Abstract
We employed phylogenomic methods to study molecular evolutionary processes and phylogeny in the geographically widely dispersed New World diploid cottons (Gossypium, subg. Houzingenia). Whole genome resequencing data (average of 33× genomic coverage) were generated to reassess the phylogenetic history of the subgenus and provide a temporal framework for its diversification. Phylogenetic analyses indicate that the subgenus likely originated following transoceanic dispersal from Africa about 6.6 Ma, but that nearly all of the biodiversity evolved following rapid diversification in the mid-Pleistocene (0.5–2.0 Ma), with multiple long-distance dispersals required to account for range expansion to Arizona, the Galapagos Islands, and Peru. Comparative analyses of cpDNAversus nuclear data indicate that this history was accompanied by several clear cases of interspecific introgression. Repetitive DNAs contribute roughly half of the total 880 Mb genome, but most transposable element families are relatively old and stable among species. In the genic fraction, pairwise synonymous mutation rates average 1% per Myr, with nonsynonymous changes being about seven times less frequent. Over 1.1 million indels were detected and phylogenetically polarized, revealing a 2-fold bias toward deletions over small insertions. We suggest that this genome down-sizing bias counteracts genome size growth by TE amplification and insertions, and helps explain the relatively small genomes that are restricted to this subgenus. Compared with the rate of nucleotide substitution, the rate of indel occurrence is much lower averaging about 17 nucleotide substitutions per indel event.
Highlights
The American, diploid “D-genome” cottons comprise a monophyletic clade of cytogenetically and morphologically distinct species largely distributed from Southwest Mexico to Arizona, with additional disjunct species distributions in Peru and the Galapagos Islands (Fryxell 1979; Endrizzi et al 1985; Alvarez et al 2005; Wendel and Grover 2015)
All accessions were assembled via ABySS using multiple kmer values and the assembly with the greatest E-size (Salzberg et al 2012) was selected to represent each species. These representative assemblies were improved with the reference-based scaffolder Chromosomer (Tamazian et al 2016) using the closely related G. raimondii genome (Paterson et al 2012), producing assemblies that range in size from 585 to 775 Mbp and cover 67–85% of each genome
This suggests a general completeness of the gene space, with an average of 87% complete BUSCOs recovered from each accession and less than 3.5% redundancy on average
Summary
The American, diploid “D-genome” cottons (subgenus Houzingenia) comprise a monophyletic clade of cytogenetically and morphologically distinct species largely distributed from Southwest Mexico to Arizona, with additional disjunct species distributions in Peru and the Galapagos Islands (Fryxell 1979; Endrizzi et al 1985; Alvarez et al 2005; Wendel and Grover 2015) (fig. 1). The American, diploid “D-genome” cottons (subgenus Houzingenia) comprise a monophyletic clade of cytogenetically and morphologically distinct species largely distributed from Southwest Mexico to Arizona, with additional disjunct species distributions in Peru and the Galapagos Islands (Fryxell 1979; Endrizzi et al 1985; Alvarez et al 2005; Wendel and Grover 2015) Evol. 11(1):53–71. doi:10.1093/gbe/evy256 Advance Access publication November 23, 2018
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