ARS | Publication request: Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres

Submitted to: Nature
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 21, 2012
Publication Date: December 20, 2012
Citation: Paterson, A.H., Wendel, J.F., Gundlach, H., Guo, H., Jenkins, J., Jin, D., Llewellyn, D., Showmaker, K.C., Shu, S., Udall, J., Duke, M.V., Scheffler, B.E., Scheffler, J.A. 2012. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature. 492:423-428.

Interpretive Summary: Cotton is a tetraploid genome meaning it has a set of chromosomes from two different but related wild cotton species. Therefore cultivated upland cotton has an ‘A’ and a ‘D’ genome. G. herbaceum ‘A’ and Gossypium raimondii ‘D’ are believed to be the closest relatives to the wild species that gave rise to cultivated cotton. This paper deals with genome sequencing of Gossypium raimondii ‘D’ using a high quality standard for final assembly so that it can be used as a reference genome to compare to other cotton species. A specific comparison was made to two diploid genomes using a technique called re-sequencing to look at the evolution of fiber. The species were G. herbaceum ‘A’ which produces spinnable fiber and G. longicalyx ‘F’ which does not produce spinnable fiber. Comparisons of these three genomes with a cultivated tetraploid cotton genome gives an indication as to how exchanges between the two genomes in the tetraploid along with new mutations give rise to phenotypic innovation (superior phenotypic traits) and/or ecological adaptation.

Technical Abstract: Emergent phenotypes are common in polyploids relative to their diploid progenitors, a phenomenon exemplified by spinnable cotton fibers. Following 15-18 fold paleopolyploidy, allopolyploidy 1-2 million years ago reunited divergent Gossypium genomes, imparting new combinatorial complexity that might be unraveled by comparison to extant diploids. Similar gene content and order makes a Gossypium raimondii ‘D’ reference sequence suitable as outgroup for elucidating fiber evolution by comparing monophyletic spinnable-fibered G. herbaceum ‘A’ and non-spinnable G. longicalyx ‘F’ genomes. Comparison to the allopolyploid G. hirsutum ‘AtDt’ genome exemplifies how polyploids may achieve phenotypic innovation and/or ecological adaptation by commingling new mutations with bi-directional but asymmetric exchanges between ‘subgenomes’, recombining alleles from the D-genome progenitor native to its New World habitat and the A-genome progenitor in which spinnable fiber evolved. Patterns of diversity, expression, paleo- and neo-evolution implicate specific gene families and coordinately regulated gene clusters in fiber evolution and its elaboration in polyploids.