Ancient Gene Duplicates in Gossypium (Cotton) Exhibit Near-Complete Expression Divergence

作者：Renny Byfield Simon; Gallagher Joseph P; Grover Corrinne E; Szadkowski Emmanuel; Page Justin T; Udall Joshua A; Wang Xiyin; Paterson Andrew H; Wendel Jonathan F^*

来源：Genome Biology and Evolution, 2014, 6(3): 559-571.

DOI：10.1093/gbe/evu037

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 similar to 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, withmost 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 similar to 60 Ma.

• 出版日期2014