Ancestral polyploidy in seed plants and angiosperms

Abstract

Whole-genome duplication (WGD), or polyploidy, followed by gene loss and diploidization has long been recognized as an important evolutionary force in animals, fungi and other organisms, especially plants. The success of angiosperms has been attributed, in part, to innovations associated with gene or whole-genome duplications, but evidence for proposed ancient genome duplications pre-dating the divergence of monocots and eudicots remains equivocal in analyses of conserved gene order. Here we use comprehensive phylogenomic analyses of sequenced plant genomes and more than 12.6 million new expressed-sequence-tag sequences from phylogenetically pivotal lineages to elucidate two groups of ancient gene duplications-one in the common ancestor of extant seed plants and the other in the common ancestor of extant angiosperms. Gene duplication events were intensely concentrated around 319 and 192 million years ago, implicating two WGDs in ancestral lineages shortly before the diversification of extant seed plants and extant angiosperms, respectively. Significantly, these ancestral WGDs resulted in the diversification of regulatory genes important to seed and flower development, suggesting that they were involved in major innovations that ultimately contributed to the rise and eventual dominance of seed plants and angiosperms.

The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

“…Phylogenomic analysis. To infer the timing of genome duplication events relative to speciation events, all annotated Musa genes were sorted based on best BLASTP hit into the gene family clusters circumscribed by Jiao et al 52 and the PlantTribes database 53 (http://fgp.bio.psu.edu/tribedb/), including sequenced eudicotyledons and monocotyledons, along with transcriptome assemblies for other non-grass monocotyledons (Supplementary Text). Gene family clusters were queried for Sorghum 18 and Musa orthologues mapping to syntenic blocks, and maximum likelihood gene trees were estimated for these gene families using the GTR1GAMMA model of molecular evolution in RAxML 54 .…”

How life changes itself: The Read–Write (RW) genome

“…Moreover, the genome sequence record provides abundant evidence for hybridization as a powerful driver of "hybrid speciation" in plants and animals [121,122]. Darwin's "abominable mystery" of rapid seed plant (angiosperm) diversification results from the ease of interspecific hybridization and the capacity for self-fertilization by hybrids in these organisms [123].…”

Life at the extreme: lessons from the genome

“…In most plants, including T. parvula , genomes enriched by polyploidy have subsequently experienced extensive gene losses [33]. Their modern genomes reflect this.…”