Re-evaluating the phylogeny of allopolyploid Gossypium L.

Abstract

The formation of allopolyploid cotton precipitated a rapid diversification and colonization of dry coastal American tropical and subtropical regions. Previous phylogenetic analyses, combined with molecular divergence analyses, have offered a temporal framework for this radiation, but provide only weak support for some of the resolved branches. Moreover, these earlier analyses did not include the recently recognized sixth polyploid species, G. ekmanianum Wittmack. Here we use targeted sequence capture of multiple loci in conjunction with both concatenated and Bayesian concordance analyses to reevaluate the phylogeny of allopolyploid cotton species. Although phylogenetic resolution afforded by individual genes is often low, sufficient signal was attained both through the concatenated and concordance analyses to provide robust support for the Gossypium polyploid clade, which is reported here.

Assessment of Genetic Diversity, Population Structure, and Evolutionary Relationship of Uncharacterized Genes in a Novel Germplasm Collection of Diploid and Allotetraploid Gossypium Accessions Using EST and Genomic SSR Markers

“…The results are quite congruent to prior taxonomic studies [2,3,66]. The average genetic distance (GD = 0.325) revealed the overall level of genetic diversity to be high among semi-wild and cultivated accessions; this finding is similar to earlier reports [26,67,68].…”

Uncovering SNP and indel variations of tetraploid cottons by SLAF-seq

“…The phylogenetic analysis has been reported in a previous study [37], and it was based on the targeted genes sequence capture method. Here, we used high-throughput sequencing to reconstruct the phylogenetic trees that showed a high concordance with the historically hypothesized phylogeny, providing strong support for the phylogenetic relationships in diploid and allotetraploid cottons (Fig.…”

Epigenomic and functional analyses reveal roles of epialleles in the loss of photoperiod sensitivity during domestication of allotetraploid cottons

“…1a). The allotetraploid diverged into five or more species [32, 34]. Two of them, Gossypium hirsutum (Gh, Upland cotton) and Gossypium barbadense (Gb, Pima cotton), were independently domesticated for higher fiber yield and wider geographical distribution; these characteristics were accompanied by extraordinary morphological changes including loss of photoperiod sensitivity, reduction in seed dormancy, and conversion from tree-like wild species to an annual crop [31, 33, 35].…”