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The fate of duplicated genes in a polyploid plant genome
Author(s) -
Roulin Anne,
Auer Paul L.,
Libault Marc,
Schlueter Jessica,
Farmer Andrew,
May Greg,
Stacey Gary,
Doerge Rebecca W.,
Jackson Scott A.
Publication year - 2013
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.12026
Subject(s) - biology , gene , genome , genetics , polyploid , gene duplication , epigenetics , gene expression
Summary Polyploidy is generally not tolerated in animals, but is widespread in plant genomes and may result in extensive genetic redundancy. The fate of duplicated genes is poorly understood, both functionally and evolutionarily. Soybean ( G lycine max L .) has undergone two separate polyploidy events (13 and 59 million years ago) that have resulted in 75% of its genes being present in multiple copies. It therefore constitutes a good model to study the impact of whole‐genome duplication on gene expression. Using RNA ‐seq, we tested the functional fate of a set of approximately 18 000 duplicated genes. Across seven tissues tested, approximately 50% of paralogs were differentially expressed and thus had undergone expression sub‐functionalization. Based on gene ontology and expression data, our analysis also revealed that only a small proportion of the duplicated genes have been neo‐functionalized or non‐functionalized. In addition, duplicated genes were often found in collinear blocks, and several blocks of duplicated genes were co‐regulated, suggesting some type of epigenetic or positional regulation. We also found that transcription factors and ribosomal protein genes were differentially expressed in many tissues, suggesting that the main consequence of polyploidy in soybean may be at the regulatory level.