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Hierarchically Aligning 10 Legume Genomes Establishes a Family-Level Genomics Platform.
Wang, Jinpeng; Sun, Pengchuan; Li, Yuxian; Liu, Yinzhe; Yu, Jigao; Ma, Xuelian; Sun, Sangrong; Yang, Nanshan; Xia, Ruiyan; Lei, Tianyu; Liu, Xiaojian; Jiao, Beibei; Xing, Yue; Ge, Weina; Wang, Li; Wang, Zhenyi; Song, Xiaoming; Yuan, Min; Guo, Di; Zhang, Lan; Zhang, Jiaqi; Jin, Dianchuan; Chen, Wei; Pan, Yuxin; Liu, Tao; Jin, Ling; Sun, Jinshuai; Yu, Jiaxiang; Cheng, Rui; Duan, Xueqian; Shen, Shaoqi; Qin, Jun; Zhang, Meng-Chen; Paterson, Andrew H; Wang, Xiyin.
Afiliação
  • Wang J; School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L
  • Sun P; Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and.
  • Li Y; Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.).
  • Liu Y; School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L
  • Yu J; Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and.
  • Ma X; Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.).
  • Sun S; School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L
  • Yang N; Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and.
  • Xia R; Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.).
  • Lei T; School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L
  • Liu X; Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and.
  • Jiao B; Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.).
  • Xing Y; School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L
  • Ge W; Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and.
  • Wang L; Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.).
  • Wang Z; School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L
  • Song X; Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and.
  • Yuan M; Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.).
  • Guo D; School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L
  • Zhang L; Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and.
  • Zhang J; Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.).
  • Jin D; School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L
  • Chen W; Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and.
  • Pan Y; Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.).
  • Liu T; School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L
  • Jin L; Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and.
  • Sun J; Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.).
  • Yu J; School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L
  • Cheng R; Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and.
  • Duan X; Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.).
  • Shen S; School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L
  • Qin J; Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and.
  • Zhang MC; Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.).
  • Paterson AH; School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L
  • Wang X; Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and.
Plant Physiol ; 174(1): 284-300, 2017 May.
Article em En | MEDLINE | ID: mdl-28325848
ABSTRACT
Mainly due to their economic importance, genomes of 10 legumes, including soybean (Glycine max), wild peanut (Arachis duranensis and Arachis ipaensis), and barrel medic (Medicago truncatula), have been sequenced. However, a family-level comparative genomics analysis has been unavailable. With grape (Vitis vinifera) and selected legume genomes as outgroups, we managed to perform a hierarchical and event-related alignment of these genomes and deconvoluted layers of homologous regions produced by ancestral polyploidizations or speciations. Consequently, we illustrated genomic fractionation characterized by widespread gene losses after the polyploidizations. Notably, high similarity in gene retention between recently duplicated chromosomes in soybean supported the likely autopolyploidy nature of its tetraploid ancestor. Moreover, although most gene losses were nearly random, largely but not fully described by geometric distribution, we showed that polyploidization contributed divergently to the copy number variation of important gene families. Besides, we showed significantly divergent evolutionary levels among legumes and, by performing synonymous nucleotide substitutions at synonymous sites correction, redated major evolutionary events during their expansion. This effort laid a solid foundation for further genomics exploration in the legume research community and beyond. We describe only a tiny fraction of legume comparative genomics analysis that we performed; more information was stored in the newly constructed Legume Comparative Genomics Research Platform (www.legumegrp.org).
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Filogenia / Genoma de Planta / Genômica / Fabaceae Idioma: En Revista: Plant Physiol Ano de publicação: 2017 Tipo de documento: Article
Texto completo
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XML
PubMed Links
Buscar no Google

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Filogenia / Genoma de Planta / Genômica / Fabaceae Idioma: En Revista: Plant Physiol Ano de publicação: 2017 Tipo de documento: Article