Govaerts, R. How many species of seed plants are there? TAXON 50, 10851090 (2001).<\/p>\n
Google Scholar <\/p>\n
Friis, E. M., Pedersen, K. R. & Crane, P. R. Cretaceous angiosperm flowers: Innovation and evolution in plant reproduction. Palaeogeogr., Palaeoclimatol., Palaeoecol. 232, 251293 (2006).<\/p>\n
Google Scholar <\/p>\n
Magalln, S., Gmez-Acevedo, S., Snchez-Reyes, L. L. & Hernndez-Hernndez, T. A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity. N. Phytol. 207, 437453 (2015).<\/p>\n
Google Scholar <\/p>\n
Jiao, Y. et al. Ancestral polyploidy in seed plants and angiosperms. Nature 473, 97100 (2011).<\/p>\n
ADS CAS PubMed Google Scholar <\/p>\n
Amborella Genome Project. The Amborella genome and the evolution of flowering plants. Science 342, 1241089 (2013).<\/p>\n
Google Scholar <\/p>\n
Schranz, M. E., Mohammadin, S. & Edger, P. P. Ancient whole genome duplications, novelty and diversification: the WGD Radiation Lag-Time Model. Curr. Opin. Plant Biol. 15, 147153 (2012).<\/p>\n
PubMed Google Scholar <\/p>\n
Vanneste, K., Maere, S. & Peer, deY. V. Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution. Philos. Trans. R. Soc. B 369, 20130353 (2014).<\/p>\n
Google Scholar <\/p>\n
Tank, D. C. et al. Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications. N. Phytologist 207, 454467 (2015).<\/p>\n
Google Scholar <\/p>\n
Soltis, P. S. & Soltis, D. E. Ancient WGD events as drivers of key innovations in angiosperms. Curr. Opin. Plant Biol. 30, 159165 (2016).<\/p>\n
PubMed Google Scholar <\/p>\n
Landis, J. B. et al. Impact of whole-genome duplication events on diversification rates in angiosperms. Am. J. Bot. 105, 348363 (2018).<\/p>\n
PubMed Google Scholar <\/p>\n
Cantino, P. D. et al. Towards a phylogenetic nomenclature of Tracheophyta. Taxon 56, 1E44E (2007).<\/p>\n
Google Scholar <\/p>\n
Jaillon, O. et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449, 463467 (2007).<\/p>\n
ADS CAS PubMed Google Scholar <\/p>\n
Jiao, Y. et al. A genome triplication associated with early diversification of the core eudicots. Genome Biol. 13, R3 (2012).<\/p>\n
PubMed PubMed Central Google Scholar <\/p>\n
Vekemans, D. et al. Gamma paleohexaploidy in the stem-lineage of core eudicots: significance for MADS-box gene and species diversification. Mol. Biol. Evol. https:\/\/doi.org\/10.1093\/molbev\/mss183<\/a> (2012).<\/p>\n Chanderbali, A. S., Berger, B. A., Howarth, D. G., Soltis, D. E. & Soltis, P. S. Evolution of floral diversity: genomics, genes and gamma. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 372, 20150509 (2017).<\/p>\n Soltis, D. E. et al. Gunnerales are sister to other core eudicots: implications for the evolution of pentamery. Am. J. Bot. 90, 461470 (2003).<\/p>\n PubMed Google Scholar <\/p>\n Endress, P. K. In Advances in Botanical Research 44: Developmental Genetics of the Flower (eds. Soltis, D. E., Leebens-Mack, J. H. & Soltis, P. S.) 161 (Elsevier, 2006).<\/p>\n Endress, P. K. Flower structure and trends of evolution in eudicots and their major subclades. Ann. Mo. Botanical Gard. 97, 541583 (2010).<\/p>\n Google Scholar <\/p>\n Soltis, D. E. et al. Angiosperm phylogeny: 17 genes, 640 taxa. Am. J. Bot. 98, 704730 (2011).<\/p>\n PubMed Google Scholar <\/p>\n Ohno, S. Evolution by Gene Duplication (Springer-Verlag, 1970).<\/p>\n Lyons, E., Pedersen, B., Kane, J. & Freeling, M. The value of nonmodel genomes and an example using SynMap within CoGe to dissect the hexaploidy that predates the rosids. Tropical Plant Biol. 1, 181190 (2008).<\/p>\n CAS Google Scholar <\/p>\n Ming, R. et al. Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biol. 14, R41 (2013).<\/p>\n PubMed PubMed Central Google Scholar <\/p>\n Tang, H. et al. Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Res. 18, 19441954 (2008).<\/p>\n CAS PubMed PubMed Central Google Scholar <\/p>\n Akz, G. & Nordborg, M. The Aquilegia genome reveals a hybrid origin of core eudicots. Genome Biol. 20, 256 (2019).<\/p>\n PubMed PubMed Central Google Scholar <\/p>\n Velasco, R. et al. A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS ONE 2, e1326 (2007).<\/p>\n ADS PubMed PubMed Central Google Scholar <\/p>\n Worberg, A. et al. Phylogeny of basal eudicots: insights from non-coding and rapidly evolving DNA. Org. Diversity Evolution 7, 5577 (2007).<\/p>\n Google Scholar <\/p>\n Ruhfel, B. R., Gitzendanner, M. A., Soltis, P. S., Soltis, D. E. & Burleigh, J. G. From algae to angiospermsinferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Evolut. Biol. 14, 23 (2014).<\/p>\n Google Scholar <\/p>\n Moore, M. J., Soltis, P. S., Bell, C. D., Burleigh, J. G. & Soltis, D. E. Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots. Proc. Natl Acad. Sci. USA 107, 46234628 (2010).<\/p>\n ADS CAS PubMed PubMed Central Google Scholar <\/p>\n Sun, Y. et al. Phylogenomic and structural analyses of 18 complete plastomes across nearly all families of early-diverging eudicots, including an angiosperm-wide analysis of IR gene content evolution. Mol. Phylogenet. Evol. 96, 93101 (2016).<\/p>\n PubMed Google Scholar <\/p>\n Leebens-Mack, J. H. et al. One thousand plant transcriptomes and the phylogenomics of green plants. Nature 574, 679685 (2019).<\/p>\n Google Scholar <\/p>\n Filiault, D. L. et al. The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history. Elife 7, e36426 (2018).<\/p>\n Strijk, J. S., Hinsinger, D. D., Zhang, F. & Cao, K. Trochodendron aralioides, the first chromosome-level draft genome in Trochodendrales and a valuable resource for basal eudicot research. Gigascience 8, giz136 (2019).<\/p>\n Liu, P.-L. et al. The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements. Genome Biol. 21, 291 (2020).<\/p>\n CAS PubMed PubMed Central Google Scholar <\/p>\n Xu, Q., Jin, L., Zheng, C., Leebens-Mack, J. & Sankoff, D. in Lecture Notes in Bioinformatics Vol. 12686 (2021).<\/p>\n Chin, C.-S. et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nat. Methods 13, 10501054 (2016).<\/p>\n CAS PubMed PubMed Central Google Scholar <\/p>\n Ghurye, J. et al. Integrating Hi-C links with assembly graphs for chromosome-scale assembly. PLoS Comput. Biol. 15, e1007273 (2019).<\/p>\n Yang, X., Lu, S. & Peng, H. Cytological studies on the eastern Asian family Trochodendraceae. Bot. J. Linn. Soc. 158, 332335 (2008).<\/p>\n Google Scholar <\/p>\n Van Laere, K., Hermans, D., Leus, L. & Van Huylenbroeck, J. Genetic relationships in European and Asiatic Buxus species based on AFLP markers, genome sizes and chromosome numbers. Plant Syst. Evolution 293, 111 (2011).<\/p>\n Google Scholar <\/p>\n Simo, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 32103212 (2015).<\/p>\n PubMed Google Scholar <\/p>\n Seppey, M., Manni, M. & Zdobnov, E. M. in Gene Prediction: Methods and Protocols (ed. Kollmar, M.) 227245 (Springer, 2019).<\/p>\n Ratter, J. A. & Milne, C. in Notes from the Royal Botanic Garden Edinburgh (UK) (1976).<\/p>\n Dodsworth, S., Chase, M. W. & Leitch, A. R. Is post-polyploidization diploidization the key to the evolutionary success of angiosperms?. Botanical J. Linn. Soc. 180, 15 (2016).<\/p>\n Google Scholar <\/p>\n Waterhouse, R. M. et al. BUSCO applications from quality assessments to gene prediction and phylogenomics. Mol. Biol. Evol. 35, 543548 (2018).<\/p>\n CAS PubMed Google Scholar <\/p>\n Johnson, M. G. et al. A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering. Syst. Biol. 68, 594606 (2019).<\/p>\n CAS PubMed Google Scholar <\/p>\n Emms, D. M. & Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20, 238 (2019).<\/p>\n PubMed PubMed Central Google Scholar <\/p>\n Mirarab, S. & Warnow, T. ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics 31, i44i52 (2015).<\/p>\n CAS PubMed PubMed Central Google Scholar <\/p>\n Sankoff, D., Zheng, C., Lyons, E. & Tang, H. in Algorithms for Computational Biology (eds. Botn-Fernndez, M., Martn-Vide, C., Santander-Jimnez, S. & Vega-Rodrguez, M. A.) 314 (Springer International Publishing, 2016).<\/p>\n Sankoff, D. & Zheng, C. in Comparative Genomics: Methods and Protocols (eds. Setubal, J. C., Stoye, J. & Stadler, P. F.) 291315 (Springer, 2018).<\/p>\n Murat, F., Armero, A., Pont, C., Klopp, C. & Salse, J. Reconstructing the genome of the most recent common ancestor of flowering plants. Nat. Genet 49, 490496 (2017).<\/p>\n CAS PubMed Google Scholar <\/p>\n Roach, M. J., Schmidt, S. A. & Borneman, A. R. Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies. BMC Bioinforma. 19, 460 (2018).<\/p>\n CAS Google Scholar <\/p>\n Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 21142120 (2014).<\/p>\n CAS PubMed PubMed Central Google Scholar <\/p>\n Grabherr, M. G. et al. Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nat. Biotechnol. 29, 644652 (2011).<\/p>\n CAS PubMed PubMed Central Google Scholar <\/p>\n Holt, C. & Yandell, M. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinforma. 12, 491 (2011).<\/p>\n Google Scholar <\/p>\n Campbell, M. S. et al. MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiol. 164, 513524 (2014).<\/p>\n CAS PubMed Google Scholar <\/p>\n Ellinghaus, D., Kurtz, S. & Willhoeft, U. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinforma. 9, 18 (2008).<\/p>\n Google Scholar <\/p>\n Steinbiss, S., Willhoeft, U., Gremme, G. & Kurtz, S. Fine-grained annotation and classification of de novo predicted LTR retrotransposons. Nucleic Acids Res. 37, 70027013 (2009).<\/p>\n CAS PubMed PubMed Central Google Scholar <\/p>\n <\/p>\n See original here: Govaerts, R. How many species of seed plants are there? Continue reading
\nBuxus and Tetracentron genomes help resolve eudicot genome history - Nature.com<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"