title: The fate of duplicated genes in a polyploid plant genome.
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.
authors.affiliation: Institute for Plant Breeding, Genetics and Genomics, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA.|Zoologisches Institut, Universität Basel, Vesalgasse 1, CH-4051, Basel, Switzerland.
authors.forename: Anne
authors.initials: A
authors.lastname: Roulin
authors.affiliation: Department of Statistics, Purdue University, West Lafayette, IN, 47907, USA.|Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
authors.forename: Paul L
authors.initials: PL
authors.lastname: Auer
authors.affiliation: Divisions of Plant Science and Biochemistry, University of Missouri, Columbia, MO, 65211, USA.|Department of Botany and Microbiology, University of Oklahoma, Norman, OK, 73019, USA.
authors.forename: Marc
authors.initials: M
authors.lastname: Libault
authors.affiliation: Institute for Plant Breeding, Genetics and Genomics, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA.|College of Computing and Informatics, University of North Carolina Charlotte, Charlotte, NC, 28223, USA.
authors.forename: Jessica
authors.initials: J
authors.lastname: Schlueter
authors.affiliation: National Center for Genome Resources, Santa Fe, NM, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Farmer
authors.affiliation: National Center for Genome Resources, Santa Fe, NM, USA.
authors.forename: Greg
authors.initials: G
authors.lastname: May
authors.affiliation: Divisions of Plant Science and Biochemistry, University of Missouri, Columbia, MO, 65211, USA.
authors.forename: Gary
authors.initials: G
authors.lastname: Stacey
authors.affiliation: Department of Statistics, Purdue University, West Lafayette, IN, 47907, USA.
authors.forename: Rebecca W
authors.initials: RW
authors.lastname: Doerge
authors.affiliation: Institute for Plant Breeding, Genetics and Genomics, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Jackson
mesh_terms: D020440:Gene Duplication / Q000235:genetics* / Q000502:physiology; D018506:Gene Expression Regulation, Plant / Q000235:genetics / Q000502:physiology; D018745:Genome, Plant / Q000235:genetics* / Q000502:physiology; D018514:Plant Structures / Q000378:metabolism / Q000502:physiology; D011123:Polyploidy; D013025:Glycine max / Q000235:genetics / Q000502:physiology