Comparative genomic de‐convolution of the cotton genome revealed a decaploid ancestor and widespread chromosomal fractionation

Abstract

SummaryThe 'apparently' simple genomes of many angiosperms mask complex evolutionary histories. The reference genome sequence for cotton (Gossypium spp.) revealed a ploidy change of a complexity unprecedented to date, indeed that could not be distinguished as to its exact dosage.Herein, by developing several comparative, computational and statistical approaches, we revealed a 59 multiplication in the cotton lineage of an ancestral genome common to cotton and cacao, and proposed evolutionary models to show how such a decaploid ancestor formed.The c. 70% gene loss necessary to bring the ancestral decaploid to its current gene count appears to fit an approximate geometrical model; that is, although many genes may be lost by single-gene deletion events, some may be lost in groups of consecutive genes. Gene loss following cotton decaploidy has largely just reduced gene copy numbers of some homologous groups.We designed a novel approach to deconvolute layers of chromosome homology, providing definitive information on gene orthology and paralogy across broad evolutionary distances, both of fundamental value and serving as an important platform to support further studies in and beyond cotton and genomics communities.

Hierarchically Aligning 10 Legume Genomes Establishes a Family-Level Genomics Platform

“…The details inferring orthology and paralogy can be found in "Materials and Methods" and Supplemental Text S1. Similar analyses have been described for grass genomes and the cotton (Gossypium hirsutum) genome (Paterson et al, 2012;Wang et al, 2015Wang et al, , 2016. In that an extra LCT is shared by all legumes, there would be an expected 1:2 ratio of orthologous regions between grape and most legumes, with the additional SST conferring a 1:4 ratio between grape and soybean.…”

A Malvaceae mystery: A mallow maelstrom of genome multiplications and maybe misleading methods?

“…Even in sampling genomic‐scale data for eight of the nine subfamilies in the Malvaceae, it is still uncertain as to whether cotton has undergone a 5‐ or 6‐fold multiplication (Paterson et al ; Wang et al ), and whether this same history is shared by other subfamilies in the Malvaceae. Nonetheless, our data suggest two alternative hypotheses, which are quite different despite both invoking two autotetraploidy events and one allopolyploidy event.…”

“…Genomic evidence for WGM in the Malvaceae was first described in the publication of the Gossypium raimondii genome, where collinearity data supported an ancient 5‐ to 6‐fold WGM sometime after its divergence from chocolate ( Theobroma cacao ), estimated at approximately 90 million years ago (Paterson et al ). Subsequent analyses (using various lines of evidence) have attempted to infer whether this event consisted of two successive whole genome duplication/triplication events, or a single deca‐ or dodecaploidization event (Wang et al ). In addition, studies have investigated if any other Malvaceae taxa show evidence of the same event(s), namely Durio zibethinus (Teh et al ) and Firmiana danxiaensis (Chen et al ).…”

Overlooked polyploidies in lycophytes generalize their roles during the evolution of vascular plants

“…The availability of whole-genome sequences provides evidence of ancient polyploidies that one can see other than infer. However, as mentioned previously, there have been quite some failures in deconvoluting these large-scale events (Paterson et al 2005;Wang et al 2005;Li et al 2015;Wang et al 2016b). The initial analysis of Selagillana genome overlooked these large-scale evolutionary events.…”

“…There occurred quite several times that certain ancestral polyploidies eluded from genome analysis, resulting in problematic interpretation of the structure, evolution, and/or functional innovation of whole genomes and key gene families (Paterson et al 2005;Wang et al 2005;Li et al 2015;Wang et al 2016b). In sake of much time, energy, and money invested in a genome project, this can be a nonelected pity.…”