DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton.

Justin T Page,Amanda M Hulse-Kemp,Hamid Ashrafi,David M Stelly,Rich H Alexander,Allen Van Deynze,Kimberly Clemons,Zach S Liechty,Joshua A Udall,Kirsten Bomblies

doi:10.1371/journal.pgen.1006012

Justin T Page, Amanda M Hulse-Kemp + Show 8 more

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https://doi.org/10.1371/journal.pgen.1006012

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Abstract

Allotetraploid cotton species are a vital source of spinnable fiber for textiles. The polyploid nature of the cotton genome raises many evolutionary questions as to the relationships between duplicated genomes. We describe the evolution of the cotton genome (SNPs and structural variants) with the greatly improved resolution of 34 deeply re-sequenced genomes. We also explore the evolution of homoeologous regions in the AT- and DT-genomes and especially the phenomenon of conversion between genomes. We did not find any compelling evidence for homoeologous conversion between genomes. These findings are very different from other recent reports of frequent conversion events between genomes. We also identified several distinct regions of the genome that have been introgressed between G. hirsutum and G. barbadense, which presumably resulted from breeding efforts targeting associated beneficial alleles. Finally, the genotypic data resulting from this study provides access to a wealth of diversity sorely needed in the narrow germplasm of cotton cultivars.

Highlights

Domesticated cotton has a polyploid genome consisting of an AT- and DT-genome
We we examine the comparative evolution and genetic diversity of the polyploid cotton species and genomes by mapping reads to the diploid A- and D-genome reference sequences of G. arboreum [19] and G. raimondii [20], as well as to the recently published drafts of the cotton tetraploid genomes [21,22]
3) The duplication/deletion events do not have the same start and stop sites. We suggest that this possible conversion event—the only major event suggested by our sequencing data—was likely not a true conversion event because a complex series of introgression and selection that would be needed to occur to find it in two separate species of cotton

Summary

Introduction

Domesticated cotton has a polyploid genome consisting of an AT- and DT-genome (the “T” subscript indicates tetraploid nucleus). 1 mya, a polyploidization event gave rise to six described AD allotetraploid species with genome sizes ~2400 Mbp, mostly native to Central and South America [1,2,3,4]. There are two major clades among the six tetraploid species, one containing G. hirsutum (AD1) and the other containing G. barbadense (AD2). Both of these species were independently domesticated and produce long spinnable fiber. The remaining tetraploid species (AD3 –AD6) AD1 is the source of the vast majority (~90%) of worldwide cotton production [5]. Introgression of genetic material from AD2 into AD1 (or vice versa) is of particular interest

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