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Soybean Genome Structure and Organization

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Part of the book series: Plant Genetics and Genomics: Crops and Models ((PGG,volume 2))

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References

  • Adams, K. and Wendel, J. (2005) Polyploidy and genome evolution in plants. Current Opinion in Plant Biology 8,135–141.

    Article  PubMed  CAS  Google Scholar 

  • Arabidopsis Genome Initiative. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796–815.

    Article  Google Scholar 

  • Bender, J. (2004) DNA methylation and epigenetics. Annu Rev Plant Biol 55, 41–68.

    Article  PubMed  CAS  Google Scholar 

  • Bennetzen, J. L. and Kellogg, E. A. (1997) Do plants have a one-way ticket to genomic obesity? Plant Cell 9, 1509–1514.

    Article  PubMed  CAS  Google Scholar 

  • Blanc, G., and Wolfe, K.H., (2004) Widespread paleopolyploidy in model plant species inferred from age distributions of duploicate genes. Plant Cell 16, 1667–1678.

    Article  PubMed  CAS  Google Scholar 

  • Boutin, S.R., Young, N.D., Olson, Yu, Z.-H., Shoemaker, R.C., and Vallejos C.E. (1995) Genome conservation among three legume genera detected with DNA markers. Genome 38, 928–937.

    CAS  PubMed  Google Scholar 

  • Bowers, J.E., Chapman, B.A., Rong, J., Paterson, A.H. (2003) Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422, 433–438.

    Article  PubMed  CAS  Google Scholar 

  • Cannon, S.B., McCombie, W.R., Sato, S., Tabata, S., Denny, R., Palmer, L., Katari, M., Young, N.D., Stacey, G. (2003) Evolution and microsynteny of the apyrase gene family in three legume genomes. Mol Genet Genomics 270, 347–361.

    Article  PubMed  CAS  Google Scholar 

  • Choi, H.K., Kim, D., Uhm, T., Limpens, E., Lim, H., Mun, J.H., Kalo, P., Penmetsa, R.V., Seres, A., Kulikova, O., Roe, B.A., Bisseling, T., Kiss, G.B., Cook, D.R. (2004a) A sequence-based genetic map of Medicago truncatula and comparison of marker colinearity with M. sativa. Genetics 166, 1463–1502.

    Article  CAS  Google Scholar 

  • Choi, H.K., Mun, J.H., Kim, D.J., Zhu, H., Baek, J.M., Mudge, J., Roe, B., Ellis, N., Doyle, J., Kiss, G.B., Young, N.D., Cook, D.R. (2004b) Estimating genome conservation between crop and model legume species. Proc Natl Acad Sci USA 101, 15289–15294.

    Article  CAS  Google Scholar 

  • Devos, K.M., Brown, J.K.M., and Bennetzen, J.L. (2002) Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res. 12, 1075–1079.

    Article  PubMed  CAS  Google Scholar 

  • Doyle, J.J., Luckow, M.A. (2003) The rest of the iceberg. Legume diversity and evolution in a phylogenetic context. Plant Physiol 131, 900–910.

    Article  PubMed  CAS  Google Scholar 

  • Foster-Hartnett, D., Mudge, J., Danesh, D., Yan, H., Larsen, D., Denny, R., and Young N.D. (2002) Comparative genomic analysis of sequences sampled from a small region on soybean molecular linkage group ‘G’. Genome 45, 634–645.

    Article  PubMed  CAS  Google Scholar 

  • Goldberg, R. B. (1978) DNA sequence organization in the soybean plant. Biochem Genet 16, 45–68.

    Article  PubMed  CAS  Google Scholar 

  • Grant, D. Cregan, P., and Shoemaker, R.C. (2000) Genome organization in dicots: genome duplication in Arabidopsis and synteny between soybean and Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 94, 4168–4173.

    Article  Google Scholar 

  • Grover, C.E., Kim, H, Wing, R., Paterson A.H., and Wendel, J.F. (2004) Incongruent patterns of local and global genome size evolution in cotton. Genome Res. 14, 1474–1482.

    Article  PubMed  CAS  Google Scholar 

  • Gurley, W. B., Hepburn, A. G., Key, J.L. (1979) Sequence organization of the soybean genome. Biochem Biophys Acta 561, 167–183.

    PubMed  CAS  Google Scholar 

  • Illic, K., SanMiguel, P.J., and Bennetzen, J.L. (2003) A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes. Proc. Natl. Acad. Sci. U.S.A. 100, 12265–12270.

    Article  CAS  Google Scholar 

  • Langham, R.J., Walsh, J., Dunn, M., Ko, C., Goff, S.A., and Freeling, M. (2004) Genome duplication, fractionation and the origin of regulatory novelty. Genetics 166, 935–945.

    Article  PubMed  CAS  Google Scholar 

  • Lee, J.M., Bush A., Specht J.E., and Shoemaker R. (1999) Mapping duplicate genes in soybean. Genome 42, 829–836.

    Article  CAS  Google Scholar 

  • Lee, J.M., Grant, D.,Vallejos C.E., and Shoemaker R. (2001) Genome organization in dicots. II. Arabidopsis as a ‘bridging species’ to resolve genome evolution events among legumes. Theor. Appl. Genet. 103, 765–773.

    Article  CAS  Google Scholar 

  • Lin, J. Y., Jacobus, B. H., SanMiguel, P., Walling, J.G., Yuan, Y., Shoemaker, R.C., Young, N.D., Jackson, S.A. (2005) Pericentromeric regions of soybean (Glycine max L. Merr.) chromosomes consist of retroelements and tandemly repeated DNA and are structurally and evolutionarily labile. Genetics 170, 1221–1230.

    Article  PubMed  CAS  Google Scholar 

  • Lockton, S., and Gaut, B.S. (2005) Plant conserved non-coding sequences and paralogue evolution. Trends in Genet. 21, 80–86.

    Google Scholar 

  • Ma, J., SanMiguel, P., Lai, J., Messing, J. and Bennetizen, J.L. (2005) DNA rearrangement in orthologous Orp regions of the maize, rice and sorghum genomes. Genetics 170, 1209–1220.

    Article  PubMed  CAS  Google Scholar 

  • Marek, L.F., Mudge, J., Darnielle, L., Grant, D., Hanson, N., Paz, M., Huihuang, Y., Denny, R., Larson, K., Foster-Hartnett, D., Cooper, A., Danesh, D., Larsen, D., Schmidt, T., Staggs, R., Crow, J.A., Retzel, E., Young, N.D., and Shoemaker, R.C. (2001) Soybean genomic survey: BAC-end sequences near RFLP and SSR markers. Genome 44, 572–581.

    Article  PubMed  CAS  Google Scholar 

  • Masterson, J. (1994) Stomatal size in fossil plants: evidence for polyploidy in majority of angiosperms. Science (Washington, D.C.), 264, 421–424.

    Article  CAS  Google Scholar 

  • Menacio-Hautea, D., Fatokum, C.A., Kumar, L., Danesh, D., Young, N.D. (1993) Comparative genome analysis of mungbean (Vigna radiata (L.) Wilczek) and cowpea (V. unguiculata (L.) Walpers) using RFLP mapping data. Theor Appl Genet 86, 797–810.

    Article  Google Scholar 

  • Messing, J., Bharti, A. K., Karlowski, W.M., Gundlach, H., Kinm H.R., Yu, Y., Wei, F., Fuks, G., Soderlund, C.A., Mayer, K.F., Wing, R.A. (2004) Sequence composition and genome organization of maize. PNAS 101, 14349–14354.

    Article  PubMed  CAS  Google Scholar 

  • Mudge, J., Huihuang, Yan, Denny, R. L., Howe, D. K., Danesh, D., Marek, L. F., Retzel, E., Shoemaker, R. C., and Young, N. D. (2004) Soybean bacterial artificial chromosome contigs anchored with RFLPs: insights into genome duplication and gene clustering. Genome 47, 361–372.

    Article  PubMed  CAS  Google Scholar 

  • Mudge, J., Cannon, S.B., Kalo, P., Oldroyd, G.E.D., Roe, B.A., Town, C.D., and Young, N.D. (2005) Highly syntenic regions in the genomes of soybean, Medicago truncatula and Arabidopsis thaliana. BMC Plant Biology 5, 15.

    Article  PubMed  CAS  Google Scholar 

  • Nunberg, A., Bedell, J. A., Budiman, M.A., Citek, R., Clifton, S.W., Fulton, L., Pape, D., Cai, Z., Joshi, T., Nguyen, H., Xu, D., Stacey, G. (2006) Survey sequencing of soybean elucidates the genome structure, composition and identifies novel repeats. Functional Plant Biology 33, 765–773.

    Article  Google Scholar 

  • Ohno, S. (1970) Evolution by Gene Duplication, Springer-Verlag, New York.

    Google Scholar 

  • Pagel, J., Walling, J.G., Young, N.D., Shoemaker, R.C., Jackson, S.A. (2004) Segmental duplications within the Glycine max genome revealed by fluorescence in situ hybridization of bacterial artificial chromosomes. Genome 47, 764–768.

    Article  PubMed  CAS  Google Scholar 

  • Petrov, D.A. (2001) Evolution of genome size: new approaches to an old problem. Trends in Genetics 17, 23–28.

    Article  PubMed  CAS  Google Scholar 

  • Pfeil, B.E., Schlueter, J.A., Shoemaker, R.C., Doyle, J.J. (2005) Placing paleopolyploidy in relation to taxon divergence: a phylogenetic analysis in legumes using 39 gene families. Systematic Biology 54(3), 441–454.

    Article  PubMed  CAS  Google Scholar 

  • Schlueter, J.A., Dixon, P., Granger, C. Grant, D., Clark, L., Doyle, J.J., and Shoemaker, R.C. (2004) Mining EST databases to resolve evolutionary events in major crop species. Genome 47, 868–876.

    Article  PubMed  CAS  Google Scholar 

  • Schlueter, J.A., Scheffler, B.E.,, Schlueter, S.D., and Shoemaker, R.C. (2006) Sequence conservation of homeologous Bacterial Artificial Chromosomes and transcription of homeologous genes in soybean (Glycine max L. Merr.). Genetics 174, 1017–1028.

    Article  PubMed  CAS  Google Scholar 

  • Schlueter, J., Lin, J.-Y., Schlueter, S., Vasylenko-Sanders, I., Deshpandem, S., Yi, J., O’Bleness, M., Roe, B., Nelson R., Scheffler, B., Jackson, S. and Shoemaker, R., (2007a) Gene duplication and paleopolypoloidy in soybean and the implications for whole genome sequencing. BMC Genomics 8, 330.

    Article  CAS  Google Scholar 

  • Schlueter, J.A., Vasylendo-Sanders, I.F., Deshpande, S., Yi, J., Siegfried, M., Roe, B.A., Schlueter, S.D., Scheffler, B.E. and R.C. Shoemaker. (2007b) The FAD2 gene family of soybean: insights into the structural and functional divergence of a paleopolyploid genome. The Plant Genome 1, 14–26.

    Google Scholar 

  • Shi, L., Zhu, T., Keim, P. (1996) Ribosomal RNA genes in soybean and common bean : chromosomal organization, expression, and evolution. Theor Appl Genet 93, 136–141.

    Article  CAS  Google Scholar 

  • Shoemaker, R., Polzin K., Labate J., Specht J., Brummer E.C., Olson T., Young N., Concibido V., Wilcox J., Tamulonis J., Kochert, G., and Boerma H.R. (1996) Genome duplication in soybean (Glycine subgenus soja). Genetics 144, 329–338.

    PubMed  CAS  Google Scholar 

  • Vahedian, M., Shi, L., Zhu, T., Okimoto, R., Danna, K., Keim, P. (1995) Genomic organization and evolution of the soybean SB92 satellite sequence. Plant Molecular Biology 29, 857–862.

    Article  PubMed  CAS  Google Scholar 

  • Vision, T.J, Brown, D.G., and Tanksley, S.D. (2000) The origins of genomic duplications in Arabidopsis. Science 290, 2114–2117.

    Article  PubMed  CAS  Google Scholar 

  • Walling, J. G., Shoemaker, R. C., Young, N., Mudge, J., Jackson, S. (2006) Chromosome level homeology in paleopolyploid soybean (Glycine max) revealed through integration of genetic and chromosome maps. Genetics 172, 1893–1900.

    Article  PubMed  CAS  Google Scholar 

  • Weeden, N.F., Muehlbauer, F.J., Ladizinsky, G. (1992) Extensive conservation of linkage relationships between pea and lentil genetic maps. J Hered 83, 123–129.

    Google Scholar 

  • Yan, H.H., Mudge, J., Kim, D.-J., Shoemaker, R.C., Cook, D.R., Young, N.D. (2003) Estimates of conserved microsynteny among the genomes of Glycine max, Medicago truncatula, and Arabidopsis thaliana. Theor Appl Genet 106, 1256–1265.

    PubMed  CAS  Google Scholar 

  • Young, N.D., Mudge, J., Ellis, T.N. (2003) Legume genomes: more than peas in a pod. Curr. Opin. Plant Biol. 6, 199–204.

    Article  PubMed  CAS  Google Scholar 

  • Young, N.D., Cannon, S.B., Sato, S., Kim, K., Cook, D.R., Town, C.D., Roe, B.A., Tabata, S. (2005) Sequencing the Genespaces of Medicago truncatula and Lotus japonicus. Plant Phys 137, 1174–1181.

    Article  CAS  Google Scholar 

  • Zhu, H., Kim, D.J., Baek, J.M., Choi, H.K., Ellis, L.C., Kuester, H., McCombie, W.R., Peng, H.M., Cook, D.R. (2003) Syntenic relationships between Medicago truncatula and Arabidopsis reveal extensive divergence of genome organization. Plant Physiol 131, 1018–1026.

    Article  PubMed  CAS  Google Scholar 

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Shoemaker, R.C., Schlueter, J.A., Jackson, S.A. (2008). Soybean Genome Structure and Organization. In: Stacey, G. (eds) Genetics and Genomics of Soybean. Plant Genetics and Genomics: Crops and Models, vol 2. Springer, New York, NY. https://doi.org/10.1007/978-0-387-72299-3_6

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