked fragments failed to identify either PARs or evolutionary strata in the XY sex systems of the clade Ispecies T. muris and T. suis. Only 0.06% of the T. muris X-linked sequences have Y-linked counterparts. Their Y chromosomes have probably become completely degenerated, as suggested by a previous cytogenetic study of T. muris65, so that few fragments can be assembled.

Given that non-recombining regions have recently formed between sex chromosomes of both nematodes and schistosomes, it is interesting to ask whether genes in these regions followed the evolutionary trajectory of canonical ancestral sex chromosomes, including evolution of dosage compensation (DC), and a different distribution of sex-biased genes relative to autosomes66,67.

Genetic degeneration of Y-linked genes is expected to reduce transcript abundances of hemizygous X-linked genes below the ancestral level, favouring the evolution of dosage compensation (DC), either in individual genes (incomplete DC, iDC) or of the entire X chromosome (chDC)68. Dosage compensation likely initially involves an upregulation of X-linked genes in males (as in Drosophila69), but this may be followed by downregulation in females (as in mammals70 and C. elegans71). The opposite changes are expected in species with ZW systems68. S. mansoni was reported to have chDC in the cercarial stage, but iDC after sexual differentiation20,72. Meiotic sex chromosome inactivation (MSCI) in male gonads can also lead to evolution of an underrepresentation of male-biased genes on X chromosomes, as reported in C. elegans73 and Drosophila74. Because of its inheritance pattern and selection differences between the sexes66,75, the X chromosome is also expected to accumulate genes with female-biased expression (feminisation) and become depleted for genes with male-biased expression (demasculinisation) if the mutations are expressed in heterozygotes (wholly or partially dominant), while the Y chromosome should become masculinised. These changes occur either through expression changes, or relocation of individual genes between chromosomes. Both feminisation and demasculinisation have been reported for numerous insects29,74 and some nematode species76, and affect relative expression levels of sex-linked and autosomal genes, in addition to the effects of MSCI and dosage compensation.

Comparisons of the transcriptomes from whole adults between fully X-linked versus autosomal genes in males (X/A ratios), and between the sexes (M/F ratios for X-linked genes), suggest very diverse forms and extents of DC in our seven representative nematode species (Fig.4a, b). All the nematode species studied showed X/A expression ratios below 1 in males (based on between 782 to 2742 X-linked genes and 5398 to 10,490 autosomal genes, depending on the species, and Wilcoxon tests yielding P<0.05 for all species, see Supplementary Data7). These patterns were the same, regardless of whether we included strongly sex-biased genes (2-fold transcriptional difference between sexes) or not (Supplementary Fig.13). This supports the genomic coverage data showing degeneration of the Y chromosome, though, because the tissues analysed included gonads, MSCI of the male X chromosome may also contribute (Fig.4a).

a Transcription levels of autosomal (blue) and X-linked genes (red) of different nematode species in males and females. The dotted line shows the median log2 normalised transcription levels of autosomal genes. b Male/female transcription ratios of autosomal (blue) and X-linked genes (red) in nematodes. c Transcription levels of B. malayi and O. volvulus genes divided into different chromosome regions, with autosomes (A) in blue, pseudoautosomal regions (PAR) in green, and different evolutionary strata (S0-S4) in different colours. The dotted line is the median log2 normalised transcription level of autosome genes. Overall the whole-genome transcription level is male-biased. The two-sided Wilcoxon rank-sum tests yielding P<0.05 in all species (based on between 782 to 2742 X-linked genes and 5398 to 10,490 autosomal genes, see Supplementary Data7). The boxplots show the 25th percentile, median, and 75th percentile, and whiskers are set within 1.5 times the interquartile range. d Percentages of male- (blue) and female- (red) biased genes, showing, respectively, deficiency and enrichment on the X relative to the autosomes across the studied nematode species (based on between 7568 to 13,129 genes). Significant deficiencies or enrichments by two-sided Chi-square tests are indicated with blue asterisks (male-biased gene), and with red asterisks (female-biased gene): *P<0.05; **P<0.01; ***P<0.001. e Transcription patterns for autosomal O. volvulus genes (Ovol_A) that are homologous to the Y-linked genes of B. malayi (Bmal_Y) in males (M) and females (F), or vice versa. Species abbreviation: Tmur: T. muris, Tsui: T. suis, Spap: S. papillosus, Bmal: B. malayi, Ovol: O. volvulus, Hcon: H. contortus, Ppac: P. pacificus.

However, in clade I and cladeIII species, most X-linked genes in females, despite having twice the genomic copy number compared with males, exhibited whole-body transcription levels similar to, or even lower than, in males. This suggested either upregulation of X-linked gene expression in males, or adownregulation in females for nematodesin these clades (Fig.4a). While autosomal genes have the same genomic copy numbers between sexes, they are expected to exhibit an equal transcription level between sexes. However, autosomal genes of all studied species of these two clades exhibited a significantly (P<0.05, Wilcoxon test) lower transcription level in females than in males. Particularly in O. volvulus, the median transcription level of autosomal genes was four times higher in males than in females. In addition, the transcription levels of autosomal genes in male O. volvulus were similar to those of their orthologs in B. malayi or other species in clade I groups (see Methods, Fig.4c, Supplementary Fig.14). These findingssuggested that genome-wide downregulation of transcription levels in females not restricted to the X chromosome, probably accounted for a similar or even male-biased transcription pattern on the X chromosome (Fig.4a, Supplementary Fig.14). The female-biased sex ratio of O. volvulus77 may reflect selection for lower female transcription to resolve sexual conflict, as suggested in ref. 75. Intriguingly, in both B. malayi and O. volvulus females, estimated M/F transcription ratios of X-linked S0 region genes were closer to 1 than for autosomal genes (Fig.4c) and appeared to show iDC.

In the clade IV and clade V species studied, however, transcription levels of X-linked genes in females were lower than those of autosomal ones (Fig.4b), except for H. contortus, suggesting a chDC mechanism similar to that inC. elegans. All clade IV and cladeV species M/F transcription ratios were, nevertheless, lower for X-linked genes than autosome ones probably due to MSCI in males66,75.

The X chromosomes of most nematode species studied consistently showed adepletion of male-biased genes (using the criterion of 2-fold higher transcriptional levels in males than in females), and anenrichment in female-biased genes, compared to autosomes (all species P<0.05 by Chi-square tests; Fig.4d). Feminisation of the O. volvulus X chromosome seems to have evolved more slowly than demasculinisation, as all evolutionary strata have become demasculinised, but only S0 is enriched in female-biased genes. The Y chromosomes of both O. volvulus and B. malayi show signatures of masculinisation, involving recruitment of gene duplications from autosomes. Among the total 91 O. volvulus and 219 B. malayi Y-linked genes (Supplementary Data4), we identified 10 and 13 Y-linked genes, respectively, with no homologs elsewhere in the genome, but with an autosomal homolog in the other species as their potential progenitors, and these mostly have male-biased transcript levels (Fig.4e). This suggests that the Y chromosomes of both species have preferentially fixed relocated autosomal genes with pre-existing male-related functions (Supplementary Fig.15). Among the other Y-linked genes, we found two genes (Bm2848: WBGene00223109 and Ovo-sma-5: WBGene00242293) with X-linked homologs in the S0 region of the NX element. This suggests that the ancestor of clade III species had a Y chromosome homologous to the NX element (Supplementary Data8), which has now become degenerated. The sex chromosome system of the nematode orancestor of the Rhabditida ancestor might therefore have been XX/XY rather than XX/XO (Fig.2c), contradicting the currently accepted view42,43.

Finally, we also found evidence of masculinisation of the S. mansoni Z chromosome. The overall median expression level of S. mansoni Z-linked genes in testes was significantly higher (P<0.05, Wilcoxon test) than that of autosomal genes (Supplementary Fig.16).

Having defined the ancestral sex-determining regions in which suppressed recombination first arose in schistosomes (Supplementary Fig.1), we used the available somatic and gonad tissue transcriptome data of the (hermaphroditic) trematode Clonorchis sinensis (liver fluke)78, a relatively close outgroup to schistosomes, and the (hermaphroditic) taeniid cestode Taenia multiceps79, to suggest transcription patterns in the hermaphroditic ancestor of flatworms before gonochorism evolved. C. sinensis and T. multiceps were estimated to have diverged from the gonochoristic schistosomes about 70 and 100 MYA, respectively53,79. We first examined the chromosomal rearrangements that produced the extant schistosome sex chromosomes, then looked for candidate sex-determining genes that might be responsible for the transition to gonochorism, and finally studied genome-wide transcriptional changes after the transition. Our inferences of genes potentially participating in the sex-determination pathways of flatworms and nematodes other than C. elegans used the well-characterised C. elegans genes as a reference. However, it is known that sex-determining pathway genes can undergo rapid turnovers between even related species80,81; therefore, orthologs of C. elegans genes in other nematode species, and particularly the deeply diverged flatworms do not necessarily have a sex-determining function, and need to be functionally validated in the focal species in the future. In the following, we mainly focus our description on certain genes that have functional evidence in both schistosomes and C. elegans.

Alignments of sequences of the chromosomal assemblies of S. mansoni with C. sinensis (Fig.5a, Supplementary Fig.17a) and T. multiceps (Supplementary Fig.17b) indicate that the S. mansoni Z chromosome evolved through a translocation, as first proposed in the 1980s41. Our analyses clarified that this involved two ancestral chromosomes homologous to two (CM030370 and CM030373) of the seven C. sinensis linkage groups, and to LG3 and one part of LG1 of T. multiceps, followed by intrachromosomal rearrangements (Supplementary Fig.17b). These rearrangements might have led to the suppressed recombination of the oldest schistosome stratum, S0, which is expected to carry the candidate sex-determining genes of all Schistosoma species, since the translocation boundary overlaps the S. mansoni S0/PAR boundary. Within the Z-linked S0 region of S. mansoni, we found the ortholog of the C. elegans gene mag-1, whose knockdown in C. elegans causes the hermaphrodites to produce sperm instead of oocytes82; in S. japonicum, its knockdown causes apparent cell proliferation in testicular lobes83. Functional experiments in Drosophila84 have indicated an important and evolutionarily conserved role of mag-1 during oogenesis. If gonochorism originated in a non-gonochoristic schistosome ancestor via two mutations, a possible scenario might be that recessive female-suppressing mutations have first affected mag-1s likely feminising function in the germline, leading to a transition from hermaphroditism to androdioecy as the first step in the evolution of gonochorism2. The second mutation might have given rise to the dominant demasculinising/feminising gene U2AF2, which was recently identified on the S0 region of W chromosome of S. mansoni85,86.

a Gene synteny relationships between Schistosoma mansoni chrZ (Sman-chrZ) and Clonorchis sinensis linkage group CM030370 (Csin_CM030373, red) and CM030373 (Csin_CM030373, blue). The evolutionary strata of S. mansoni are shown in different colours, and the positions of the candidate sex-determining genes U2AF2 and mag-1 on the chrZ are indicated by arrows. b The distribution of the reported genes in the C. elegans sex determination pathway on different Nigon elements. c Lineage-specific duplication of C. elegans sex-determining genes across the phylogeny of nematodes. d Density plots comparing the testis or ovary (e) transcription levels, or the testis (f) or ovary (g) transcription specificity (measured by the transcript level ratios of gonad vs. soma) of gonad-biased genes of C. sinensis (light blue or red) and their S. mansoni orthologs (dark blue or red). Masculinisation, i.e., increase of testis transcription levels, is indicated with a larger male sign, and vice versa for feminisation and demasculinsation etc. Comparison of whole-body male (h) and female (or hermaphrodite, i) transcriptomes between C. elegans (dotted line) vs. H. contortus (solid line). j Masculinised S. mansoni ortholog of C. sinensis gonad-enriched genes (defined as the former having at least 2-fold higher transcription level in testis than the latter), and demasculinised, feminised, or defeminised genes. Their testis or ovary transcription levels of each gene are shown in the heatmap, as well as its functional category, chromosome location in S. mansoni, and information about the knockdown phenotype of its C. elegans ortholog (Supplementary Data10). k A proposed model for the transition of sexual systems in platyhelminths and nematodes. We hypothesised a 2-step model for the transition from a hermaphroditic ancestor to the gonochoristic schistosomes (see text). The recent independent transitions from gonochorism to androdioecy in different Caenorhabditis species have been studied previously88,120, as have the genes reported here. Changes in gonad transcription levels in relation to the sexual systems are indicated using larger or smaller male or female/hermaphrodite symbols.

The schistosome Z-linked S0 region also had a duplication of fox-1. In C. elegans, fox-1 communicates the different ratios of X vs. autosome copy numbers between sexes to the downstream switch gene xol-1, and directs male or hermaphrodite development87. However, the duplication of fox-1 in the S0 region of the Z chromosome is specific to S. mansoni and has not been detected in S. japonicum or S. haematobium. Therefore, the fox-1 paralog of S. mansoni may not have a sex-determining function.

Duplication of orthologs of genes involved in the sex-determination pathway of C. elegans88 also seems to have occurred in other nematodes, as we found lineage-specific duplications of 12 sex-determination pathway genes on different Nigon elements (Fig.5c). For instance, the ortholog of xol-1, the direct target gene of fox-1, is present only in Caenorhabditis species89,90 but not in the other nematode species (or in the schistosome species studied here, Supplementary Data9). The fog-3 gene is critical for spermatogenesis in C. elegans91, and is duplicated in both B. malayi and O. volvulus (Supplementary Fig.18), probably in the ancestor of clade III nematode species. Interestingly, O. volvulus also has a duplication of fox-1, similar to S. mansoni.

We found no clear relationship between the numbers of sex-determining gene orthologs and the probability of particular Nigon elements being translocated to an ancestral sex chromosome pair. The NB element carries the largest number of orthologs of C. elegans sex-determining genes and has been more frequently translocated onto the ancestral sex chromosome than other Nigon elements (Fig.2d). However, the NC element, with orthologs of seven C. elegans sex-determining genes, was not involved in such a translocation in any nematode species so far studied.

Next, we compared the transcriptomes among the gonochoristic S. mansoni vs. the hermaphrodites C. sinensis and T. multiceps, and between the gonochoristic H. contortus vs. androdioecious C. elegans (Fig.5d-i, Supplementary Fig.19), in order to reveal genome-wide changes of transcription following transitions in sex systems. We focused our comparison on gonad tissues whose transcriptomes were available for the three flatwormspecies and are probably more likely to change than somatic tissues in response to the transition. We defined gonad genes as those with at least 2-fold higher transcription levels in gonads than the soma. For the two nematode species, we analysed sexed whole-body transcriptome data, as tissue-specific transcriptomes were not available.

C. sinensis and T. multiceps gonad genes had unimodal distributions of transcription levels and specificities (measured by the gonad/soma transcription ratios); in contrast, their S. mansoni orthologs exhibited bimodal distributions of both values in testes, predominantly with lower values of both measures in ovaries (Fig.5dg, j, Supplementary Figs.19, 20). In particular, there were 202 S. mansoni genes that became masculinised (i.e., had increased testis transcription levels) relative to C. sinensis, compared with 231 genes that became demasculinised (Fig.5j). In contrast, only 114 genes became feminised (i.e., had increased ovary transcription levels) compared with 389 defeminised genes (Fig.5j). A similar pattern is observed in comparisons to the more distantly related T. multiceps vs. S. mansoni (Supplementary Figs.19, 20). These transcriptome patterns suggest that the transition from a hermaphroditic ancestor (represented by C. sinensis or T. multiceps) to the ZW system in the gonochoristic S. mansoni involved mostly defeminisation, a lesser or similar extent of masculinisation and demasculinisation, and an even lower extent of feminisation of gonad gene expression. C. elegans orthologs of feminised genes in S. mansoni are enriched for mutant phenotypes related to female reproduction (e.g., egg laying, vulva development) and embryonic or germ cell development (e.g., embryonic lethal and germ cell development variant) (P<0.05, Chi-square test, Supplementary Data11). While male-related mutant phenotypes (e.g., male behaviour variant and male response to hermaphrodite variant) show enrichment only in masculinised, but not in feminised, genes (Supplementary Data12). Interestingly, we identified 65 S. mansoni genes that were both masculinised and defeminised, and 3 genes that were feminised and demasculinised relative to C. sinensis in the gonads, suggesting possible resolution of sexual conflict after the evolution of gonochorism (Fig.5j).

Similarly, the reverse transition from a gonochoristic ancestor represented by H. contortus in relation to the androdioecious C. elegans seems mainly to have involved defeminisation and masculinisation of the gene transcription (Fig.5h, i, Supplementary Figs.21, 22).

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Evolution of sexual systems, sex chromosomes and sex-linked gene transcription in flatworms and roundworms - Nature.com

Sample selection and sequencing

We selected 44 representative potato accessions, 3 of which are publicly accessible3,13, on the basis of phylogenetic relationships of 432 accessions (PRJNA378971, PRJNA394943 and PRJNA766763; genotype information is available at http://solomics.agis.org.cn/potato/ftp/Genotype_432sp/; Supplementary Fig. 1). To infer the phylogeny of the 432 accessions, reads were mapped to the DM v4 reference genome using BWA (0.7.5a-r405)49, and single-nucleotide polymorphisms (SNPs) were then extracted using SAMtools (v.1.9)50 and BCFtools (v.1.9)49. Fourfold degenerate SNPs with base quality40 and mapping quality30 were fed into IQ-TREE v.2.0.6 (ref. 51), with parameters -st DNA -m 012345 -B 1000. In addition, two non-tuber-bearing species from the Etuberosum section PG0019 (S. etuberosum) and PG0009 (S. palustre) were chosen to be used in phylogeny inference (Supplementary Table 1). Sequencing of these 44 potato accessions was performed on the Pacific Biosciences Sequel II platform, in the circular consensus sequencing (CCS) mode, and the two Etuberosum species were sequenced on the Pacific Biosciences Sequel II platform, in the continuous long read (CLR) mode. A total of 15.938.1Gb of HiFi reads was generated using CCS (https://github.com/PacificBiosciences/ccs) for the 41 newly sequenced potato accessions. For the construction of Hi-C libraries, DNA was extracted from in vitro seedlings, of which PG5068, PG0019 and E86-69 were digested with the restriction enzyme MboI, and PG6359 was digested with HindIII using the previously described Hi-C library preparation protocol52. These Hi-C libraries were sequenced on an Illumina HiSeq X Ten platform. The total RNA of 23 accessions (Supplementary Table 1) from the tissues of roots, stems, leaves, stolons, tubers and flowers was extracted for the library construction. These libraries were subsequently sequenced on the DNBSEQ-T7 system at Annoroad Gene Technology, which produced around 6Gb data for each tissue in each sample.

Genome heterozygosity was estimated using a k-mer-based approach by GenomeScope2.0 (ref. 53). Genomes of the 44 HiFi sequenced accessions were assembled by hifiasm54 (https://github.com/chhylp123/hifiasm), using default parameters. The initial output of hifiasm (v.0.13) yielded a pair of assemblies: (1) the primary assembly (in hifiasm named p_ctg), representing a mosaic haplotype without purging; and (2) the alternate assembly (in hifiasm named a_ctg), which represents the alternate haplotype absent from the primary one. To facilitate downstream analyses, including inter-genomic alignment and comparison of gene copy numbers, we generated monoploid genome assemblies, accompanied by their heterozygous assembled fragments. Haplotigs from the primary assembled contigs, with haplotypes collapsed (p_ctg.*), were then excluded using the purge_dups (v.1.01) software (https://github.com/dfguan/purge_dups) to generate the heterozygous-region-purged assemblies, which were then termed as monoploid assembled contigs (MTGs), indicative of monoploid genomes. The raw alternate assemblies from hifiasm (a_ctg.*), in addition to the contigs that have been removed by purge_dups, were concatenated as the alternate assembled contigs (ATGs) to be the heterozygous genomic segments (Supplementary Fig. 2). The two Etuberosum genomes PG0019 and PG0009 were assembled using CANU v1.8 (ref. 55), and then two rounds of Pilon v.1.23 (ref. 56) were applied for genome polishing, using available resequencing data. Pseudo-chromosomes of the seven potato accessions (A6-26, E4-63, PG6359, E86-69, RH, RH10-15 and PG5068) and one Etuberosum accession (PG0019) were built with Hi-C reads, using the Juicer (v.1.5) (ref. 57) and 3D-DNA (v.180922) (ref. 58) pipeline, with parameters -m haploid -I 15000 -r 0. The assembly completeness in genic regions was evaluated using the solanales_odb10 database (for Solanaceae species) of BUSCO v.4.1.4 (ref. 18), with default parameters.

Transposable elements (TEs) were identified by the Extensive De-Novo TE Annotator (EDTA)59 v.1.9.4, and the non-redundant TE libraries for each accession were passed into RepeatMasker v.1.332 (http://www.repeatmasker.org) to mask potential genomic repeats together with simple repeats and satellites, by default parameters.

Three distinct strategies, comprising ab initio prediction, homology search and expression evidence, were combined to generate the predicted gene models. HISAT2 (v.2.0.1-beta) (ref. 60) was used to perform splice alignment of RNA-sequencing (RNA-seq) reads to the assembled genomes, with --dta parameter. Potential transcripts were then assembled, using StringTie (v.1.3.3b) (ref. 61) with parameter --rf. BRAKER2 v.2.1.6 (ref. 62) was then run to use the transcript assemblies as hints to generate predicted gene models from AUGUSTUS (v.3.4.0) (https://github.com/Gaius-Augustus/Augustus) and to train the hidden Markov model (HMM) of GeneMark-ET (v.3.67_lic) (ref. 63). The parameters set in BRAKER2 were --nocleanup --softmasking.

Non-redundant human-curated plant homologous protein sequences, downloaded from the UniProt Swiss-Prot database (https://www.uniprot.org/downloads), combined with published peptide sequences of tomato and potato8,10,11,13,35, were used as homologous protein sequences. These and the assembled transcripts from StringTie (v.1.3.3b) were passed to MAKER2 (v.2.31.11) (ref. 64). Putative gene structures were then inferred and subsequently used as the training set to generate the HMM in SNAP (v.2013-02-16) (https://github.com/KorfLab/SNAP). MAKER2 was then run again, combining previously generated SNAP HMM, GeneMark-ET HMM and AUGUSTUS tuned species settings, along with the predicted gene models produced from the first round of MAKER2, to synthesize the final gene annotations. The longest transcript of each predicated gene model was considered as the representative.

For gene functional annotation, InterProScan 5.34-73.0 (ref. 65) was applied to predict potential protein domains, based on sequence signatures, with parameters -cli -iprlookup -tsv -appl Pfam.

All-versus-all BLASTP (v.2.2.30+) (ref. 66) results of 2,701,787 peptide sequences of protein-coding genes, annotated from 44 potato accessions and the DM v.6.1 reference genome11, were input into OrthoFinder (v.2.5.2) (ref. 67) for gene clustering, in which the MCL algorithm19 was enabled by setting the inflation factor to 1.5, resulting in 51,401 non-redundant pan-gene clusters. We classified those clusters into 4 categories: core gene clusters that were conserved in all the 45 individuals; soft-core gene clusters, which were present in 4244 samples in our collection; shell gene clusters, which were found in 241 accessions; and accession-specific gene clusters, which contained genes from only 1 sample. To facilitate these analyses, if genes from the DM reference were present in one cluster, this gene was selected as the representative; otherwise, the gene with the longest encoded protein was chosen.

Simulation of pan-genome size in terms of number of protein-coding genes was performed by PanGP (v.1.0.1) (ref. 68) using the totally random algorithm, with a number of combinations, at each given number of genomes, of 500, and with the sample replication time set to 30.

Non-synonymous/synonymous substitution ratios (Ka/Ks) within core, soft-core and shell gene clusters were computed using ParaAT (v.2.0) (ref. 69), with parameters -m muscle -f axt -k. The default parameter of KaKs_Calculator was set to estimate the Ka/Ks values, which means that the Ka/Ks value was the average of the output from 15 available algorithms comprising 7 original approximate methods (NG, method from Nei and Gojobori;LWL, method from Li, Wu and Luo;MLWL, modified method from Li, Wu and Luo;LPB, method from Li, Pamilo and Bianchi; MLPB, modified method from Li, Pamilo and Bianchi;YN, method from Yang and Nielsen;MYN, modified method from Yang and Nielsen), 7 gamma-series methods (-NG, -LWL, -MLWL, -LPB, -MLPB, -YN and -MYN) and one maximum likelihood method (GY, method from Goldman and Yang) (ref. 70). To simplify the calculation, we randomly selected 1,500 clusters from clusters of core, soft-core and shell categories. Within each cluster, Ka/Ks values between gene pairs from 50 randomly chosen combinations of 2 accessions were estimated. The non-parametric multiple comparisons KruskalWallis test was used to perform significance analyses for sample median, using the agricolae package in R v.4.0.3 (https://www.r-project.org/), as these data did not comply with a normal distribution. Multiple comparisons were performed, using the Fishers least significant difference. The level of significance used in the post-hoc test was 0.001. Functional enrichment was performed, using Fishers exact tests in R. Those functional classes with P<0.05 were regarded as significantly enriched.

Whole-genome alignment of 73 accessions, comprising 44 potato MTGs and the genomes of DM, 2 Etuberosum species, 24 tomato accessions (https://solgenomics.net/projects/tomato100, http://caastomato.biocloud.net/page/download/), and 2 outgroup species of S. americanum and S. melongena (http://eggplant-hq.cn/Eggplant/home/index)35,44,71,72 were performed by ProgressCactus (v.1.2.3) (ref. 73). The tomato genomes investigated in this study were all built using the third-generation sequencing technique (PacBio CLR and Nanopore) and are all assembled into 12 chromosomes, indicative of their relatively high qualities. The guide tree used in ProgressCactus was inferred by IQ-TREE, v.2.0.6 (ref. 51). To reduce the computation requirement, genome sequences were soft-masked and contigs shorter than 100kb were discarded. To facilitate downstream analyses, we next used PHAST toolkit v.1.5 (ref. 74) to generate 73-way multi-alignment blocks in fasta format, relative to the DM genome.

The 44 MTGs were aligned to the DM reference genome, using the nucmer program in MUMmer v.4.00rc1 (ref. 75) software with the --mum parameter, and alignments with an identity of less than 90% and length shorter than 1,000bp were discarded. We used a modified version of dotPlotly (https://github.com/tpoorten/dotPlotly/blob/master/mummerCoordsDotPlotly.R) for visualization. To assess the heterozygosity distribution of 41 diploids (excluding 3 homozygous inbred lines), their MTGs and ATGs were split into 5-kb fragments and were aligned to the DM reference genome, using the same approach described above, and alignments shorter than 5kb were discarded to reduce potential noise.

To identify syntenic gene pairs, BLASTP (v.2.2.30+) was used to calculate pairwise similarities (e-value<1105), and MCscanX76 with default parameters was then applied.

To build a super-matrix tree of 29 species (32 accessions, in which 4 are from S. tuberosum), amino-acid sequences of the longest transcripts of their annotated gene models were first extracted from the MTG genomes of 25 potatoes, 3 tomato accessions (see Supplementary Table 1 for more details)35,44,71,72, 2 Etuberosum species, S. americanum and eggplant77. All-versus-all alignments were generated using DIAMOND (v.2.0.6.144) (ref. 78). The results were then passed to OrthoFinder (v.2.5.2)67 to infer orthology. A total of 3,971 single-copy orthologues gene clusters were then generated and 32-way protein alignments for these genes were computed using MAFFT (v.7.471) (ref. 79) with default parameters. Maximum likelihood inference of phylogenetic relationships was performed using IQ-TREE v.2.0.6 (ref. 51), by automatically calculating the best-fit amino-acid substitution model via the -m MFP parameter. The consensus tree was generated specifying the number of bootstrap replicates as 1,000 by ultrafast bootstrap approximation80. We also constructed a phylogenetic tree using an additional 20 potato (including DM) and 21 tomato genomes by applying the same approach described above.

To minimize the effect of ILS, we applied a multi-species coalescent-based method incorporated in ASTRAL (v.5.7.8) (ref. 81) to generate a species tree. ASTRAL took 3,971 single-copy gene trees as input and generated a species tree estimated by searching for the species tree that was most congruent with quartets garnered from the input gene trees.

To infer the local phylogeny among the 32 representative accessions, considering the diverse nucleotide evolution rate of coding and non-coding regions, we masked coding regions according to the gene prediction in DM using the maskFastaFromBed command embedded in BEDTools (v.2.29.2) (ref. 82), and repetitive regions were then hard-masked. We split Cactus whole-genome alignment blocks into 100-kb non-overlapping windows and inferred tree topologies for each window, using IQ-TREE51 with the parameter -m GTR. Next, we filtered the window trees with three standards: (1) fully aligned length>10kb; (2) missing rate<20%; (3) mean bootstrap values>80. After filtering, we next re-estimated the tree topologies of the retained 1,899 windows, using the selected best substitution model for each window, using ModelFinder implemented into IQ-TREE (ref. 51). To help with visualization, 500 window trees were randomly selected, with an R script modified from a previous report83 (https://zenodo.org/record/3401692#.YNrvJ6e76XQ). The consensus tree topology was generated by IQ-TREE51, using concatenated single-copy protein-coding sequences identified by OrthoFinder67.

BASEML and MCMCTREE in the PAML package (v.4.9) (ref. 84) were used to estimate the divergence time. To reduce the computational burden, coding sequences (CDSs) of single-copy genes from 10 representative species (S. melongena, S. americanum, PG0019, LA716, LA2093, Heinz 1706, PG6241, PG4042, PG5068 and DM) were selected for a rough estimation of the substitution rate using BASEML with model=7. MCMCTREE was then applied to estimate the divergence time with parameters model=7, burnin=500,000, sampfreq=100, nsample=20,000. The divergence time of potatotomato (7.38.0Ma)35,85 and potatoeggplant (13.715.5Ma)85,86,87 was used for calibration. The estimation was performed for two rounds and generated very similar results.

On the basis of the genome assemblies, around 20-fold short reads of the 25 representative Petota accessions, 2 Etuberosum species, 3 tomatoes and S. americanum were simulated using WGSc (https://github.com/YaoZhou89/WGSc), and reads were mapped to the outgroup reference genome S. melongena using BWA-mem49 with the default parameters. Bi-allelic SNPs were then identified using SAMtools50 and BCFtools49. Setting S. melongena as the outgroup, an ABBA-BABA test was performed between all possible triplets among potato, tomato and Etuberosum species, using the Dtrios program within Dsuite (v.0.4 r28)88, with the -c parameter. The tree topology among these four species, inferred from the whole-genome data in Newick format, was also passed into Dtrios via the -t parameter.

The level of ILS at a given bi-allelic SNP i from the above mentioned 32-way alignment was calculated as CABBA(i) and CBABA(i) divided by the total count of segregating sites: (CBAAA(i)+CABAA(i)+CAABA(i)+2(CBBAA(i)+CBABA(i)+CABBA(i)))/3, as described previously27. The tree topology used was (((Lycopersicon, Petota), Etuberosum), S. melongena).

To evaluate the theta value for internal branch, which reflects the level of effective population size89, we divided the mutation units by coalescent units. The mutation units were inferred by IQ-TREE (ref. 51) and the coalescent units were inferred by ASTRAL.

Simulation of 20,000 gene trees with ILS among six potato accessions (S. tuberosum Group Stenotomum, S. candolleanum, Solanum lignicaule, S. chacoense, Solanum cajamarquense and Solanum bulbocastanum) were performed by DendroPy (ref. 90). The branch lengths of the estimated species tree by ASTRAL were used as an input. Frequencies between the observed and simulated gene-tree topologies from all possible four-species groups among the six potato species were plotted. The correlations were computed using the correlation function cor() in R using the pearson method.

Both read-mapping-based and assembly-based approaches were applied to identify SVs (50bp in length). SVIM (v.1.4.2) (ref. 91) was used to identify putative SVs, consisting of insertions, deletions, inversions, duplications and translocations. SVs with quality10 and number of supported reads5 were kept. Assembled genomes of each accession were first aligned to the DM v.6.1 reference using the nucmer program embedded in MUMmer v4.00rc1 (ref. 75), with the following parameters: --batch 1 -c 500 -b 500 -l 100. The alignments in delta format were passed to the delta-filter program to retain highly reliable alignments with length100bp and identity90%. Assemblytics (v.1.2.1) (ref. 92) was subsequently applied to identity SVs from the filtered alignments, setting the minimum SV size to 50bp. To make the false positive rate in our SV dataset as low as possible, we only kept SVs in terms of insertions, deletions, inversions, duplications and translocations<10kb in size, identified by SVIM. For SV10kb, only insertions and deletions reported in Assemblytics were retained. The two SV datasets for each sample were then combined, using SURVIVOR (v.1.0.7)93 merge with parameters 0 1 1 1 0 50.

To detect megabase-scale inversion events among the 20 landraces and 4 CND accessions, we applied ragtag (v.2.1.0) (ref. 94) with the default parameters, to order and orient the contig-level assemblies into 12 chromosomes, using the DM genome as the reference. Inversions were next identified using SyRI (v.1.4) (ref. 95) with parameters -k -F S. Only those inversions that located in a single contig were retained for downstream analyses.

To identify regions present in MTGs but absent in ATGs, we mapped HiFi reads of each accession to its corresponding MTGs using minimap2 (v.2.21-r1071) (ref. 96), and heterozygous deletions were detected using SVIM (v.1.4.2) (ref. 91) with default parameters (length50bp, quality10, number of supported reads2). To identify sequences present in ATGs but absent in MTGs, we aligned ATGs to MTGs from each accession and extracted the inserted regions using Assemblytics92 with parameters unique_anchor_length=10,000, min_variant_size=50, max_variant_size=10,000,000. These results were merged as heterozygous SVs, and genes overlapping with those SVs were considered as hemizygous genes, as applied in a previous report97.

Breakpoints of crossing-overs were inferred based on the 624 selfing progenies of PG6359 (ref. 3), using a method described previously7.

NLR-annotator (v.0.7) (ref. 98) was first applied to identify genomic segments containing putative nucleotide-binding domain and leucine-rich repeat (NLR) genes for each accession. A total of 7,007 amino-acid sequences of high-confidence NLR gene models, downloaded from resistance gene enrichment sequencing (RenSeq)-based NLR genes of 15 tomato accessions99, putative NLR genes in Arabidopsis100 (annotation version Araprot11) and experimentally validated NLR genes obtained from PRGdb 3.0 (ref. 101) and RefPlantNLR102, were used as homologous protein evidence. Training sets from SNAP and AUGUSTUS for each accession were then inputted to MAKER2, together with the assembled transcripts, in GFF3 format, and the homologous proteins, to predict and synthesize the final gene models. The reannotated NLR gene models were then integrated with the whole-genome annotation results, and originally predicted genes overlapping with our reannotated NLRs were removed to avoid redundancy.

To examine the completeness of NLR loci generated by our pipeline, we produced three NLR datasets of tomato accession Heinz 1706 from the predicted high-confidence and representative gene models (annotation version ITAG 4.0), predicted models using our pipeline, and previously reported RenSeq-derived models99, respectively. The RGAugury (v.2.2) (ref. 103) pipeline was then used to classify putative nucleotide-binding site (NB-ARC) domain-encoding genes into different subgroups, on the basis of domain and motif structures: TN (Toll/interleukin-1 receptor (TIR) and NB-ARC), CN (coiled-coil (CC) and NB-ARC), NL (NB-ARC and leucine rich repeat (LRR)), CNL (CC, NB-ARC and LRR), NB (NB-ARC), TNL (TIR, NB-ARC and LRR).

For identification of putatively expanded NLR clusters in potato, the annotated NLR loci from 45 potato, 22 tomato and 2 Etuberosum genomes were classified into clusters, using the method described in the pan-genome analysis. The NLR copy numbers in potato, tomato and Etuberosum accessions, in each cluster, were compared by Wilcoxon rank-sum test using the R package exactRankTests. The clusters with P<0.05 were extracted as the expanded clusters. For the potato-specific NLR analyses, the NLR protein sequences from 2 Etuberosum species and 22 tomato species were merged together, as a query, to blast against those from the 45 potato species. If the best hit of a potato NLR showed an identity<75, the NLR was defined as potato-specific. NLRs with transcripts per kilobase of exon model per million mapped reads (TPM)1 in potato stolon or tuber were extracted and considered as expressed in these tissues.

RNA-seq reads of 23 accessions (Supplementary Table 1) as well as DM (SRA030516) were mapped to the corresponding assembled genome, using HISAT2 (v.2.0.1-beta) (ref. 60), with parameters -x --dta. StringTie (v.1.3.3b) (ref. 61) was applied to compute the expression level for each predicted gene in terms of TPM values, using -e -G parameters.

Tools embedded in the PHAST package (v.1.5) (ref. 74) were used for CNSs analyses. The msa_view program was applied to extract fourfold degenerate synonymous sites and to prepare sufficient statistics, on the basis of multiple alignments and CDS annotation of the reference genome. PhyloFit was then used to train the un-conserved model, with sufficient statistics generated by msa_view. phastCons, with the parameter --most-conserved used to identify conserved regions and assign an odds score for each site. Finally, conserved regions containing gaps and overlapping with CDS were removed to generate CNSs shared among potato species. To further remove CNSs shared within outgroup species, we identified CNSs from genomes of 45 potato, 24 tomato and 2 Etuberosum species, using the same pipeline presented above. The potato conserved CNSs that shared sequences with tomato and Etuberosum species were removed. In addition, short sequences (<5bp) were excluded and sequences that were located within 10bp of each other were merged to generate the final potato-specific CNSs. ChIPseeker v.1.24.0 (ref. 104) was adopted to annotate these CNSs, in which sequences 3kb upstream from the start codon or 3kb downstream from the stop codon of a certain gene were defined as promoter or downstream regions. Genes possessing CNSs within their promoters, introns, upstream regions, downstream regions or UTRs were defined as CNS-associated genes. pyGenomeTracks v.3.6 was applied to visualize the CNS region105. Sequences flanking IT1 CNS regions were extracted from the 71-way multiple alignment and were imported into MView (v.1.67) (ref. 106) to generate the multiple comparisons figure.

The diploid S. tuberosum Group Phureja S15-65 clone was used for gene editing in this study. The 19-nucleotide single-guide RNA sequence for IT1 from the S15-65 clone was incorporated into the CRISPRCas9 vector pKSE401 (ref. 107). Three-week-old plantlets were used for transformation. Agrobacterium-mediated transformation of potato internodes was conducted as previously described6: after two days of pre-culture, the explants were co-cultured with Agrobacterium containing pKSE401 with the target sequence for two days, in the presence of 2mgl1 -naphthaleneacetic acid and 1mgl1 zeatin, followed by callus induction and regeneration mediated by 0.01mgl1 -naphthaleneacetic acid and 2mgl1 zeatin until shoot proliferation. Positive transformants were screened on the basis of growth on the medium containing 50mgl1 kanamycin.

The cDNA of S15-65 stolons was used to construct the cDNA library for yeast-two hybrid by using the CloneMiner II cDNA Library Construction Kit. The library was screened, with the IT1 as bait, according to the Matchmaker Gold Yeast Two-Hybrid System User Manual. To further validate the interaction between IT1 and SP6A, the CDSs of IT1 and SP6A were inserted into pGADT7 and pGBKT7 vectors, respectively, and co-transfected into the yeast strain AH109, and the yeast cells were then plated on SD/Leu/Trp medium and SD/Leu/Trp/His medium and cultivated at 30C for 5 days.

The CDSs of SP6A and IT1 were fused in the pCAMBIA-nLUC-GW and pCAMBIA-cLUC-GW vectors, respectively108. The vectors were transformed into Agrobacterium strain GV3101, and infiltrated into Nicotiana benthamiana leaves. After 3 days, the detached leaves were sprayed with 100mM luciferin and kept in the dark for 10min. The leaves were observed under a low-light cooled charge-coupled device imaging apparatus, Lumazone 1300B (Roper Bioscience).

The seeds of potato inbred line E4-63 and Etuberosum species PG0019 were planted in soil and cultivated under long-day conditions (16-h light, 8-h dark) for one month, and then half of the plants were transferred to short-day (8-h light, 16-h dark) conditions. When flower buds developed in the long-day plants (usually two months after sowing), the fourth leaf of both long-day and short-day plants was harvested at ZT4 to investigate SP6A gene expression. The total leaf RNA was extracted using an RNAprep Pure Plant Kit (DP441), and a PrimeScript RT Reagent Kit (RR047A) was used to reversely transcribe the RNA to cDNA. Quantitative PCR was performed using SYBR Premix Ex Taq II (RR820A) on a 7500 Fast Real-Time PCR system (Applied Biosystems), according to standard instructions. EF1A was used as the internal reference. The specific primers used are listed in Supplementary Table 17.

To plot syntenic relationships around the R3a locus, collinear blocks between the given two species were identified by MCScanX (Python version)109. Syntenic genes around R3a loci were extracted and plotted using in-house R scripts. For a synteny plot of the SP6A loci, the SP6A genomic sequences from different species were extracted and aligned using MAFFT, with --auto parameter79. In-house Python scripts were used to transfer aligned regions between two species to the BED format required by MCScanX. The micro-synteny plot between the two species was then generated. Finally, synteny plots among different species were merged using Adobe Illustrator.

Further information on research design is available in theNature Research Reporting Summary linked to this paper.

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Genome evolution and diversity of wild and cultivated potatoes - Nature.com

DALLAS, June 10, 2022 /PRNewswire/ -- A golden opportunity for youth to embark on a professional journey as Target Evolution has come up with its latest venture. The organization proudly announces its partnership with renowned national brand, Macy's smaller, off-mall concept, Market by Macy's at The Highlands of Flower Mound. With the fruitful collaboration between the two companies, Trail Blaze Shop has emerged in the market. It is a retail store especially built for the young entrepreneurs, belonging to the age group of 12-19 years old. The organization is offering opportunities for youth to grow while paving their way to success.

Considering the fall of the global employment rate and effects of the pandemic, many people, especially youth, are trying to find alternative sources to earn. Target Evolution thrives to empower those youngsters who have the passion for entrepreneurship. The latest Trail Blaze Shop is not only offering an opportunity to earn at a young age, but also letting teenagers learn more about entrepreneurship along with financial literacy. Currently, the organization has its own retail shops in two shopping malls, and now is looking to expand even further.

The stores are situated in Houston and Dallas, Texas. The organization is also working with a national mall owner to execute expansion. With the goal to establish stores in the other top cities, the organization also collaborated with Market by Macy's, Macy's smaller, off-mall concept. It's going to host 2-day pop-ups for youth entrepreneurs in Texas. Teens and youth can join the event by signing up online or at Trail Blaze Shops to be featured in Market by Macy's at The Highlands of Flower Mound. Market by Macy's is a smaller format retail store than its larger full-line stores, approximately 20,000 square feet, offering an even more curated assortment of Macy's branded fashion, within an easy-to-shop and open environment.

"We are proud to partner with such an incredible organization, such as Target Evolution," said Loren Payne, store manager for Market by Macy's at the Highlands of Flower Mound, "Their impactful work plays a vital role in supporting and enriching our local community and beyond."

Target Evolution is a Texas based, 501(c)3 nonprofit organization, founded in 2011 established to provide solutions to the common problem of youth unemployment that has broken many dreams. Offering hope, inspiration, and professional help to youth; the organization ensures the young generation is capable of running their own businesses. It offers opportunities for youth to work and sell products while nourishing their entrepreneurship skills. The partnership with Macy's is offering a chance for youngsters to work at the world's largest department store offering adequate exposure and experience. Working with a reputed organization allows students to have a better grasp of the competitive market.

April Pelton is one of the youths of this organization who set a record by earning $1000 in just two hours. Talking about her experience she said, "They help children like me every day, and I'm proud to be a part of the Target Evolution family." It is evident that the organization is always ready to reach teenagers with their helping hand.

Currently, this organization is looking forward to establishing retail stores in the top 10 cities within the next two years. The latest partnership with Macy's is just the beginning of a prolific journey into the future. Find out morewww.targetevolution.org.

About Macy's

Macy's, the largest retail brand of Macy's, Inc. serves as the style source for generations of customers. With one of the nation's largest e-commerce platformspowered by macys.com and mobile app,paired with anationwide network of stores, Macy's delivers the most convenient and seamless shopping experience, offering great values in apparel, home, beauty, accessories and more. Macy's gives customers even more ways to shop and own their stylethrough an off-price assortment at Macy's Backstage and at our highly curated and smaller store format, Market by Macy's. Each year, Macy's provides millions with unforgettable experiences through Macy's 4th of July Fireworks and Macy's Thanksgiving Day Parade and helps customerscelebrate special moments, big and small. We're guided by our purpose to create a brighter future with bold representation that empowers more voice, choice and ownership for our colleagues, customers, and communities.

Crystal VictoriaTarget Evolution866-922-6686[emailprotected]

SOURCE Target Evolution Incorporated

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Target Evolution is Collaborating with Market by Macy's to Empower Teen Entrepreneurs - PR Newswire

When the Celtics drafted Jaylen Brown third overall in 2016, they had Avery Bradley and Jae Crowder starting on the wings with Marcus Smart and Terry Rozier coming off the bench. Even as he walked across the podium with a hat that had Lucky the leprechaun on it, Brown wasn't sure he was Boston bound or if it was where his career would flourish.

As Brown put it Thursday: "Fast forward, things turned out pretty good."

Kyle Terada-USA TODAY Sports

But with his team in the middle of the NBA Finals, it's understandably difficult for Brown to take time to reflect on the journey he and the Celtics are on.

"It's hard for me to reflect on moments when I'm in the heart of the storm. All the adversity, all (of) the ups and downs, all the negative things, indirectly and directly, has helped build me to where I'm at. Things weren't given to me here. I felt like I haven't always been put in the best position to be the best version of myself, and that's aided me into getting better; into working harder.

"Sometimes, the things that you complain about most can be your biggest blessings. So, everything that I've learned and acquired here, directly or indirectly, has helped me, and I think it's going to help me going forward, so if I would have to reflect, I'm just grateful for each and every experience that you go through because it just makes you who you are."

Kyle Terada-USA TODAY Sports

Regarding Brown's evolution, Ime Udoka said it's "all around, honestly. The things he does, (and) the versatility he gives us on the defensive end. I think that goes down, trickles down with Marcus and our bigs as well as our big wings."

Udoka added: "He's one of the guys that probably has had to restructure what he did as a defender. He's usually a guy that locks in on an assignment. On-ball, off-ball, and takes that guy out. Well, we're asking, more communication, more recognition, and he's one of the guys that's improved throughout the season as far as that."

Kyle Terada-USA TODAY Sports

Along with his contributions to the NBA's top-ranked defense, in Boston's 116-100 win over the Warriors in Game 3, Brown registered a team-high 27 points, pairing it with nine rebounds, five assists, and only two turnovers.

Thursday, Brown said about his facilitating and what makes the difference when a kickout pass is available a step or two sooner: "Spacing. It's been like that all season. Spacing is the key. We get the floor nice and spaced, (and) you can see everything a lot easier. A lot of times during the year, we'll get on top of each other, and we'll drive, (and) there are no outlets. And that's when you start to see a lot of the turnovers."

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Brown's head coach labeled his performance in Wednesday's win a "culmination of last night was his playmaking ability and his scoring for himself. I think it was one of his best games of getting guys organized into spots he wanted, getting our spacing correct, and then attacking from there. So, I think it was almost a perfect night as far as the reads he made with his aggression looking to score but also, one-two dribbles and finding guys all over the court.

"That growth, as well as Jayson('s), was a big point of emphasis coming into the season. I think he did a hell of a job last night."

Further Reading

Tony Parker Sizes Up the NBA Finals, Talks Ime Udoka and His Collaboration with MTN Dew LEGEND

Celtics' Playoff Run Highlighting Robert Williams' Impact and Maturation: 'We're very fortunate to have a guy like that'

Jayson Tatum and Jaylen Brown's Defensive Commitment Helps Enforce Celtics' Culture

The Top 5 Plays of Game 3 of NBA Finals Between Celtics and Warriors

Celtics Feed Off Home Crowd in Game 3 Win Over Warriors: 'They give us so much energy and so much juice'

What Stood Out in Game 3 of the NBA Finals: Celtics More Assertive on Both Ends; Earn 2-1 Lead

The Anatomy of the Celtics' Fourth-Quarter Comeback in Game 1 of NBA Finals

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Celtics, Jaylen Brown Discuss His Evolution: 'Sometimes, the things that you complain about most can be your biggest blessings' - Sports Illustrated

Karen Hopkin: This is Scientific Americans 60-Second Science. Im Karen Hopkin.

Hedgehogs are a lot of things. Theyre small and spiky, covered in quills. And some people even say theyre cute. Now, a new study says that they are also the origin of resistance to methicillin, an antibiotic derived from penicillin. That pointed observation appears in the journal Nature.

Antibiotic resistance is a huge clinical problem. And methicillin-resistant Staphylococcus aureusotherwise known as M-R-S-A or MRSAcan be difficult to treat as many have developed resistance to a handful of our frontline therapeutics.

Jesper Larsen: Historically it has been assumed that resistance in disease-causing bacteria, including Staph aureus, is a modern phenomenon driven by clinical use of antibiotics.

Hopkin: Jesper Larsen is a senior scientist at the Statens Serum Institute in Copenhagen

Larsen: which is the Danish equivalent of the CDC in the US.

Hopkin: Methicillin resistance was thought to be tied to prescription, in part because methicillin-resistant bugs were first isolated from British hospitals just a year after the drug became available for clinical use.

Larsen: But a couple of years ago we found out by chance that MecC M-R-S-A is present in more than 60 percent of hedgehogs from Denmark and Sweden.

Hopkin: Ok, whats MecC M-R-S-A? Methicillin and penicillin belong to the so-called beta lactam family of antibiotics. They kill bacteria by inhibiting enzymes the bugs use to build their protective cell walls. MecCand a related gene MecAencode versions of the enzymes that the antibiotics dont latch onto as well.

Larsen: Staph aureus bacteria that carry these genes are therefore resistant to most beta lactam antibiotics.

Hopkin: But where did these resistance genes come from? Theyve been spotted not only In folks with Staph infections, but in livestocklike pigs and cattleand in some wild animals. And in Sweden, Larsen found that mecC is really common in hedgehogs.

Larsen: So the big question was, why hedgehogs carry so much mecC MRSA.

Hopkin: To find out, Larsen went to the library

Larsen: where I came across an old study from the 1960s which showed that a particular fungus in hedgehogs is able to produce a penicillin-like antibiotic that is very similar to methicillin.

Hopkin: So hedgehogs with this particular skin fungus would naturally be exposed to penicillin. And that could have launched an evolutionary arms race that drove the hedgehogs resident bacteria to evolve resistance.

Larsen: This was a real eureka moment and led us to hypothesize that wild hedgehogs have been a natural reservoir of mecC MRSA long before penicillin and methicillin came on the market.

Hopkin: To confirm this suspicion, Larsen and his colleagues screened hedgehogs from Europe and New Zealand and found that hedgehogs in Scandinavia and the UK harbor a heavy load of mecC MRSA. And they also found that the fungus carried by those hedgehogs had all the genes they needed to produce penicillin.

Larsen: We then went on and sequenced and analyzed the genomes of around one thousand mecC MRSA isolates. Which showed that they first appeared in hedgehogs in the early 1800s long before we started to use antibiotics in human and veterinary medicine.

Hopkin: Now, that doesnt mean that we should feel free to use antibiotics all over the place, because its not our faultits the hedgehogs. Because if having antibiotics around encourages bacteria to evolve resistance, taking antibiotics away robs them of their superpowerand leaves them a little bit weaker than their non-resistant kin.

Larsen: It is often very energy consuming to produce the enzymes that inactivate the antibiotics. This means that resistant bacteria will often be outcompeted by susceptible bacteria in periods when they are not exposed to antibiotics.

Hopkin: So if we really want to show MRSA no mercy, we should keep the methicillin to a minimum. And maybe keep at least a quills-length away from Scandinavian hedgehogs.

For Scientific Americans 60-Second Science, Im Karen Hopkin.

[The above text is a transcript of this podcast.]

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Hedgehogs Host the Evolution of Antibiotic Resistance - Scientific American