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Phylogeny and molecular evolution of the DMC1 gene within the StH genome species in Triticeae (Poaceae)

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Abstract

To estimate the phylogeny and molecular evolution of a single-copy nuclear disrupted meiotic cDNA (DMC1) gene within the StH genome species, two DMC1 homoeologous sequences were isolated from nearly all the sampled StH genome species and were analyzed with those from seven diploid taxa representing the St and H genomes in Triticeae. Sequence diversity patterns and genealogical analysis suggested that (1) there is a close relationship among North American StH genome species; (2) the DMC1 gene sequences of the StH genome species from North America and Eurasia are evolutionarily distinct; (3) the StH genome polyploids have higher levels of sequence diversity in the St genome homoeolog than the H genome homoeolog; (4) the DMC1 sequence may evolve faster in the polyploid species than in the diploids; (5) high dN and dN/dS values in the St genome within polyploid species could be caused by low selective constraints or AT-biased mutation pressure. Our result provides some insight on evolutionary dynamics of duplicate DMC1 gene, the polyploidization events and phylogeny of the StH genome species.

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References

  • Anderson LK and Stack SM (2002) Meiotic recombination in plants. Curr. Genomics 3:507–525.

    Article  CAS  Google Scholar 

  • Bianco PR, Tracy RB and Kowalczykowski SC (1998) DNA strand exchange proteins: a biochemical and physical comparison. Front. Biosci. 3:570–603.

    Google Scholar 

  • Bishop DK, Park D, Xu L and Kleckner N (1992) DMC1: A meiosis specific yeast homolog of E. coli recA required for recombination, synaptonemal complex formation and cell cycle progression. Cell 69:439–456.

    Article  PubMed  CAS  Google Scholar 

  • Caldewell KS, Dvorak J, Laqudah ES, Akhunov E, Luo MC, Wolters P and Powell W (2004) Sequence polymorphism in polyploid wheat and their D-genome diploid ancestor. Genetics 167:941–947.

    Article  Google Scholar 

  • Chapman BA, Bower JE, Feltus EA and Paterson AH (2006) Buffering of crucial functionas by paleologous duplicated genes may contribute cylicality to angiosperm genome duplication. Proc. Natl. Acad. Sci. USA 103:2730–2735.

    Article  PubMed  CAS  Google Scholar 

  • Chittela RK and Sainis JK (2010) Plant DNA recombinases: A long way to go. J. Nucleic Acids 2010:646109.

    PubMed  Google Scholar 

  • Deng ZY and Wang T (2007) OsDMC1 is required or homologous pairing in Oryza Sativa. Plant Mol. Biol. 65:31–42.

    Article  PubMed  CAS  Google Scholar 

  • Dewey DR (1984) The genome system of classification as a guide to intergeneric hybridization with the perennial Triticeae. Gene manipulation in plant improvement, J.P. Gustafson, ed., Plenum Press, New York

    Google Scholar 

  • Doyle JJ and Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15.

    Google Scholar 

  • Fan X, Sha LN, Yang RW, Zhang HQ, Kang HY, Zhang L, Ding CB, Zheng YL and Zhou YH (2009) Phylogeny and evolutionary history of Leymus (Triticeae; Poaceae) based on a single-copy nuclear gene encoding plastid acetyl-CoA carboxylase. BMC Evol. Biol. 9:247 doi:10.1186/1471-2148-9-247.

    Article  PubMed  Google Scholar 

  • Fu YX and Li WH (1993) Statistical tests of neutrality of mutations. Genetics 133:693–709.

    PubMed  CAS  Google Scholar 

  • George S, Behl P, DeGuzman R, Lee M, Rusyniak S, Hotta Y, Hiratsuka K, Takase H and Hasenkampf C (2002) DMC1 fluorescent foci in prophase I nuclei of diploid, triploid and hybrid lilies. Chromosoma 111:96–105.

    Article  PubMed  CAS  Google Scholar 

  • Gong PC and Bao Y (2008) Nucleotide diveristy of the homoelogous adh1 loci in the American allotetraploid Oryza species. Plant Syst. Evol. 276:243–253.

    Article  CAS  Google Scholar 

  • Hudson RR (1990) Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology. D. Futuyma and J. Antonovics, eds., Oxford University Press, New York, pp.1–44.

    Google Scholar 

  • Jaaska V (1992) Isoenzyme variation in the grass genus Elymus (Poaceae). Hereditas 117:11–22.

    Article  CAS  Google Scholar 

  • Kathiresan A, Khush GS and Bennett J (2002) Two rice DMC1 genes are differentially expressed during meiosis and haploid and diploi mitosis. Sex. Plant Reprod. 14: 257–267.

    Article  CAS  Google Scholar 

  • Klimyuk VI and Jones JD (1997) AtDMC1, the Arabidopsis honologue of the yeast DMC1 gene: characterization, transposon-induced allelic variation and meisis-associated expression. Plant J. 11:1–14.

    Article  PubMed  CAS  Google Scholar 

  • Lawton-Rauh AL, Robichaux RH and Purugganan MD (2003) Patterns of nucleotide variation in homoeologous regulatory genes in the allotetraploid Hawaiian silversword alliance (Asteraceae). Mol. Ecol. 12:1301–13.

    Article  PubMed  CAS  Google Scholar 

  • Linde-Laursen I, Seberg O and Salomon B (1994) Comparison of the Gniemsa C-banded and N-banded karyotypes of two Elymus species, E. dentatus and E. glaucescens (Poaceae: Triticeae). Plant Syst. Evol. 192:165–176.

    Article  Google Scholar 

  • Löve Á (1984) Conspectus of the Triticeae. Feddes Rep. 95:425–521.

    Google Scholar 

  • Mason-Gamer RJ, Burns MM and Naum M (2010) Reticulate evolutionary history of a complex group of grasses: Phylogeny of Elymus StStHH allotetraploids based on three nuclear genes. Plos One 5:e10989.

    Article  PubMed  Google Scholar 

  • Moench C (1794) Methodus Plantas Horti Botanici et Agri Marburgensis a Staminum Situ Describendi. Margburgi Cattorum

  • Neale MJ and Keeney S (2006) Clarifying the mechanics of DNA strand exchange in meiotic recombination. Nature 442:153–158.

    Article  PubMed  CAS  Google Scholar 

  • Petersen G and Seberg O (2000) Phylogenetic evidence for excision of Stowaway miniature inverted-repeat transposable elements in Triticeae (Poaceae). Mol. Biol. Evol. 17:1589–1596.

    Article  PubMed  CAS  Google Scholar 

  • Petersen G and Seberg O (2002) Molecular evolution and phylogenetic application of DMC1. Mol. Phylogenet. Evol. 22:43–50.

    Article  PubMed  CAS  Google Scholar 

  • Posada D and Crandall KA (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 14:817–818.

    Article  PubMed  CAS  Google Scholar 

  • Rose PP and Korber BT (2000) Detecting hypermutations in viral sequences with an emphasis on G → A hypermutation. Bioinformatics 16:400–401.

    Article  PubMed  CAS  Google Scholar 

  • Rozas J, Sánchez-DelBarrio JC, Messeguer X and Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496–2497.

    Article  PubMed  CAS  Google Scholar 

  • Sha LN, Fan X, Yang RW, Kang HY, Ding CB, Zhang L, Zheng YL and Zhou YH (2010) Phylogenetic relationships between Hystrix and its closely related genera (Triticeae; Poaceae) based on nuclear Acc1, DMC1 and chloroplast trnL-F sequences. Mol. Phylogenet. Evol. 54:327–335.

    Article  PubMed  CAS  Google Scholar 

  • Small RL and Wendel JF (2000) Copy number lability and evolutionary dynamics of the Adh gene family in diploid and tetraploid cotton (Gossypium). Genetics 155:1913–1926.

    PubMed  CAS  Google Scholar 

  • Small RL and Wendel JF (2002) Differential evolutionary dynamics of duplicated paralogous Adh loci in allotetraploid cotton (Gossypium). Mol. Biol. Evol. 19:597–607.

    Article  PubMed  CAS  Google Scholar 

  • Soltis DE, Soltis PS and Tate JA. (2003) Advances in the study of polyploidy since Plant Speciation. New Phytol. 161:173–191.

    Article  Google Scholar 

  • Sun GL, Daley T and Ni Y (2007) Molecular evolution and genome divergence at RPB2 gene of the St and H genome in Elymus species. Plant Mol. Biol. 64:645–665.

    Article  PubMed  CAS  Google Scholar 

  • Sun GL, Ni Y and Daley T (2008) Molecular phylogeny of RPB2 gene reveals multiple origin, geographic differentiation of H genome, and the relationship of the Y genome to other genomes in Elymus species. Mol. Phylogenet. Evol. 46:897–907.

    Article  PubMed  CAS  Google Scholar 

  • Swofford DL (2003) PAUP*: Phylogenetic analysis using parsimony (*and other method) Version 4.0b10. Sinauer Associates, Sunderland, Massachusetts, USA.

    Google Scholar 

  • Tajima F (1989) Statistical method for testing the neutral mutation of hypothesis by DNA polymorphism. Genetics 123:585–595.

    PubMed  CAS  Google Scholar 

  • Tamura K, Dudley J and Nei M Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596–1599.

    Article  PubMed  CAS  Google Scholar 

  • Thompson JD, Higgins DG and Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22:4673–4680.

    Article  PubMed  CAS  Google Scholar 

  • Wakeley J and Hey J (1997) Estimating ancestral population parameters. Genetics 145:847–855.

    PubMed  CAS  Google Scholar 

  • Watterson GA (1975) On the number of segregation sites in genetic models without recombination. Theor. Popul. Biol. 7:256–276.

    Article  PubMed  CAS  Google Scholar 

  • Williams EJB and Hurst LD (2000) The proteins of linked genes evolve at similar rates. Nature 407:900–903.

    Article  PubMed  CAS  Google Scholar 

  • Wilson FD (1963) Revision of Sitanion (Triticeae, Grameneae). Brittonia 15:303–323.

    Article  Google Scholar 

  • Xia X and Xie Z (2001) DAMBE: Data analysis in molecular biology and evolution. J. Hered. 92:371–373.

    Article  PubMed  CAS  Google Scholar 

  • Yoshida K, Kondoh G, Matsuda Y, Habu T, Nishimune Y and Morita T (1998) The mouse RecA-like gene DMC1 is required for honomlogous chromosome synapsis during meiosis. Mol. Cell. 1:707–718.

    Article  PubMed  CAS  Google Scholar 

  • Zhang Z, Inomata N, Ohba T, Cariou ML and Yamazaki T (2002) Codon bias differentiates between the duplicated amylase Loci following gene duplication in Drosophila. Genetics 161:1187–1196.

    PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, Sichuan, China

    Xiao-Li Wang, Xing Fan, Li-Na Sha, Hai-Qin Zhang, Hou-Yang Kang & Yong-Hong Zhou

  2. Key Laboratory of Genetic Resources and Crop Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, Sichuan, China

    Xiao-Li Wang & Yong-Hong Zhou

  3. College of Biology and Science, Sichuan Agricultural University, Yaan, 625014, Sichuan, China

    Xiao-Li Wang, Rui-Wu Yang, Li Zhang & Chun-Bang Ding

  4. College of Resources and Environment, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China

    Jian Zeng

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  1. Xiao-Li Wang
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  2. Xing Fan
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  3. Jian Zeng
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  4. Li-Na Sha
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  10. Yong-Hong Zhou
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Correspondence to Yong-Hong Zhou.

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Wang, XL., Fan, X., Zeng, J. et al. Phylogeny and molecular evolution of the DMC1 gene within the StH genome species in Triticeae (Poaceae). Genes Genom 34, 237–244 (2012). https://doi.org/10.1007/s13258-011-0169-z

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  • DOI: https://doi.org/10.1007/s13258-011-0169-z

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