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Plant J. 2013 Jan;73(1):143-53. doi: 10.1111/tpj.12026. Epub 2012 Oct 22.

The fate of duplicated genes in a polyploid plant genome.

Author information

1
Institute for Plant Breeding, Genetics and Genomics, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA.
2
Zoologisches Institut, Universität Basel, Vesalgasse 1, CH-4051, Basel, Switzerland.
3
Department of Statistics, Purdue University, West Lafayette, IN, 47907, USA.
4
Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
5
Divisions of Plant Science and Biochemistry, University of Missouri, Columbia, MO, 65211, USA.
6
Department of Botany and Microbiology, University of Oklahoma, Norman, OK, 73019, USA.
7
College of Computing and Informatics, University of North Carolina Charlotte, Charlotte, NC, 28223, USA.
8
National Center for Genome Resources, Santa Fe, NM, USA.

Abstract

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 (Glycine 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.

KEYWORDS:

Glycine max; RNA-seq; duplicated gene expression; genome evolution; polyploidy; sub-functionalization

PMID:
22974547
DOI:
10.1111/tpj.12026
[Indexed for MEDLINE]
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