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In silico SSRs Analysis of Mitochondrial Genome (mtDNA) of Oryza rufipogon Griff.

Year 2012, Volume: 2012 Issue: 1, - , 01.06.2012

Abstract

Cultivated rice is one of the most important crops for human diet. The Oryza genus includes 21 wild species and 2 cultivated species. Oryza rufipogon Griff. is the wild ancestor of cultivated rice and has AA genome structure as cultivated rice species (Oryza sativa L. and Oryza glaberrima Steud. ). Microsatellites also known as simple sequence repeats (SSRs) are small tandem repeats (1-6 bp) that are interspersed throughout the genome. In this study, in silico we identified mitochondrial SSRs (mtSSR) in O. rufipogon mitochondrial genome (mtDNA) by using bioinformatics tools. We determined 594 SSRs in the mitochondrial genome with an average of 1 SSR/1.06 kb and a total of 4% mtSSRs were observed in genic regions while a total of 96% mtSSRs were observed in intergenic regions. Trinucleotide SSRs were the most abundant repeats in mitochondrial genome while mononucleotide SSRs were predominant in genic regions. The most frequent motifs were A/T (85.5%) for mononucleotide repeats, AG/CT (70.59%) for dinucleotide repeats , AAG/CTT (30.9%) for trinucleotide repeats, AAAG/CTTT (24.5%) for tetranucleotide repeats, AAATT/AATTT, AAGAT/ATCTT, AATTC/GAATT and CCCGG/CCGGG were equal (16.7%) for pentanucleotide repeats and AAAAAT/ATTTTT (100%) for hexanucleotide repeats. In conclusion, this study results provide scientific basis for phylogenetics, evolutionary genetics, genetic mapping and diversity studies based on mtSSRs for different Oryza species in future.

References

  • Bellon, M.R., Brar, D.S., Lu, B.R., Pham J.L. 1998. Rice genetic resources. In: Dwoling NG, Greenfield SM, Fischer KS (eds) Sustainability of rice in the global food system, Chapter 16,Davis, California (USA). Pacific Basin Study Center and IRRI, Manila, 251–283.
  • Gandhi, S.G., Awasthi, P. and Bedi, Y.S. 2010. Analysis of SSR dynamics in chloroplast genomes of Brassicaceae family. Bioinformation, 5(1), 16-20.
  • Gao, L.Z. 1997. Studies on genetic variation of three wild rice (Oryza spp.) in China and their conservation biology. Ph.D. Dissertation, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China.
  • Gao, L.Z., Zhang, C.H., Li, D.Y., Pan, D.J., Jia, J.Z., Dong, Y.S. 2006. Genetic diversity within Oryza rufipogon germplasms preserved in Chinese field gene banks of wild rice as revealed by microsatellite markers. Biodiversity and Conservation, 15, 4059–4077.
  • Khush, G.S. 1997. Origin, dispersal, cultivation and variation of rice. Plant Molecular Biology, 35, 25–34.
  • Kuntal, H., Sharma V. 2011. In Silico Analysis of SSRs in Mitochondrial Genomes of Plants. OMICS: A Journal of Integrative Biology, Vol. 15, No. 11, 783-789.
  • Li, Y.C., Korol, A.B., Fahima, T. and Nevo, E. 2004. Microsatellites Within Genes: Structure, Function, and Evolution. Mol. Biol. Evol., 21(6), 991–1007.
  • Londo, J.P., Chiang, Y.C., Hung, K.H., Chiang, T.Y., Schaal, B.A. 2006. Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. PNAS, 103: 25, 9578–9583.
  • Mackenzie, S., He, S., Lyznik, A. 1994. The Elusive Plant Mitochondrion as a Genetic System. Plant Physiol., 105, 775–780.
  • Metzgar, D., Bytof, J., Wills, C. 2000. Selection Against Frameshift Mutations Limits Microsatellite Expansion in Coding DNA. Genome Res., 10, 72-80.
  • Morgante, M., Hanafey, M. and Powell, W. 2002. Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat. Genet., 30, 194–200.
  • Nishikawa, T., Vaughan, D.A., Kadowaki, K. 2005. Phylogenetic analysis of Oryza species, based on simple sequence repeats and their flanking nucleotide sequences from the mitochondrial and chloroplast genomes. Theor Appl Genet, 110, 696–705.
  • Oka, H.I. 1988. Origin of cultivated rice. Japanese Scientific Societies Press, Tokyo. Oliveira, E. J., Pádua, J. G., Zucchi, M.I., Vencovsky, R., Vieira, M.L.C. 2006. Origin, evolution and genome distribution of microsatellites, Genetics and Molecular Biology, 29(2), 294-307.
  • Palmer, J.D., Adams, K.L., Cho, Y., Parkinson, C.L., Qiu, Y.L., and Song, K. 2000. Dynamic evolution of plant mitochondrial genomes: mobile genes and introns, and highly variable mutation rates. Proc. Natl. Acad. Sci. USA, 97, 6960-6966.
  • Rajendrakumar, P., Biswal, A.K., Balachandran, S.M., Srinivasarao, K. and Sundaram, R.M. 2007. Simple sequence repeats in organellar genomes of rice: frequency and distribution in genic and intergenic regions. Bioinformatics, 23, 1–4.
  • Rajendrakumar, P., Biswal, A.K., Balachandran, S.M., Sundaram, R.M. 2008. In silico analysis of microsatellites in organellar genomes of major cereals for understanding the phylogenetic relationships. In Silico Biology, 8, 9-18.
  • Xu, J.H., Cheng, C., Tsuchimoto, S., Ohtsubo, H., Ohtsubo, E. 2007. Phylogenetic analysis of Oryza rufipogon strains and their relationship to Oryza sativa strains by insertion polymorphism of rice SINEs. Genes Genet. Syst., 82, 217-229.
  • Varshney, R.K., Thiel, T., Stein, N., Langridge, P. and Graner, A. 2002. In Silico Analysis on Frequency and Distribution of Microsatellites in ESTs of Some Cereal Species. Cellular & Molecular Biology Letters, 7, 537 – 546.
  • Varshney, R.K., Graner, A., Sorrells, M.E. 2005. Genic microsatellite markers in plants: features and applications. TRENDS in Biotechnology, Vol.23, No.1. Victoria, F.C., Maia, L.C., Oliveira, A.C. 2011. In silico comparative analysis of SSR markers in plants. BMC Plant Biology, 11,15.
  • Yuan, L.P., Virmani, S.S., Mao, C.X. 1989. Hybrid rice: achievements and further outlook. In: Progress in irrigated rice research. International Rice Research Institute, Manila, The Philippines, 219–223.

Oryza rufipogon Griff. Mitokondri Genomunun (mtDNA) In silico SSR Analizi

Year 2012, Volume: 2012 Issue: 1, - , 01.06.2012

Abstract

Kültüvarı yapılan çeltik türleri, insan beslenmesi için en önemli ürünlerden biridir. Oryza cinsi 21 yabani ve 2 kültüvar tür barındırmaktadır. Oryza rufipogon Griff. kültüvar çeltiğin yabani atasıdır ve aynen kültüvar çeltik türleri gibi (Oryza sativa L. ve Oryza glaberrima Steud. ) AA genom yapısına sahiptir. Basit dizi tekrarları (SSRs) olarak da bilinen mikrosatellitler, bütün genomda dağılmış halde bulunan küçük ve birbirini izleyen tekrarlardır (1-6 bç). Bu çalışmada, biyoenformatik araçlar kullanılarak in silico O. rufipogon mitokondriyal genomunda SSR’ları (mtSSR) tanımladık. Mitokondriyal genomda 594 SSR ortalama 1 SSR/1.06 kb olarak belirledik ve mtSSR’ların %96’sının kodlama yapmayan bölgelerde olmasına karşın mtSSR’ların %4’ü kodlama yapan bölgelerde gözlemlendi. Tek nükleotid SSR’lar kodlama bölgelerinde baskın olmasına karşın üç nükleotid SSR’lar mitokondriyal genomda en fazla bulunan tekrarlardır. Tek nükleotid tekrarları için en sık tekrar A/T (85.5%), ikili nükleotid tekrarları için AG/CT (70.59%), üçlü nükleotid tekrarları için AAG/CTT (30.9%), dörtlü nükleotid tekrarları için AAAG/CTTT (24.5%), beşli nükleotid tekrarları için eşit AAATT/AATTT, AAGAT/ATCTT, AATTC/GAATT ve CCCGG/CCGGG (16.7%), altılı nükleotid tekrarları için AAAAAT/ATTTTT (100%) bulunmuştur. Sonuç olarak, bu çalışmanın bulguları gelecekte farklı Oryza türleri için filogenetik, evrimsel genetik, genetik haritalama ve mtSSR temelli genetik çeşitlilik çalışmalarına bilimsel bir zemin sağlayacaktır.

References

  • Bellon, M.R., Brar, D.S., Lu, B.R., Pham J.L. 1998. Rice genetic resources. In: Dwoling NG, Greenfield SM, Fischer KS (eds) Sustainability of rice in the global food system, Chapter 16,Davis, California (USA). Pacific Basin Study Center and IRRI, Manila, 251–283.
  • Gandhi, S.G., Awasthi, P. and Bedi, Y.S. 2010. Analysis of SSR dynamics in chloroplast genomes of Brassicaceae family. Bioinformation, 5(1), 16-20.
  • Gao, L.Z. 1997. Studies on genetic variation of three wild rice (Oryza spp.) in China and their conservation biology. Ph.D. Dissertation, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China.
  • Gao, L.Z., Zhang, C.H., Li, D.Y., Pan, D.J., Jia, J.Z., Dong, Y.S. 2006. Genetic diversity within Oryza rufipogon germplasms preserved in Chinese field gene banks of wild rice as revealed by microsatellite markers. Biodiversity and Conservation, 15, 4059–4077.
  • Khush, G.S. 1997. Origin, dispersal, cultivation and variation of rice. Plant Molecular Biology, 35, 25–34.
  • Kuntal, H., Sharma V. 2011. In Silico Analysis of SSRs in Mitochondrial Genomes of Plants. OMICS: A Journal of Integrative Biology, Vol. 15, No. 11, 783-789.
  • Li, Y.C., Korol, A.B., Fahima, T. and Nevo, E. 2004. Microsatellites Within Genes: Structure, Function, and Evolution. Mol. Biol. Evol., 21(6), 991–1007.
  • Londo, J.P., Chiang, Y.C., Hung, K.H., Chiang, T.Y., Schaal, B.A. 2006. Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. PNAS, 103: 25, 9578–9583.
  • Mackenzie, S., He, S., Lyznik, A. 1994. The Elusive Plant Mitochondrion as a Genetic System. Plant Physiol., 105, 775–780.
  • Metzgar, D., Bytof, J., Wills, C. 2000. Selection Against Frameshift Mutations Limits Microsatellite Expansion in Coding DNA. Genome Res., 10, 72-80.
  • Morgante, M., Hanafey, M. and Powell, W. 2002. Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat. Genet., 30, 194–200.
  • Nishikawa, T., Vaughan, D.A., Kadowaki, K. 2005. Phylogenetic analysis of Oryza species, based on simple sequence repeats and their flanking nucleotide sequences from the mitochondrial and chloroplast genomes. Theor Appl Genet, 110, 696–705.
  • Oka, H.I. 1988. Origin of cultivated rice. Japanese Scientific Societies Press, Tokyo. Oliveira, E. J., Pádua, J. G., Zucchi, M.I., Vencovsky, R., Vieira, M.L.C. 2006. Origin, evolution and genome distribution of microsatellites, Genetics and Molecular Biology, 29(2), 294-307.
  • Palmer, J.D., Adams, K.L., Cho, Y., Parkinson, C.L., Qiu, Y.L., and Song, K. 2000. Dynamic evolution of plant mitochondrial genomes: mobile genes and introns, and highly variable mutation rates. Proc. Natl. Acad. Sci. USA, 97, 6960-6966.
  • Rajendrakumar, P., Biswal, A.K., Balachandran, S.M., Srinivasarao, K. and Sundaram, R.M. 2007. Simple sequence repeats in organellar genomes of rice: frequency and distribution in genic and intergenic regions. Bioinformatics, 23, 1–4.
  • Rajendrakumar, P., Biswal, A.K., Balachandran, S.M., Sundaram, R.M. 2008. In silico analysis of microsatellites in organellar genomes of major cereals for understanding the phylogenetic relationships. In Silico Biology, 8, 9-18.
  • Xu, J.H., Cheng, C., Tsuchimoto, S., Ohtsubo, H., Ohtsubo, E. 2007. Phylogenetic analysis of Oryza rufipogon strains and their relationship to Oryza sativa strains by insertion polymorphism of rice SINEs. Genes Genet. Syst., 82, 217-229.
  • Varshney, R.K., Thiel, T., Stein, N., Langridge, P. and Graner, A. 2002. In Silico Analysis on Frequency and Distribution of Microsatellites in ESTs of Some Cereal Species. Cellular & Molecular Biology Letters, 7, 537 – 546.
  • Varshney, R.K., Graner, A., Sorrells, M.E. 2005. Genic microsatellite markers in plants: features and applications. TRENDS in Biotechnology, Vol.23, No.1. Victoria, F.C., Maia, L.C., Oliveira, A.C. 2011. In silico comparative analysis of SSR markers in plants. BMC Plant Biology, 11,15.
  • Yuan, L.P., Virmani, S.S., Mao, C.X. 1989. Hybrid rice: achievements and further outlook. In: Progress in irrigated rice research. International Rice Research Institute, Manila, The Philippines, 219–223.
There are 20 citations in total.

Details

Primary Language Turkish
Journal Section Research Articles
Authors

Ertuğrul Filiz This is me

Publication Date June 1, 2012
Published in Issue Year 2012 Volume: 2012 Issue: 1

Cite

APA Filiz, E. (2012). Oryza rufipogon Griff. Mitokondri Genomunun (mtDNA) In silico SSR Analizi. Journal of Agricultural Faculty of Gaziosmanpaşa University (JAFAG), 2012(1).