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Status of SSR, cSSR, iSSR and VNTR motifs in Leptosphaeria maculans based on high throughput sequencing data | ||
| Mycologia Iranica | ||
| دوره 8، شماره 2، اسفند 2021، صفحه 95-107 اصل مقاله (1.44 M) | ||
| نوع مقاله: Original Article | ||
| شناسه دیجیتال (DOI): 10.22092/MI.2022.359536.1225 | ||
| نویسندگان | ||
| Ali Zamanmirabadi1؛ Roghayeh Hemmati* 1؛ Aria Dolatabadian2؛ Jacqueline Batley3 | ||
| 1Department of Plant Protection, Faculty of Agriculture, University of Zanjan, Zanjan, Iran | ||
| 2Department of Plant Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada | ||
| 3UWA School of Biological Sciences and the UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, WA, Australia | ||
| چکیده | ||
| Leptosphaeria maculans is a fungus of the phylum Ascomycota that is a causal agent of blackleg disease on canola (Brassica napus L.). Due to the high diversity and worldwide distribution, L. maculans has been widely studied as a model phytopathogenic fungus. Simple sequence repeats (SSRs) are robust molecular markers widely used for population diversity research. This study utilized whole-genome sequencing data of four Iranian L. maculans isolates (Pk4, Ar3, Ar5, and Alam10). We compared them with the JN3 reference genome to identify and compare different types of SSRs, including perfect (SSRs), compound (cSSR), imperfect (iSSR) and variable tandem number repeats (VNTR) motifs. The average length of SSRs was estimated to be 155.692 kb, accounting for 0.36% of the total genome. An average of 7138 SSR motifs with a frequency of one SSR per 169.5 bp, including an average of 33.86% tri, 25.69% di, 14.48% mono, 10.87% tetra, 8.52% hexa, 6.58% penta-nucleotide repeats, were identified from assembled genomic sequences. Of the total SSRs identified in the Pk4 isolate, 459 motifs were identified in CDS regions. Approximately 13% of the identified SSRs were linked to cSSRs. The average cSSR loci density for four isolates was 487.32 bp/Mb, and C, AG and AC were the most frequent SSR motifs. The assessed isolates' cSSRs lengths ranged from 24 to 295 bp. The largest common cSSRs in four isolates were identified as a motif (GA)26-(CAGAGA)15 with a length of 142 bp. The tri-nucleotide (AAT) was the most common iSSRs motif, followed by di, tetra, mono, hexa, and penta-nucleotides. About 30% of iSSRs contained the AAT, AT, and AAG motifs. Among the 7 to 30 nucleotide motifs, 7, 8, 9, and 10 motifs showed the most occurrences. In addition, 11 motifs with more than 100 nucleotides were found in the studied isolates and the reference genome. The data demonstrate that these results can be used to characterize L. maculans isolates from diverse hosts and geographic locations and are transferable to other isolates of L. maculans. | ||
| کلیدواژه‌ها | ||
| Blackleg؛ SSRs؛ Leptosphaeria maculans؛ NGS | ||
| مراجع | ||
|
Bayraktar, H., Sara Dolar, F., and Tör, M. 2007. Determination of genetic diversity within Ascochyta Rabiei (Pass.) Labr., the cause of Ascochyta blight of Chickpea in Turkey Determinatıon Of Fungi That Cause Cluster and Fruıt Diseases On Hazelnut in Ordu Giresun and Trabzon Provinces and Reactions of C. JSTOR. [Online] Available: https://www.researchgate.net/publication/242758035 [2020 Mar. 30].
Bull, L.N., Pabón-Peña, C.R., and Freimer, N.. 1999. Compound Microsatellite Repeats: Practical and Theoretical Features. Genome Res. 9: 830-838.
Chambers, G.K., and MacAvoy, E.S. 2000. Microsatellites: consensus and controversy. Comp Biochem Physiol B Biochem Mol Biol. 126: 455–76.
Doyle, J.J., and Doyle, J.L. 1990. A rapid total DNA preparation procedure for fresh plant tissue. Focus (Madison). 12: 13–15.
Du, L., Zhang, C., Liu, Q., Zhang, X., and Yue, B. 2018. Krait: an ultrafast tool for genome-wide survey of microsatellites and primer design. Bioinformatics 34: 681–683.
Duran, C., Appleby, N., Edwards, D., and Batley, J. 2009. Molecular Genetic Markers: Discovery, Applications, Data Storage and Visualisation. Curr. Bioinform. 4: 16–27. doi:10.2174/157489309787158198.
Dutech, C., Enjalbert, J., Fournier, E., Delmotte, F., Barrès, B., Carlier, J., Tharreau, D., and Giraud, T. 2007a. Challenges of microsatellite isolation in fungi. Fungal Genet. Biol. 44: 933–949. doi:10.1016/j.fgb.2007.05.003.
Dutech, C., Enjalbert, J., Fournier, E., Delmotte, F., Barrès, B., Carlier, J., Tharreau, D., Giraud, T., Biology, F.D.-… G. and, 2007, undefined, Delmotte, F., Barrès, B., Carlier, J., Tharreau, D., and Giraud, T. 2007b. Challenges of microsatellite isolation in fungi. Fungal Genet. Biol. 44: 933–949.
Engelbrecht, J., Duong, T.A., Reports, N. vd B.-S., 2017, U., and Berg, N. V.D. 2017. New microsatellite markers for population studies of Phytophthora cinnamomi, an important global pathogen. Sci. Rep. 7: 1–10. Springer US. doi:10.1038/s41598-017-17799-9.
Fitt, B.D.L.L., Brun, H., Barbetti, M.J., and Rimmer, S.R. 2006. Worldwide importance of phoma stem canker (Leptosphaeria maculans and L. biglobosa) on oilseed Rape (Brassica napus). Eur. J. Plant Pathol. 114: 3–15. doi:10.1007/s10658-005-2233-5.
Guichoux, E., Lagache, L., Wagner, S., Chaumeil, P., Léger, P., Lepais, O., Lepoittevin, C., Malausa, T., Revardel, E., Salin, F., and Petit, R.J. 2011. Current trends in microsatellite genotyping. Molecular Ecology Resources. 4: 591–611.
Gurjar, M.S., Aggarwal, R., Jogawat, A., Kulshreshtha, D., Sharma, S., Solanke, A.U., Dubey, H., and Jain, R.K. 2019. De novo genome sequencing and secretome analysis of Tilletia indica inciting Karnal bunt of wheat provides pathogenesis-related genes. 3 Biotech 9: 1–11. Springer International Publishing. doi:10.1007/s13205-019-1743-3.
Hayden, H.L., Cozijnsen, A.J., and Howlett, B.J. 2007. Microsatellite and Minisatellite Analysis of Leptosphaeria maculans in Australia Reveals Regional Genetic Differentiation. Phytopathology 97: 879–887. Scientific Societies. doi:10.1094/phyto-97-7-0879.
Howlett, B.J. 2004. Current knowledge of the interaction between Brassica napus and Leptosphaeria maculans. Can. J. Plant Pathol. 26: 245–252.
Jana, T., Sharma, T.R., and Singh, N.K. 2005. {SSR}-based detection of genetic variability in the charcoal root rot pathogen Macrophomina phaseolina. Mycol. Res. 109: 81–86. Elsevier {BV}. doi:10.1017/s0953756204001364.
Jarne, P., and Lagoda, P.J.L. 1996. Microsatellites, from molecules to populations and back. Trends Ecol. Evol. 11: 424–429.
Karaoglu, H., Lee, C.M.Y., and Meyer, W. 2005. Survey of simple sequence repeats in completed fungal genomes. Mol. Biol. Evol. 22: 639–649. doi:10.1093/molbev/msi057.
Kashyap, P.L., Kumar, S., Kumar, R.S., Tripathi, R., Sharma, P., Sharma, A., Jasrotia, P., and Singh, G.P. 2020. Identification of Novel Microsatellite Markers to Assess the Population Structure and Genetic Differentiation of Ustilago hordei Causing Covered Smut of Barley. Front. Microbiol. 10. Frontiers Media S.A. doi:10.3389/fmicb.2019.02929.
Katti, M. V, Ranjekar, P.K., and Gupta, V.S. 2001. Differential distribution of simple sequence repeats in eukaryotic genome sequences. Mol. Biol. Evol. 18: 1161–7. Society for Molecular Biology and Evolution. doi:10.1093/oxfordjournals.molbev.a003903.
Kofler, R., Schlötterer, C., Luschützky, E., and Lelley, T. 2008. Survey of microsatellite clustering in eight fully sequenced species sheds light on the origin of compound microsatellites. BMC Genomics 9: 1–14. doi:10.1186/1471-2164-9-612.
Li, C.Y., Liu, L., Yang, J., Li, J.B., Su, Y., Zhang, Y., Wang, Y.Y., and Zhu, Y.Y. 2009. Genome-wide analysis of microsatellite sequence in seven filamentous fungi. Interdiscip. Sci. Comput. Life Sci. 1: 141-150.
Liban, S.H., Cross, D.J., Kutcher, H.R., Peng, G., and Fernando, W.G.D. 2016. Race structure and frequency of avirulence genes in the western Canadian Leptosphaeria maculans pathogen population, the causal agent of blackleg in brassica species. Plant Pathol. 65: 1161–1169. Wiley.
Luo, H., Wang, X., Zhan, G., Wei, G., Zhou, X., Zhao, J., Huang, L., and Kang, Z. 2015. Genome-wide analysis of simple sequence repeats and efficient development of polymorphic SSR markers based on whole genome resequencing of multiple isolates of the wheat stripe rust fungus. PLoS One 10.
Manawasinghe, I.S., Zhang, W., Li, X., Zhao, W., Chethana, K.W.T., Xu, J., Chen, Z., Dissanayaka, A.J., Mugnai, L., Úrbez-Torres, J.R., Savocchia, S., Hyde, K.D., and Yan, J. 2018. Novel microsatellite markers reveal multiple origins of Botryosphaeria dothidea causing the Chinese grapevine trunk disease. Fungal Ecol. 33: 134–142. Elsevier Ltd.
Marulanda, M.L., López, A.M., Isaza, L., and López, P. 2014. Microsatellite isolation and characterisation for Colletotrichum spp, causal agent of anthracnose in Andean blackberry. Genet. Mol. Res. 13: 7673–7685. Genetics and Molecular Research.
Metzgar, D., Bytof, J., and Wills, C. 2000. Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genome Res. 10: 72–80.
Moges, A.D., Admassu, B., Belew, D., Yesuf, M., Njuguna, J., Kyalo, M., and Ghimire, S.R. 2016. Development of microsatellite markers and analysis of genetic diversity and population structure of colletotrichum gloeosporioides from Ethiopia. PLoS One 11: 1–18. Public Library of Science. doi:10.1371/journal.pone.0151257.
Murat, C., Riccioni, C., Belfiori, B., Cichocki, N., Labbé, J., Morin, E., Tisserant, E., Paolocci, F., Rubini, A., and Martin, F. 2011. Distribution and localisation of microsatellites in the Perigord black truffle genome and identification of new molecular markers. Fungal Genet. Biol. 48: 592–601.
Neik, T.X., Barbetti, M.J., Batley, J., Fernandez-Aparicio, M., An, H., Peng, G., Bruce, C., Gossen, D., Batley, J., Neik, T.X., Barbetti, M.J., Batley, J., Fernandez-Aparicio, M., An, H., Peng, G., Bruce, C., Gossen, D., Batley, J., Neik, T.X., Barbetti, M.J., and Batley, J. 2017. Current status and challenges in identifying disease resistance genes in Brassica napus. Front. Plant Sci. 8: 1788. Frontiers Media S.A.
Owati, A., Agindotan, B., Burrows, M., Biology, M.B.-F., and 2019, U. 2019. First microsatellite markers developed and applied for the genetic diversity study and population structure of Didymella pisi associated with ascochyta blight of dry pea in Montana. Fungal Biol. 123: 384–392. Elsevier Ltd.
Raman, R., Taylor, B., Marcroft, S., Stiller, J., Eckermann, P., Coombes, N., Rehman, A., Lindbeck, K., Luckett, D., Wratten, N., Batley, J., Edwards, D., Wang, X., and Raman, H. 2012. Molecular mapping of qualitative and quantitative loci for resistance to Leptosphaeria maculans causing blackleg disease in canola (Brassica napus L.). Theor. Appl. Genet. 125: 405–418. Springer Science and Business Media {LLC}.
Riju, A. 2009. SSR - Identification from EST. Nat. Preced. doi:10.1038/npre.2009.3908.1.
Rizatto, S., de Araújo Batista, C.E., Bajay, M.M., Sigrist, M.S., Ito, M.F., Monteiro, M., Cavallari, M.M., Pinheiro, J.B., and Zucchi, M.I. 2009. A new set of microsatellite markers for the genetic characterisation of Ceratocystis fimbriata, an economically important plant pathogen. Conserv. Genet. Resour. 2: 55–58. Springer Science and Business Media {LLC}.
Robinson, A.J., Love, C.G., Batley, J., Barker, G., and Edwards, D. 2004. Simple sequence repeat marker loci discovery using SSR primer. Bioinformatics 20: 1475–1476.
Rouxel, T., Grandaubert, J., Hane, J. K., Hoede, C., Van De Wouw, A.P., Couloux, A., Dominguez, V., Anthouard, V., Bally, P., Bourras, S., Cozijnsen, A. J., Ciuffetti, L. M., Degrave, A., Dilmaghani, A., Duret, L., Fudal, I., Goodwin, S. B., Gout, L., Glaser, N., Linglin, J., Kema, G. H. J., Lapalu, N., Lawrence, C. B., May, K., Meyer, M., Ollivier, B., Poulain, J., Schoch, C. L., Simon, A., Spatafora, J. W., Stachowiak, A., Turgeon, B.G., Tyler, B. M., Vincent, D., Weissenbach, J., Amselem, J., Quesneville, H., Oliver, R. P., Wincker, P., Balesdent, M.-H., and Howlett, B.J. 2011. Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations. Nat. Commun.
Rouxel, T., Grandaubert, J., Hane, J.K., Hoede, C., Van De Wouw, A.P., Couloux, A., Dominguez, V., Anthouard, V., Bally, P., Bourras, S., Cozijnsen, A.J., Ciuffetti, L.M., Degrave, A., Dilmaghani, A., Duret, L., Fudal, I., Goodwin, S.B., Gout, L., Glaser, N., Linglin, J., Kema, G.H.J., Lapalu, N., Lawrence, C.B., May, K., Meyer, M., Ollivier, B., Poulain, J., Schoch, C.L., Simon, A., Spatafora, J.W., Stachowiak, A., Turgeon, B.G., Tyler, B.M., Vincent, D., Weissenbach, J., Amselem, J., Quesneville, H., Oliver, R.P., Wincker, P., Balesdent, M.H., and Howlett, B.J. 2011. Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations. Nat. Commun. 2: 202. Nature Publishing Group.
Singh, A.K., Singh, P.K., Arya, M., Singh, N.K., and Singh, U.S. 2015. Molecular screening of blast resistance genes in Rice using SSR markers. Plant Pathol. J. 31: 12–24. Korean Society of Plant Pathology.
Srivastava, S., Avvaru, A.K., Sowpati, D.T., and Mishra, R.K. 2019. Patterns of microsatellite distribution across eukaryotic genomes. BMC Genomics 20. BioMed Central Ltd.
Stachowiak, A., Olechnowicz, J., Jedryczka, M., Rouxel, T., Balesdent, M.-H.H., Happstadius, I., Gladders, P., Latunde-Dada, A., and Evans, N. 2006. Frequency of avirulence alleles in field populations of Leptosphaeria maculans in Europe. Eur. J. Plant Pathol. 114: 67–75. Springer Science and Business Media {LLC}.
Szabo, L.J., and Kolmer, J.A. 2007. Development of simple sequence repeat markers for the plant pathogenic rust fungus Puccinia triticina. Mol. Ecol. Notes 7: 708–710. Wiley.
Taheri, S., Abdullah, T.L., Yusop, M.R., Hanafi, M.M., Sahebi, M., Azizi, P., and Shamshiri, R.R. 2018. Mining and development of novel SSR markers using Next Generation Sequencing (NGS) data in plants. Molecules 23.
Tautz, D. 1989. Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res. 17: 6463–6471.
Temnykh, S., DeClerck, G., Lukashova, A., Lipovich, L., Cart inhour, S., and McCouch, S. 2001. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 11: 1441-1452.
Wang, X., Yang, S., Chen, Y., Zhang, S., Zhao, Q., Li, M., Gao, Y., Yang, L., and Bennetzen, J.L. 2018. Comparative genome-wide characterisation leading to simple sequence repeat marker development for Nicotiana. BMC Genomics 19: 1–12.
Weber, J.L. 1990. Informativeness of human (dC-dA)n · (dG-dT)n polymorphisms. Genomics 7: 524–530. Academic Press.
Winton, L.M., Krohn, A.L., and Leiner, R.H. 2007. Microsatellite markers for Sclerotinia subarctica nom. prov., a new vegetable pathogen of the High North. Mol. Ecol. Notes 7: 1077–1079. Wiley.
Zamanmirabadi, A., Hemmati, R., Dolatabadian, A., and Batley, J. 2021. Current progress in studying blackleg disease ( Leptosphaeria maculans and L . biglobosa ) of canola in Iran : Where do we stand now ? Plant Pathol.: 1–12.
Zamanmirabadi, A., Hemmati, R., Dolatabadian, A., and Batley, J. 2022. Genetic structure and phylogenetic relationships of Leptosphaeria maculans and L. biglobosa in Northern regions of Iran. Arch. Phytopathol. Plant Prot.: 1-20.
Zamanmirabadi, A., Rahnama, K., Sadravi, M., and Mehdi Alamdarlou, R.M. 2008. First report of Leptosphaeria maculans teleomorph on canola stem in the north of Iran (short article). Rostaniha 9: 128–130. [Online] Available: http://en.journals.sid.ir/ViewPaper.aspx?ID=122787 [2018 Jan. 12]. | ||
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