Monthly Archives: September 2021

In 1990, an international team of scientists began an ambitious attempt to sequence the human genome. By 2001 the Human Genome Project (HGP) had prepared a rough draft, and in April 2003, the draft sequence was declared finished. But Karen Miga, a geneticist now at the University of California, Santa Cruz and the associate director of the UCSC Genomics Institute, knew that while the work might have wrapped up, the sequencing was far from complete.

The HGP was able to sequence the 90% of human DNA that geneticists call euchromatin, which is loosely folded and contains nearly all of the genes that are actively making proteins. But Miga specialized in heterochromatin, the tightly packed sections of DNA with highly repetitive sequences near the ends (telomeres) and centers (centromeres) of chromosomes. At the time, scientists couldnt sequence heterochromatin, so despite the celebratory hubbub and champagne toasts, almost 10% of the genome went unsequenced.

It stayed that way for almost 20 years. The problem nagged at Miga, in part because she didnt believe that the regions were as unimportant as some geneticists thought. (Without a sequence, how could you tell?) Over the years, Miga continued to push the genomics field to complete the project they had started so many years before. As DNA sequencing technologies enabled researchers to read longer and longer stretches of the genome in one go, Miga could see that scientists were inching closer to the possibility of cracking the problem open.

Together with Adam Phillippy, a computational biologist at the National Human Genome Research Institute, Miga launched the Telomere-to-Telomere (T2T) consortium in 2018 to finally sequence every last nucleotide of human DNA. Then, just as the team was finding its footing, the pandemic struck.

But COVID-19 didnt stop their progress. In June, Miga, Phillippy and their colleagues published the first complete genome sequence on the preprint server biorxiv.org. Three decades after it began, the human genome was finally complete.

Quanta sat down with Miga in a video chat to discuss her years of work and what the consortiums accomplishment might mean for science. The interview has been condensed and edited for clarity.

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Karen Miga Fills In the Missing Pieces of Our Genome - Quanta Magazine

A UB team has developed a new model of how information in the genome is organized, called the novel genome archipelago model (GAM). The model provides new insights into how a multitude of interactions among genes may affect normal development, as well as mutations that lead to cancer and other diseases.

GAM offers a physical basis for the idea of systems genomics, which has begun to emerge in recent years, in which individual genome elements are integrated into an organism-like entity, says Michal K. Stachowiak, professor in the Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences at UB.

Stachowiak is senior author on thepaper that describes the GAM, which was published in a special edition of the International Journal of Molecular Sciences entitled Molecular Mechanisms of Neural Stem Cells Systems Approach.

The study advances the idea that the GAM is created through the interactions of distant chromosome regions and even different chromosomes.

Stachowiak says the study shows that tens of thousands of genes may engage in hundreds of millions of interactions, and that through these associations, genomic function is executed.

This vast interactome, as we call it, truly constitutes a new code for the information that is stored and executed by the genome, he says.

The interactions were mapped by first author Brandon Decker when he was working in Stachowiaks laboratory as a graduate student in UBs Genetics, Genomics and Bioinformatics program. Decker is now a postdoctoral associate at the National Institute on Aging, part of the National Institutes of Health.

Stachowiak explains that the GAM is based on the idea that the genome is an archipelago of constantly changing islands, and that when the islands form, they provide a blueprint for specific parts of the body and specific functions.

A single small mutation may have broad impact on genomic function by disrupting multi-genome interactions or their control mechanism, he says. It is the understanding of these interactions that may bring our therapeutic efforts to new, unprecedented levels.

Stachowiak says they assign the central role in organizing the GAM to a nuclear form of the protein FGFR1, which, through its Integrative Nuclear FGFR1 Signaling (INFS) mechanism, discovered in his lab, offers a new paradigm for genomic regulation of an organisms development. He notes that recent studies by teams at other institutions have shown that INFS plays an important role in cancers, including breast cancer.

This is an example of how an advanced basic science becomes translated into clinical medicine andmay offer new strategies for cancer treatments, he says.

Stachowiak named his model to reflect his lifelong inspiration by the travels of Charles Darwin, who developed his theory of evolution after happening upon the islands of Galapagos. We refer to different islands that form in the cell nucleus and, as we propose, orchestrate ontogenesis, Stachowiak says.

In addition to Decker and Stachowiak, other UB authors are Yongho Bae and Ewa Stachowiak, both of the Department of Pathology and Anatomical Sciences; Josep M. Jornet, associate professor of electrical engineering at Northeastern University; and Donald Yergeau, associate director of genomic technologies in UBs New York State Center of Excellence in Bioinformatics and Life Sciences.

Co-authors are Hussam Abdellatif, a doctoral student at the Institute for the Wireless Internet of Things at Northeastern University, who trained with Jornet, and Michal Liput, a doctoral student at the Mossakowski Medical Research Center, Polish Academy of Sciences, who trained with Stachowiak at UB.

This research was funded by three consecutive grants from the National Science Foundation, with additional support from New York State Department of Health and the Patrick P. Lee Foundation.

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UB team proposes genome 'archipelago' as new model of how genomic information influences development, disease - UB Now: News and views for UB faculty...

NEW YORK A team of US researchers led by the Broad Institute's Feng Zhang has discovered a new class of transposon-encoded RNA-guided DNA nucleases, which they said could be used for genome editing in human cells and hold potential for biotechnology.

In a paper published on Thursday in Science, the researchers wrote that the IscB proteins which are the likely ancestors of the RNA-guided endonuclease Cas9 are putative nucleases encoded in a distinct family of IS200/IS605 transposons. Using evolutionary analysis, RNA-seq, and biochemical experiments, they reconstructed the evolution of CRISPR-Cas9 systems from IS200/IS605 transposons and showed that IscB utilized a single non-coding RNA for RNA-guided cleavage of double-stranded DNA.

The researchers also experimented with the RNA-guided nuclease activity of TnpB, another IS200/605 transposon-encoded protein and the likely ancestor of Cas12 endonucleases. Overall, they said, this work revealed a widespread class of transposon-encoded RNA-guided nucleases, which they named OMEGA, for Obligate Mobile Element Guided Activity.

IscB is about 400 amino acids long and has an architecture similar to that of Cas9 it contains an RuvC endonuclease domain split by the insertion of a bridge helix as well as an HNH endonuclease domain. When the researchers performed a comprehensive search for proteins containing an HNH or a split RuvC endonuclease domain, they found that Cas9 and IscB were the only proteins that contained both domains. Clustering and phylogenetic analyses of the combined RuvC, BH, and HNH domains strongly suggested that all extant Cas9s descended from a single ancestral IscB.

Using a previously established protospacer adjacent motif (PAM)-discovery assay, they further observed that CRISPR-associated IscBs are reprogrammable RNA-guided nucleases. Additional experiments showed that IscB functionally associated with CRISPR at least once, and likely on additional occasions, suggesting that IscB systems more generally shared a core ancestral ncRNA gene that was prone to evolving into a CRISPR array or a separate trans-acting tracrRNA.

The researchers also investigated the evolutionary relationships between IscB, Cas9, and other homologous proteins to gain a broader insight into the evolution of RNA-guided mechanisms. In searching for proteins containing split RuvC domains, they detected another group of shorter IscB homologs that were about 350 amino acids long and were also encoded in IS200/605 superfamily transposons. They renamed these proteins IsrB (Insertion sequence RuvC-like OrfB).

In addition to IscB and IsrB, they further identified a family of even smaller (about 180 amino acids) proteins that only contained the PLMP domain and HNH domain but no RuvC domain, which they named IshB (Insertion sequence HNH-like OrfB).

In investigating the relationships between these proteins, they found that IsrB, IscB, and Cas9 formed distinct, strongly supported clades, suggesting that each of these nucleases originated from a unique evolutionary event. Additionally, they were able to identify two distinct groups of Cas9s. The first was a new subtype called II-D a group of relatively small Cas9s about 700 amino acids long that are not associated with any other known cas genes. The second is a distinct clade branching from within the II-C subtype, which includes exceptionally large Cas9s (more than 1,700 amino acids) that are associated with tnpA.

"Through the exploration of Cas9 evolution, we discovered the programmable RNA-guided mechanism of three highly abundant but previously uncharacterized transposon-encoded nucleases: IscB, IsrB, and TnpB, which we collectively refer to as OMEGA because the mobile element localization and movement likely determines the identity of their guides," the authors concluded. "Although the biological functions of [OMEGA] systems remain unknown, several hypotheses are compatible with the available evidence, including roles in facilitating TnpA-catalyzed, RNA-guided transposition, or acting as a toxin."

They further noted that the TnpB family is far more abundant and diverse than the IscB family, and that TnpBs might represent a vast diversity of RNA-guided mechanisms present not only in prokaryotes, but also in eukaryotes.

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New Class of Transposon-Encoded RNA-Guided Nucleases May Add to Genome Editing Toolbox - GenomeWeb

Genetic "dark matter" may drive the emergence of new species, new research finds.

These long, repeating stretches of the genome, called satellite DNA, may ultimately prevent incompatible animals from mating by scrambling the chromosomes in their hybrid babies, according to the study. And if animals from different populations can't mate, they will diverge over time, leading to speciation.

Just 1% of the 3 billion letters, or nucleotides, in the human genome make the proteins that determine traits such as eye color and height. Other stretches of DNA may tell the body how many copies of a protein to make, or turn genes on or off in different tissues, among other functions. Yet nearly 10% of the human genome is composed of long, repeating stretches of satellite DNA that, for many years, scientists didn't think did much of anything, said study co-author Madhav Jagannathan, currently an assistant professor at the ETH Zurich Institute of Biochemistry in Switzerland.

Related: Genes of 500-million-year-old sea monsters live inside us

"Satellite DNA repeats were very abundant in species and widely observed in eukaryotes," or life-forms with cell nuclei, Jagannathan told Live Science in an email. "Despite this, they were largely dismissed as junk DNA."

However, in a 2018 study, Jagannathan, who was then at the Massachusetts Institute of Technology (MIT), and his former postdoctoral adviser, biologist Yukiko Yamashita, also at MIT, discovered that some of this DNA served a critical purpose: It organizes DNA within a cell's nucleus. That study found that certain proteins grab DNA molecules and arrange them in densely packed bundles of chromosomes called chromocenters. Satellite DNA, they found, tells these grabby proteins how to bundle and organize chromosomes.

In the newest study, published July 24 in the journal Molecular Biology and Evolution, Jagannathan and Yamashita found another role for satellite DNA: driving speciation. The team was investigating fertility in the fruit-fly species Drosophila melanogaster. When the researchers deleted a gene that codes for a protein called prod, which binds to satellite DNA to form chromocenters, the flies' chromosomes scattered outside the nucleus. Without the ability to correctly organize chromosomes, the flies died.

This was fascinating, Jagannathan said, because the deleted protein is unique to D. melanogaster. That meant that these rapidly evolving satellite DNA sequences must also have rapidly evolving proteins that bind to them.

To test this idea, Jagannathan bred D. melanogaster females with males of a different species, Drosophila simulans. As expected, the hybrids did not live long. When the researchers looked into the flies' cells, they saw misshapen nuclei with DNA scattered throughout the cells, just as they had when they deleted the prod protein in previous experiments.

So why does that mean satellite DNA could drive speciation? The team suspects that, if satellite DNA evolves quickly and two creatures make different satellite-DNA-binding proteins, they won't produce healthy offspring. As chromocenter binding proteins and satellite DNA segments evolve differently in separate populations or species, this incompatibility could arise rather quickly.

To test this hypothesis, they mutated satellite DNA-binding genes that led to the incompatibility in both parents. When they rewrote the flies' genomes to be compatible, they produced healthy hybrids.

Such satellite DNA disagreements could be a big factor in the evolution of new species, Jagannathan suspects. He hopes further research can test their model of hybrid incompatibility with other species. Ultimately, this research could lead to a way for scientists to rescue "doomed" hybrids, or hybrids that don't survive long after birth. This could pave the way for using hybridization as a method for rescuing critically endangered species, such as the Northern White Rhino, of which only two females survive.

Ultimately, the new research confirmed Jagannathan's hunch that satellite DNA served a purpose.

"I thought that there was no way evolution could be so wasteful," Jagannathan said.

Originally published on Live Science.

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Dark regions of the genome may drive the evolution of new species - Livescience.com

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A genomic sequencing report submitted to the Karnataka government has suggested that the SARS-CoV-2 virus is changing. Currently, the Delta and sub-lineages of Delta are spreading across Bengaluru Urban and picking up new mutations.

The report said that of these mutations, the N439 mutant has already exhibited the potential to increase the fitness of the virus.

The report cautioned: "We need to monitor any increase in the frequency of these mutations. As that might be a signal for a new variant, which may not be covered by the protection from vaccines," the report quoted in bold letters.

This report comes ahead of a similar account of results of 300 samples sent for genomic sequencing that is expected to be released soon. The results will be discussed by the Committee for COVID-19 Whole Genome Sequencing (WGS), which is to meet on Thursday for discussing the findings.

Strand Precision Medicine Sciences, a genomics-based research and diagnostics company mandated to conduct genomic sequencing by the Karnataka government to help detect trends in mutations, has submitted its report to the health ministry on September 1.

The report has also been sent to the Karnataka Covid Task Force, Chairman of Genomic Surveillance Committee, Karnataka; Bruhat Bengaluru Mahanagara Palike (BBMP) Commissioner and health commissioner BBMP.

Samples processed include 34 sequences from children, 28 sequences from partially and fully vaccinated individuals, and 6 from fully vaccinated individuals. The investigations were conducted on 298 complete sequences.

The outputs suggested the identification of four lineages, and all were Delta or sub-lineages of Delta. The report also said three lineages of Delta and two sub-lineages of Delta AY.4 and AY.12 were found across all groups of Bengaluru Urban.

The report also spoke about new mutations. "This sequencing showed 133 mutations in spike protein alone. Many of these are known mutations," the report said.

"We found several new mutations at low frequency (0.3%

N439K mutant found in 7 sequences, N440Y/T/F mutant in 8 sequences, L441Y/S/G/A/C/D/V found in 7 sequences, D4421/V/Y/F in 9 sequences, S443E/V/Y/W/F in 7 sequences, K444F/N/V/T/S/V mutants found in 7 sequences.

However, experts opine that genomic sequencing results are not a cause for worry as most samples are collected from persons treated at home.

Strand Precision Medicine Solutions was tasked with studying mutations through genome sequencing by the Covid Task Force in Karnataka. The sequencing indicated 30% mutation in the Delta AY.4 variant and 3% in AY.12 mutant.

Total 298 swabs were collected from COVID-19 patients in Bengaluru for genomic sequencing. It also showed that Delta and its sub-lineages AY4 & A12 were dominant across different age groups in Bengaluru.

The test also showed that the COVID-19 virus was changing and Delta's sub-lineages are spreading across Bengaluru urban areas with new mutations being reported.

**

The above article has been published from a wire agency with minimal modifications to the headline and text.

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Genome Sequencing Results Show that SARS-CoV2 is Picking Up New Mutations in Karnataka | The Weather Channel - Articles from The Weather Channel |...

By analysing genomic data from more than 30,000 people, an international research team has revealed thousands of new regulatory regions that control disease-linked genes. Their findings, published in the journal Nature Genetics, have been described as a significant step forward for genomics-driven precision medicine and could help identify markers that reveal which patients will benefit most from which treatment.

In this study we have provided an entirely new view of genetic regulation by uncovering an in-depth picture of how genes and disease are linked, said co-senior author Associate Professor Joseph Powell, Director of the Garvan-Weizmann Centre for Cellular Genomics and Deputy Director of the UNSW Cellular Genomics Futures Institute. It is the most comprehensive analysis of how human genetic variation affects gene expression to date.

To study how human genetic variation affects our risk of disease, researchers often carry out genome-wide association studies, which scan the genomes of patients and look for genetic variants more commonly associated with a specific condition. But interpreting these results is not straightforward instead of directly driving disease, many genetic variants instead regulate the activity of genes, influencing how much of a protein is produced.

By pinpointing these regulatory regions, known as expression quantitative trait loci (eQTLs), researchers are able to better understand which genes directly contribute to disease risk and which could be targeted with precision treatments. In this study, the team used specialised machine learning algorithms to analyse genomic data from the blood samples of 31,684 individuals.

Thanks to the statistical power of this large dataset, we were able to uncover new regulatory regions on the human genome, Assoc Prof Powell said. Instead of just cataloguing the regulatory gene locations that were adjacent (known as cis-eQTLs), we were able to reveal genes that modulated the activity of more distant genes (known as trans-eQTLs).

Out of the millions of genes they investigated, the researchers found not only that 88% had a cis-eQTL effect, but that 32% of genes also had a trans-eQTL effect further away in the genome, more than half of which they could assign to a biological impact, such as cardiovascular and immune diseases.

While its clear that genetic variants are almost always a root cause of disease, the mechanism by which they influence disease is far less clear, Assoc Prof Powell said. For instance, while a specific condition may be linked to hundreds of genetic variants, the vast majority contribute to disease by regulating gene activity.

Understanding which genes this regulation converges on will be invaluable to identify targets for new potential medicines. If a pharmaceutical company develops a therapy that targets a certain molecule, our resource can help identify how its expression is regulated and if the genetic background of different patients is likely to impact its efficacy.

What weve discovered is an entirely new level of genomic information, providing a deeper understanding of biology and disease.

The teams resource is now available to researchers worldwide via http://www.eqtlgen.org.

Image credit: stock.adobe.com/au/Tartila

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New regulatory regions uncovered on the human genome - Lab + Life Scientist

Species invasions into novel habitats mark major transitions in the evolution of life on Earth. Some of these are relatively ancient, such as the vertebrate transition from the oceans to life on land (375 Mya) or the evolution of arboreal vertebrate species (160 Mya). When divergent lineages transition to the same novel habitat, it provides an opportunity to investigate the mechanisms that permit these adaptations and the relationship between similar phenotypes among lineages and the underlying genetic basis. Convergent processes may utilize homologous genomic regions in different lineages to achieve similar phenotypes (1). Alternatively, distinct, genomic processes may be possible (2), or genetic drift may lead to different options for divergent lineages. Relatively recent transitions may be the most informative, on the assumption that extended periods of evolution may obscure the relationship between genomic differences and the original adaptations. A system well suited to this investigation is the adaptation of divergent, terrestrial mammalian lineages to life in aquatic environments.

Marine mammals, broadly defined as mammals whose terrestrial predecessors entered the sea and who obtain all or most of their food from a marine environment, comprise at least 129 extant species divided into three orders (3). Cetartiodactyla includes cetaceans (whales, dolphins, and porpoises); Carnivora includes pinnipeds (walruses, sea lions, and seals), sea otters, and polar bears; and Sirenia includes sea cows (now extinct), manatees, and dugongs (3). Of these, cetaceans, pinnipeds, and sirenians are considered the oldest groups of marine mammals (3). In contrast, sea otters and the polar bear emerged relatively recently so much so that the polar bear can still hybridize with terrestrial sister taxa (35). The most species-rich group of marine mammals is Cetacea, which comprises 90 species (3). Cetaceans, pinnipeds, and sirenians represent an exceptional case of convergent evolutionthe emergence of similar phenotypic traits in species separated by millions of years of evolution (6). In these separate lineages of marine mammals, phenotypic convergence is observed in all major physiological systems (7, 8). The degree to which convergence is reflected at the molecular level can now be partially answered using genomics. However, the interpretation of such results has hitherto been restricted by the limited number of high-quality genomes from marine mammals (6, 9). Remaining uncertainties include the phylogenetic relationships between and within marine mammal groups and their demographic history. To address these questions, we assembled and annotated 17 marine mammal genomes (11 cetaceans and six pinnipeds). Based on more comprehensive genomic data, we identified many putative genetic innovations for the aquatic adaptation of mammals, including those associated with thermoregulation and skeletal systems.

We performed the sequencing and de novo assembly of 17 marine mammal genomes (11 cetaceans and six pinnipeds) (SI Appendix, Table S1). Among these, 14 were assembled by Supernova (10) with 10 Genomics data (average scaffold N50 = 28.66 Mb and contig N50 = 142.33 kb) (Table 1 and SI Appendix, Tables S1S3). The remaining three genomes were assembled using Illumina paired-end reads (SI Appendix, Tables S1S3). Eight of the assemblies were further improved by Hi-C chromosome anchoring (SI Appendix, Fig. S1). The assembled genomes of the 17 marine mammal species range in size from 2.37 to 2.62 Gb, which is similar to k-merbased estimations using GCE (11) (SI Appendix, Table S4) and those of published marine mammal genomes (SI Appendix, Table S5). More than 95% of each species short reads could be mapped to their respective assembly (SI Appendix, Fig. S2). BUSCO (Benchmarking Universal Single-Copy Orthologs) (version 3.0.2) (12) was used to assess the quality of the assemblies, revealing an average genome completeness of 90.98% (SI Appendix, Table S6). Analysis of syntenic relationships, comparing genome assemblies of closely related species, also showed high continuity of these genomes (SI Appendix, Fig. S3).

Assembly statistics for the 17 novel marine mammal genomes generated for this study

We employed de novo and homology-based prediction methods to annotate the genes and repeat sequences of the assembled genomes (SI Appendix, Tables S7 and S8). Annotated protein-coding genes ranged from 20,083 to 20,947 per species (Table 1). The average gene lengths were similar to those of closely related species (SI Appendix, Fig. S4), and we recovered an average 96.44% of the BUSCO Mammalia gene set (4,104 genes) (Table 1). Overall, we generated high-quality genome sequences for 17 marine mammals, providing a good foundation for developing a better understanding of aquatic adaptation in marine mammals across three divergent ancestral lineages.

Combining published genome data with our 17 genomes, we were able to provide a detailed phylogenomic reconstruction of marine mammal species. Two nucleotide datasets were used (SI Appendix, Table S9): ortholog sequences from whole-genome alignment and reciprocal best hit ortholog genes from gene annotations. The maximum-likelihood trees generated from the alignments of the individual loci of the two datasets were used as input for the coalescent-based phylogenetic method ASTRAL-III (13), and these two datasets generated a consensus topology (SI Appendix, Fig. S5 and Fig. 1A). The overall phylogenetic relationship of three lineages of marine mammals is consistent with previous studies (8, 1416). For cetaceans, they support the monophyly of Physeteroidea + Kogiidae, Delphinidae, Monodontidae + Phocoenidae, and Ziphiidae among odontocete taxa, with Physeteroidea as the most basal clade of odontocetes, consistent with a recent large-scale phylogenomic analysis of cetaceans (17). For pinnipeds, there is support for a sister group relationship between Musteloidea and Pinnipedia and the monophyly of Odobenidae + Otariidae, consistent with studies based on mitochondrial DNA (18).

Phylogeny and population changes of marine mammals. (A) A maximum likelihood phylogenetic tree of 35 marine mammal species and 16 outgroup mammal species. Three lineages of marine mammals are distinguished by columns of different colors: Cetacea (blue), Pinnipedia (green), and Sirenia (red). Red stars represent the species differentiation node mentioned in the main text. (B) Population size history of three lineages of marine mammals. The normalized effective population size (Ne) of each species was estimated using pairwise sequentially Markovian coalescent. The Ne for each group of marine mammals is shown.

We further assessed divergence times for each marine mammal phylogenetic tree node (SI Appendix, Fig. S7). The divergence time between Cetacea and Hippopotamidae was estimated to be 55.5 Mya, which coincides with the PaleoceneEocene transition and a global temperature rise, which possibly prompted terrestrial mammals to enter the sea (19). The initial split of Mysticeti (baleen whales) and Odontoceti (toothed whales) was about 37.7 Mya. The emergence of Pinnipedia was estimated to be 27.4 Mya, while the divergence time between Odobenidae and Otariidae was about 18.6 Mya. The divergence time of sirenians and the African savanna elephant, their closest land relative, was estimated to be 63.9 Mya.

We also reconstructed the demographic histories of cetaceans, pinnipeds, and sirenians (SI Appendix, Table S10). The three marine mammal lineages were found to experience different historical changes in population size (see normalized average effective population size, Ne, in Fig. 1B and individual species profiles in SI Appendix, Fig. S8). Specifically, the Ne of cetaceans experienced a rapid decline during the last 500,000 y. Consistently, the heterozygosity rate of most cetaceans is even lower than the endangered giant panda [1.32 (20, 21)] (SI Appendix, Table S11), highlighting the ongoing conservation needs of cetacean species.

We compared the genome sizes of the three marine mammal lineages with their terrestrial relatives: Cetacea versus Ruminantia, Pinnipedia versus Canidae, and Sirenia versus Proboscidea. The average genome size of Pinnipedia (2.4 Gb) and Sirenia (3.1 Gb) was similar to their terrestrial sister taxa (Fig. 2B). In contrast, the genome size of cetaceans ranged from 2.4 to 2.6 Gb and displayed a decreasing trend compared to Ruminantia (2.8 Gb in reindeer, cattle, and goat), their most closely related lineage (Fig. 2B). Consistent with the genome size comparisons, pinnipeds and sirenians present similar repeat contents to their terrestrial sister taxa, while cetacean genomes have 10% fewer repeats than ruminants. Five subtypes of repeats are more abundant in ruminant species (SI Appendix, Table S12), including LINE/RTE-BovB, LTR/ERV1, LTR/ERVK, SINE/Core-RTE, and SINE/tRNA-Core-RTE. In addition to several reported large fragments in ruminant genomes (22), we found 11 large (>1.5 Mb) deletions and three large insertions (SI Appendix, Tables S13S15) in cetaceans, compared to their terrestrial counterpart cattle.

Structural characteristics and chromosome evolution of marine mammal genomes. (A) Circos plot of representative genomes of marine mammals: sperm whale, Indo-Pacific bottlenose dolphin (IPB dolphin), South American fur seal (SA fur seal), and spotted seal. (B) Genome sizes and transposable element content analysis of representative genomes of marine mammals. We selected three Ruminantia species, three cetacean species, three Canidae species, three pinniped species, an elephant, and a manatee. (C) Chromosome evolution of Cetacea and Pinnipedia. We reconstructed 23 and 19 ancestral chromosomes of Cetacea and Pinnipedia, respectively. The chromosome assignment to ancestral chromosomes is shown by colored bars, Indo-Pacific humpback dolphin (IPH dolphin).

Based on the eight chromosome-level genome assemblies that we generated (SI Appendix, Fig. S1) and two publicly available chromosome-level genomes [(sperm whale (23) and Indo-Pacific humpback dolphin (24)], we reconstructed the ancestral chromosomes of Cetacea (using the Indo-Pacific bottlenose dolphin as the reference genome) and Pinnipedia (using the South American sea lion as the reference genome) with DESCHRAMBLER (25) at 300-kb resolution (Fig. 2C). In Cetacea, we identified 1,308 conserved segments and reconstructed 23 ancestral predicted chromosome fragments (APCFs), with a total length of 2.09 Gb. In Pinnipedia, we identified 194 conserved segments and reconstructed 19 APCFs, with a total length of 1.84 Gb. We traced back the source of these APCFs for both lineages and found there are fewer chromosome rearrangement events in Pinnipedia than in Cetacea (Fig. 2C).

We next assessed the expansion and contraction of gene families, positively selected genes (PSGs), and rapidly evolving genes (REGs) in the three marine mammal lineages. In total, 44, 29, and 212 gene families were identified as expanded, and 87, 15, and 12 gene families were contracted in the ancestor node of Cetacea, Pinnipedia, and Sirenia, respectively (SI Appendix, Fig. S9). Functional enrichment analysis of these gene families revealed that olfactory transduction is the only shared contracted Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway (SI Appendix, Table S16). Several expanded gene family-associated KEGG pathways are shared among two types of marine mammals: thermogenesis and oxidative phosphorylation in Cetacea and Pinnipedia and neural plasticity (as suggested by the alcoholism pathway) and estrogen signaling in Pinnipedia and Sirenia (SI Appendix, Table S17).

To assess the selective pressures acting on marine mammal genomes, we estimated the dN/dS ratio () using 7,252 orthologous, protein-coding genes. When compared with terrestrial outgroups, marine mammal branches always had a higher dN/dS ratio (SI Appendix, Fig. S10). We identified 5, 11, and 16 PSGs and 21, 17, and 295 REGs in the ancestral branches of Cetacea, Pinnipedia, and Sirenia, respectively (SI Appendix, Tables S18 and S19 and Fig. S9) (2 test, P < 0.05). We found that cystic fibrosis transmembrane conductance regulator (CFTR) underwent rapid evolution in both Pinnipedia and Sirenia. CFTR plays a vital role in the transport of various ions across the cell membrane, water transport, and fluid homeostasis (26, 27).

We identified 4,518,724 and 4,341,059 conserved noncoding elements (CNEs) in Cetacea and Pinnipedia, respectively. We further performed assay for transposase-accessible chromatin sequencing (ATAC-seq) (28) of two cetaceans (Indo-Pacific bottlenose dolphin and Rissos dolphin) and two pinnipeds (Baikal seal and South American sea lion) to identify CNEs associated with open chromatin (i.e., accessible to the transcriptional machinery). A total of 1,158 and 1,684 genes in Cetacea and Pinnipedia, respectively, have CNEs with ATAC-seq signal peaks within 3 kb upstream or downstream (SI Appendix, Tables S21 and 22). Of these genes, 371 have CNE peaks in both marine orders (SI Appendix, Table S23 and Fig. S11). Although further experimental work could be a worthwhile attempt to assess the contribution of these CNEs, our results provide a valuable resource for further studies on gene regulation in marine mammal species.

The evolution of marine mammals, the adaptation of terrestrial mammalian lineages to life histories dependent on the marine environment, is considered a seminal example of convergent evolution. The degree to which convergence is reflected at the molecular level can be addressed using genomics. Understanding this phenomenon addresses key questions about redundancy, pleiotropy, and the relationship between genotype and phenotype. We applied the Convergence at Conservative Sites method (29) to investigate convergent genes in the three lineages of marine mammals. Orthologous genes were assigned by synteny alignment (SI Appendix, SI Materials and Methods). We identified 195 convergent amino acid substitutions in 172 genes among marine mammals (SI Appendix, Tables S24). Only three genes (FAM20B, NFIA, and KYAT1) share convergent amino acid substitution in all three marine mammal lineages. Six genes (HERC1, MITF, EPG5, FAT1, SYNE1, and ATM) show convergent mutations at different amino acid positions in cetacean manatee and pinniped manatee. For example, MITF has an L10F substitution in cetaceans and sirenians (the manatee) and a T570A substitution in pinnipeds and the manatee. Among the 94 genes with convergent amino acid substitutions in the fully aquatic cetaceans and Sirenia, but not between the amphibious pinnipeds in either cetaceans or Sirenia, five genes are within the KEGG pathway dopaminergic synapse (though the adjusted P value is not significant at the 0.05 level: P = 0.51; SI Appendix, Table S25). Previous studies indicate that UCP1 has been independently lost in many marine mammals, especially in cetaceans and sirenians (30, 31). We confirm and extend this inference, showing that a functional UCP1 is present in most pinnipeds, except for the Antarctic fur seal, which is the most polar of the species included in this assessment (SI Appendix, Table S26 and Fig. S12).

Cetaceans have many unique biological characteristics, including echolocation, deep diving, and large variation in body size. The molecular basis of echolocation has been well studied previously (3234). However, based on more comprehensive data, we systematically reanalyzed the 504 hearing-related gene sequences in 40 species, including two groups of echolocating bats (group M: big brown bat, Natal long-fingered bat, Brandts bat, and little brown bat and group G: greater horseshoe bat) and 16 toothed whales (group T) (SI Appendix, Fig. S13). A total of 64 genes were identified as convergent genes, most reported in previous studies (SI Appendix, Table S27).

We next compared the four whale species with the best diving abilities to 20 comparatively shallow-diving species to study the genetic basis of deep diving in cetaceans. The deep-diving species are sperm whale (reported to dive to 1,860 m for >1 h) (35), Blainvilles beaked whale (1,251 m for 57 min) (36, 37), and dwarf and pygmy sperm whales [species in the family Kogiidae with highly similar ecology and habitat (up to 1,425 m for 43 min) (3840)]. We retrieved 1,803 genes from HypoxiaDB, a hypoxia-regulated protein database (41), and observed 39 genes with at least one specific amino acid change unique to the deep-diving group (SI Appendix, Table S28). MB encodes myoglobin, a protein critical for oxygen storage and transport (42). Deep-diving species have amino acid residue changes associated with elevated myoglobin net surface charge and maximal dive time (43). Compared with background branches, 45 genes showed significantly higher dN/dS ratios in deep-diving species (SI Appendix, Table S29) (2 test, P < 0.05). We detected 45 REGs in deep-diving cetaceans. Of these, three genes (SETX, GIF, and TMPRSS11D) had dN/dS values above 1, indicating positive selection. Seven REGs (CEP170, DHCR7, DSP, GBE1, PLD1, SETX, and TMPRSS11D) have shared amino acid mutations in the four deep-diving species.

Cetacean bodyweight spans orders of magnitude from 50 kg (the vaquita, Phocoena sinus) up to 180,000 kg (the blue whale, Balaenoptera musculus) (44). We selected a set of 1,528 genes involved in body size development and estimated their dN/dS ratios in cetaceans with large body size: the blue whale (3) and the sperm whale (3). Compared to the background, we found 102 REGs (with significantly higher dN/dS) in giant cetaceans (SI Appendix, Table S30 and Fig. S14) (2 test, P < 0.05). These REGs were enriched in the Hedgehog and Wnt signaling pathways essential for bone development (45) (SI Appendix, Table S31). Additional bone developmentrelated genes with a higher dN/dS in giant cetaceans include BMP1 in the TGF- signaling pathway and the Notch signaling pathway genes SNW1 and CTBP2.

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Comparative genomics provides insights into the aquatic adaptations of mammals - pnas.org

CRISPR/Cas9 platform announced the release of its transgene-free genome editing in plants to accelerate the research in the field of plant science for basic research.

New York, USA September 9, 2021 CRISPR/Cas9 platform, the professional division of Creative Biogene, focuses on providing comprehensive gene-editing services and products by using CRISPR/Cas9 technology. With professional products and services, CRISPR/Cas9 platform is dedicated to supporting the progress of gene editing projects. Recently, CRISPR/Cas9 platform announced the release of its transgene-free genome editing in plants to accelerate the research in the field of plant science for basic research.

CRISPR/Cas9 platform provides one-stop plant genome editing services, including gene knockout, gene knock-in and gene deletion. The service provides a variety of species, including but not limited to Arabidopsis, corn, rice, and tobacco. The specific workflow includes the design and construction of SgRNA, the delivery of Cas9 and sgRNA to plant cells, as well as targeted mutation analysis and final delivery.

CRISPR/Cas9 platform focuses on genome editing technology and provides comprehensive services to establish genome editing plants with specific genome engineering modifications on target genes/locus of interest. It also helps customers generate commercially viable target gene-edited crops, and produce non-GMO, non-regulated and sustainable genome-edited plants.

CRISPR/Cas9 platform provides GMO-free genome editing services for rice, tomato and Arabidopsis. Non-transgenic edited plants are generally obtained through genetic separation through selfing and crossing of T0 plants. Subsequently, PCR-based genotyping was used to identify T1 plants without DNA. CRISPR/Cas9 Platform also provides other strategies, such as RNP/RNA-based methods and marker-assisted transgene elimination to meet specific requirements.

CRISPR/Cas9 platform has been committed to improving plant transformation efficiency and optimizing genome editing systems for many years. Two different base editors have recently been introduced, Cytosine Base Editor (CBE) and Adenine Base Editor (ABE). CBE realizes the efficient substitution of CG to TA, and ABE mediates the transformation of AT to GC in genomic DNA. CRISPR/Cas9 Platform combines a base editor with genetic transformation technology to generate single base substitutions in the plant genome. It has been applied to precision plant breeding and transformation in agriculture.

With excellent experts and years of plant genome editing experience, we provide global customers with one-stop services from project design to genetically modified plant screening. said Marcia Brady, the marketing director of Creative Biogene, she also added, Also, we are committed to offering customized solutions to satisfy specific needs, providing professional consultation and evaluation for specific projects.

About CRISPR/Cas9 platform

CRISPR/Cas9 platform, as a professional division of Creative Biogene, is dedicated to supporting our clients conduct genetic research with comprehensive gene-editing services and products as well as experienced in-house experts. With years of effort. Creative Biogene CRISPR/Cas9 platform has become a world-recognized industry platform that supports millions of scientists worldwide.

Media ContactCompany Name: Creative BiogeneContact Person: Marcia BradyEmail: Send EmailPhone: 1-631-386-8241Country: United StatesWebsite: https://www.creative-biogene.com/crispr-cas9

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CRISPR Cas9 Platform Provides One-stop Transgene-Free Genome Editing in Plants to Support the Research of Plant Science - Digital Journal