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Identification and characterization of a new member of the SINE Au retroposon family (GmAu1) in the soybean, Glycine max (L.) Merr., genome and its potential application

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Abstract

A plant short interspersed element (SINE) was identified in Glycine max after re-sequencing of the soybean sequence characterized amplified region (SCAR) markers. Detailed analysis revealed that this newly recognized SINE element consisted of a tRNA-related region, a tRNA non-related region, direct flanking repeat sequences, and a short stretch of Ts at the 3′-terminal region. These features are similar to previously characterized SINEs. To investigate the evolution of the SINE retroposon, BLASTN was used to search against genome sequences of other plants. Since it is homologous with the retroposon Au in Aegilops umbellulata (wheat) and its homology in soybean, the SINE is named as GmAu1. Genome analysis of the Glycine max var. Willimas 82 uncovered more than 847 copies of GmAu1 per haploid genome of soybean. Examination of the regions flanking the inserted GmAu1 sequences indicated a preference for introns over exons or other noncoding regions. Considering the flanking insertion sequences, 146 primers were designed in order to detect insertion mutations by a PCR-based method. Seventy-seven primers displayed polymorphism and were used to develop corresponding GmAu1-based SCAR markers. The retroposon GmAu1 and its related SCAR markers identified in this study will prove valuable to future investigations into the genetic mapping, phylogeny, and evolution of the Glycine genus.

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References

  • Allnutt TR, Roper K, Henry C (2008) Development and application of SINE multilocus and quantitative genetic markers to study oilseed rape (Brassica napus L.) crops. J Agric Food Chem 56:426–432

    Article  PubMed  CAS  Google Scholar 

  • Chernova T, Higginson FM, Davies R, Smith AG (2008) B2 SINE retroretroposon causes polymorphic expression of mouse 5-aminolevulinic acid synthase 1 gene. Biochem Biophys Res Commun 377:515–520

    Article  PubMed  CAS  Google Scholar 

  • Deragon J, Zhang X (2006) Short interspersed elements (SINEs) in plants: origin, classification, and use as phylogenetic markers. Syst Biol 55:949–956

    Article  PubMed  Google Scholar 

  • Deragon JM, Landry BS, Pelissier T, Tutois S, Tourmente S, Picard G (1994) An analysis of retroposition in plants based on a family of SINEs from Brassica napus. J Mol Evol 39:378–386

    Article  PubMed  CAS  Google Scholar 

  • Fawcett J, Kawahara T, Watanabe H, Yasui Y (2006) A SINE family widely distributed in the plant kingdom and its evolutionary history. Plant Mol Biol 61:505–514

    Article  PubMed  CAS  Google Scholar 

  • Grillo G, Licciulli F, Liuni S, Sbisa E, Pesole G (2003) PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences. Nucleic Acids Res 31:3608–3612

    Article  PubMed  CAS  Google Scholar 

  • Lunyak VV, Prefontaine GG, Nunez E, Cramer T, Ju BG, Ohgi KA, Hutt K, Roy R, Garcia-Diaz A, Zhu X, Yung Y, Montoliu L, Glass CK, Rosenfeld MG (2007) Developmentally regulated activation of a SINE B2 repeat as a domain boundary in organogenesis. Science 317:248–251

    Article  PubMed  CAS  Google Scholar 

  • Mochizuki K, Umeda M, Ohtsubo H, Ohtsubo E (1992) Characterization of a plant SINE, p-SINE1, in rice genomes. Jpn J Genet 67:155–166

    Article  PubMed  CAS  Google Scholar 

  • Monden Y, Naito K, Okumoto Y, Saito H, Oki N, Tsukiyama T, Ideta O, Nakazaki T, Wessler SR, Tanisaka T (2009) High potential of a retroposon mPing as a marker system in japonica × japonica cross in rice. DNA Res 16:131–140

    Article  PubMed  CAS  Google Scholar 

  • Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325

    Article  PubMed  CAS  Google Scholar 

  • Ohshima K, Koishi R, Matsuo M, Okada N (1993) Several short interspersed repetitive elements (SINEs) in distant species may have originated from a common ancestral retrovirus: characterization of a squid SINE and a possible mechanism for generation of tRNA-derived retroposons. Proc Natl Acad Sci USA 90:6260–6264

    Article  PubMed  CAS  Google Scholar 

  • Okada N (1991) SINEs: short interspersed repeated elements of the eukaryotic genome. Trends Ecol Evol 6:358–361

    Article  PubMed  CAS  Google Scholar 

  • Piskurek O, Austin CC, Okada N (2006) Sauria SINEs: novel short interspersed retroposable elements that are widespread in reptile genomes. J Mol Evol 62:630–644

    Article  PubMed  CAS  Google Scholar 

  • Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365–386

    PubMed  CAS  Google Scholar 

  • Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang X-C, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183

    Article  PubMed  CAS  Google Scholar 

  • Shu Y, Li Y, Zhu Y, Zhu Z, Lv D, Bai X, Cai H, Ji W, Guo D (2010) Genome-wide identification of intron fragment insertion mutations and their potential use as SCAR molecular markers in the soybean. Theor Appl Genet 121:1–8

    Article  PubMed  CAS  Google Scholar 

  • Sun FJ, Fleurdepine S, Bousquet-Antonelli C, Caetano-Anolles G, Deragon JM (2007) Common evolutionary trends for SINE RNA structures. Trends Genet 23:26–33

    Article  PubMed  Google Scholar 

  • Takasaki N, Murata S, Saitoh M, Kobayashi T, Park L, Okada N (1994) Species-specific amplification of tRNA-derived short interspersed repetitive elements (SINEs) by retroposition: a process of parasitization of entire genomes during the evolution of salmonids. Proc Natl Acad Sci USA 91:10153–10157

    Article  PubMed  CAS  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    Article  PubMed  CAS  Google Scholar 

  • Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78

    Article  PubMed  CAS  Google Scholar 

  • Wang W, Kirkness EF (2005) Short interspersed elements (SINEs) are a major source of canine genomic diversity. Genome Res 15:1798–1808

    Article  PubMed  CAS  Google Scholar 

  • Waugh R, McLean K, Flavell AJ, Pearce SR, Kumar A, Thomas BB, Powell W (1997) Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP). Mol Gen Genet 253:687–694

    Article  PubMed  CAS  Google Scholar 

  • Yasui Y, Nasuda S, Matsuoka Y, Kawahara T (2001) The Au family, a novel short interspersed element (SINE) from Aegilops umbellulata. Theor Appl Genet 102:463–470

    Article  CAS  Google Scholar 

  • Yoshioka Y, Matsumoto S, Kojima S, Ohshima K, Okada N, Machida Y (1993) Molecular characterization of a short interspersed repetitive element from tobacco that exhibits sequence homology to specific tRNAs. Proc Natl Acad Sci USA 90:6562–6566

    Article  PubMed  CAS  Google Scholar 

  • Zhang X, Wessler SR (2005) BoS: a large and diverse family of short interspersed elements (SINEs) in Brassica oleracea. J Mol Evol 60:677–687

    Article  PubMed  CAS  Google Scholar 

  • Zhu YL, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB (2003) Single-nucleotide polymorphisms in soybean. Genetics 163:1123–1134

    PubMed  CAS  Google Scholar 

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Acknowledgments

This project was supported by Young Scholars of Harbin Normal University (KGB201010), the National “863” Program (2006AA100104, 2008AA10Z153), Aid program for Science and Technology Innovative Research Team in Higher Educational Institutions of Heilongjiang Province (2010TD10), and the Innovation Research Group of Harbin Normal University (KJTD201102).

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Correspondence to Changhong Guo or Yanming Zhu.

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Communicated by H. Jones.

Y. Shu and Y. Li contributed equally to this work.

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Shu, Y., Li, Y., Bai, X. et al. Identification and characterization of a new member of the SINE Au retroposon family (GmAu1) in the soybean, Glycine max (L.) Merr., genome and its potential application. Plant Cell Rep 30, 2207–2213 (2011). https://doi.org/10.1007/s00299-011-1126-7

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  • DOI: https://doi.org/10.1007/s00299-011-1126-7

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