Differential Accumulation of Retroelements and Diversification of NB-LRR Disease Resistance Genes in Duplicated Regions following Polyploidy in the Ancestor of Soybean
Roger W. InnesDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchCarine Ameline-TorregrosaDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchTom AshfieldDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchEthalinda K. S. CannonIndiana University BloomingtonSteven B. CannonDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchBen ChackoDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchNicolas W. G. ChenDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchArnaud CoulouxDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchAnita DalwaniDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchRoxanne DennyDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchShweta DeshpandeDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchAshley N. EganDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchNatasha GloverDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchC.S. HansDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchStacy HowellDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchDaniel C. IlutDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchScott A. JacksonDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchHongshing LaiDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchJafar MammadovDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchSara E. Martin del CampoDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchMichelle MetcalfDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchAshley NguyenDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchMajesta O’BlenessDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchBernard E. PfeilDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchRam PodichetiDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchMilind B. RatnaparkheDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchSylvie SamainDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchIryna SandersIndiana University BloomingtonBéatrice SegurensDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchMireille SévignacDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchS. Sherman-BroylesDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchVincent ThareauDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchDominic M. TuckerDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchJason G. WallingDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchAdam WawrzyńskiDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchYi JingDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchJeff J. DoyleDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchValérie GeffroyDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchBruce A. RoeDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchM. A. Saghai MaroofDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural ResearchNevin D. YoungDepartment of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural Research
2008en
ABI
Annotatsiya
The genomes of most, if not all, flowering plants have undergone whole genome duplication events during their evolution. The impact of such polyploidy events is poorly understood, as is the fate of most duplicated genes. We sequenced an approximately 1 million-bp region in soybean (Glycine max) centered on the Rpg1-b disease resistance gene and compared this region with a region duplicated 10 to 14 million years ago. These two regions were also compared with homologous regions in several related legume species (a second soybean genotype, Glycine tomentella, Phaseolus vulgaris, and Medicago truncatula), which enabled us to determine how each of the duplicated regions (homoeologues) in soybean has changed following polyploidy. The biggest change was in retroelement content, with homoeologue 2 having expanded to 3-fold the size of homoeologue 1. Despite this accumulation of retroelements, over 77% of the duplicated low-copy genes have been retained in the same order and appear to be functional. This finding contrasts with recent analyses of the maize (Zea mays) genome, in which only about one-third of duplicated genes appear to have been retained over a similar time period. Fluorescent in situ hybridization revealed that the homoeologue 2 region is located very near a centromere. Thus, pericentromeric localization, per se, does not result in a high rate of gene inactivation, despite greatly accelerated retrotransposon accumulation. In contrast to low-copy genes, nucleotide-binding-leucine-rich repeat disease resistance gene clusters have undergone dramatic species/homoeologue-specific duplications and losses, with some evidence for partitioning of subfamilies between homoeologues.
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