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Ancient Gene Duplicates in Gossypium (Cotton) Exhibit Near-Complete Expression Divergence
Genome Biology and Evolution
  • Simon Renny-Byfield, Iowa State University
  • Joseph P. Gallagher, Iowa State University
  • Corrinne E. Grover, Iowa State University
  • Emmanuel Szadkowski, Iowa State University
  • Justin T. Page, Brigham Young University - Provo
  • Joshua A. Udall, Brigham Young University - Provo
  • Xiyin Wang, University of Georgia
  • Andrew H. Paterson, University of Georgia
  • Jonathan F. Wendel, Iowa State University
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Whole genome duplication (WGD) is widespread in flowering plants and is a driving force in angiosperm diversification. The redundancy introduced by WGD allows the evolution of novel gene interactions and functions, although the patterns and processes of diversification are poorly understood. We identified ∼ 2,000 pairs of paralogous genes in Gossypium raimondii (cotton) resulting from an approximately 60 My old 5- to 6-fold ploidy increase. Gene expression analyses revealed that, in G. raimondii, 99.4% of the gene pairs exhibit differential expression in at least one of the three tissues (petal, leaf, and seed), with 93% to 94% exhibiting differential expression on a per-tissue basis. For 1,666 (85%) pairs, differential expression was observed in all tissues. These observations were mirrored in a time series of G. raimondii seed, and separately in leaf, petal, and seed of G. arboreum, indicating expression level diversification before species divergence. A generalized linear model revealed 92.4% of the paralog pairs exhibited expression divergence, with most exhibiting significant gene and tissue interactions indicating complementary expression patterns in different tissues. These data indicate massive, near-complete expression level neo- and/or subfunctionalization among ancient gene duplicates, suggesting these processes are essential in their maintenance over ∼ 60 Ma.

This article is from Genome Biology and Evolution 6 (2014): 559, doi:10.1093/gbe/evu037. Posted with permission.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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Simon Renny-Byfield, et al.
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Simon Renny-Byfield, Joseph P. Gallagher, Corrinne E. Grover, Emmanuel Szadkowski, et al.. "Ancient Gene Duplicates in Gossypium (Cotton) Exhibit Near-Complete Expression Divergence" Genome Biology and Evolution Vol. 6 Iss. 3 (2014) p. 559 - 571
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