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A deep sequencing analysis of transcriptomes and the development of EST-SSR markers in mungbean (Vigna radiata)

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Abstract

Mungbean (Vigna radiata L. Wilczek) is one of the most important leguminous food crops in Asia. We employed Illumina paired-end sequencing to analyse transcriptomes of three different mungbean genotypes. A total of 38.3–39.8 million paired-end reads with 73 bp lengths were generated. The pooled reads from the three libraries were assembled into 56,471 transcripts. Following a cluster analysis, 43,293 unigenes were obtained with an average length of 739 bp and N50 length of 1176 bp. Of the unigenes, 34,903 (80.6%) had significant similarity to known proteins in the NCBI nonredundant protein database (Nr), while 21,450 (58.4%) had BLAST hits in the Swiss-Prot database (E-value<10−5). Further, 1245 differential expression genes were detected among three mungbean genotypes. In addition, we identified 3788 expressed sequence tag-simple sequence repeat (EST-SSR) motifs that could be used as potential molecular markers. Among 320 tested loci, 310 (96.5%) yielded amplification products, and 151 (47.0%) exhibited polymorphisms among six mungbean accessions. These transcriptome data and mungbean EST-SSRs could serve as a valuable resource for novel gene discovery and the marker-assisted selective breeding of this species.

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References

  • Altschul S. F., Madden T. L., Schaffer A. A., Zhang J., Zhang Z., Miller W. et al. 1997 Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Blair M. W., Hurtado N., Chavarro C. M., Munoz-Torres M. C., Giraldo M. C., Pedraza F. et al. 2011 Gene-based ssr markers for common bean (phaseolus vulgaris l.) derived from root and leaf tissue ests: an integration of the BMC series. BMC Plant Biol. 11, 50.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen M., Wang Q. Y., Cheng X. G., Xu Z. S., Li L. C., Ye X. G. et al. 2007 Gmdreb2, a soybean dre-binding transcription factor, conferred drought and high-salt tolerance in transgenic plants. Biochem. Biophys. Res. Co. 353, 299–305.

    Article  CAS  Google Scholar 

  • Chen X., Zhu W., Azam S., Li H., Zhu F., Li H. et al. 2013 Deep sequencing analysis of the transcriptomes of peanut aerial and subterranean young pods identifies candidate genes related to early embryo abortion. Plant Biotechnol. J. 11, 115–127.

    Article  CAS  PubMed  Google Scholar 

  • Cheng X. Z. and Tian J. 2011 Status and future perspectives of Vigna (mungbean and azuki bean) production and research in China. In The 14th NIAS international workshop on genetic resources - genetic resources and comparative genomics of legumes (Glycine and Vigna) (ed. N. Tomooka, D. A. Vaughan), pp. 83–86. National Institute of Agrobiological Science, Tsukuba.

  • Conesa A., Gotz S., Garcia-Gomez J. M., Terol J., Talon M. and Robles M. 2005 Blast2go: a universal tool for annotation, visualization and analysis in functional genomics research . Bioinformatics 21, 3674–3676.

    Article  CAS  PubMed  Google Scholar 

  • Ekblom R. and Galindo J. 2011 Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity 107, 1–15.

    Article  CAS  PubMed  Google Scholar 

  • Gao J., Zhang Y., Zhang C., Qi F., Li X., Mu S. et al. 2014 Characterization of the floral transcriptome of moso bamboo (phyllostachys edulis) at different flowering developmental stages by transcriptome sequencing and RNA-seq analysis. PLoS One 9, e98910.

    Article  PubMed  PubMed Central  Google Scholar 

  • Garg R., Patel R. K., Tyagi A. K. and Jain M. 2011 De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res. 18, 53–63.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Grabherr M. G., Haas B. J., Yassour M., Levin J. Z., Thompson D. A., Amit I. et al. 2011 Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat. Biotechnol. 29, 644–652.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gupta S. K., Bansal R. and Gopalakrishna T. 2014 Development and characterization of genic SSR markers for mungbean (Vigna radiata (L.) Wilczek). Euphytica 195, 245–258.

    Article  CAS  Google Scholar 

  • Gwag J. G., Chung J. W., Chung H. K., Lee J. H. and Ma K. H. 2006 Characterization of new microsatellite markers in mungbean, Vigna radiata (L.) Mol. Ecol. Notes 6, 1132–1134.

    Article  CAS  Google Scholar 

  • Iorizzo M., Senalik D. A., Grzebelus D., Bowman M., Cavagnaro P. F., Matvienko M. et al. 2011 De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity. BMC Genomics 12, 389.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Isemura T., Kaga A., Tabata S., Somta P., Srinives P., Shimizu T. et al. 2012 Construction of a genetic linkage map and genetic analysis of domestication related traits in mungbean (Vigna radiata). PLoS One 7, e41304.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kanehisa M. and Goto S. 2000 KEGG: Kyoto encyclopedia of genes and genomes. Nucleic. Acids. Res. 28, 27–30.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kang Y. J., Kim S. K., Kim M. Y., Lestari P., Kim K. H., Ha B. K. et al. 2014 Genome sequence of mungbean and insights into evolution within Vigna species. Nat. Commun. 5, 5443.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kaur S., Pembleton L. W., Cogan N. O., Savin K. W., Leonforte T., Paull J. et al. 2012 Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers. BMC Genomics 13, 104.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kumar S. V., Tan S. G., Quah S. C. and Yusoff K. 2002 Isolation and characterization of seven tetranucleotide microsatellite loci in mungbean, Vigna radiata. Mol. Ecol. Notes 2, 293– 295.

    Article  CAS  Google Scholar 

  • Lam H. M., Xu X., Liu X., Chen W., Yang G., Wong F. L. et al. 2010 Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat. Genet. 42, 1053–1061.

    Article  CAS  PubMed  Google Scholar 

  • Lambrides C. J. and Godwin I. D. 2007 Mungbean. In Genome mapping and molecular breeding in plants (ed. C. Kole), pp. 69–90. Springer Press, Berlin.

  • Lee L. W., Zhang S., Etheridge A., Ma L., Martin D., Galas D. et al. 2010 Complexity of the microRNA repertoire revealed by next-generation sequencing. RNA 16, 2170–2180.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Leng N. and Kendziorski C. 2014 EBSeq: an R package for gene and isoform differential expression analysis of RNA-seq data. R package version 1.6.0. Available online: http://www.bioconductor.org/packages/release/bioc/html/EBSeq.html.

  • Livak K. J. and Schmittgen T. D. 2001 Analysis of relative gene expression data using real-time quantitative PCR and the 2(-delta delta c(t)) method. Methods 25, 402–408.

    Article  CAS  PubMed  Google Scholar 

  • Miyagi M., Humphry M., Ma Z. Y., Lambrides C. J., Bateson M. and Liu C. J. 2004 Construction of bacterial artificial chromosome libraries and their application in developing PCR-based markers closely linked to a major locus conditioning bruchid resistance in mungbean (Vigna radiata l. Wilczek). Theor. Appl. Genet. 110, 151–156.

    Article  CAS  PubMed  Google Scholar 

  • Moe K. T., Chung J. W., Cho Y. I., Moon J. K., Ku J. H., Jung J. K. et al. 2011 Sequence information on simple sequence repeats and single nucleotide polymorphisms through transcriptome analysis of mungbean. J. Integr. Plant. Biol. 53, 63–73.

    Article  CAS  PubMed  Google Scholar 

  • Nagalakshmi U., Wang Z., Waern K., Shou C., Raha D., Gerstein M. et al. 2008 The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344–1349.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Parida A., Raina S. N. and Narayan R. K. 1990 Quantitative DNA variation between and within chromosome complements of Vigna species (Fabaceae). Genetica 82, 125–133.

    Article  CAS  Google Scholar 

  • Porebski S., Bailey L. and Baum B. 1997 Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Mol. Biol. Rep. 15, 8–15.

    Article  CAS  Google Scholar 

  • Ren X., Chen Z., Liu Y., Zhang H., Zhang M., Liu Q. et al. 2010 Abo3, a wrky transcription factor, mediates plant responses to abscisic acid and drought tolerance in Arabidopsis. The Plant J. 63, 417–429.

    Article  CAS  PubMed  Google Scholar 

  • Rodriguez-Uribe L. and O’Connell M. A. 2006 A root-specific bzip transcription factor is responsive to water deficit stress in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris) . J. Exp. Bot. 57, 1391–1398.

    Article  CAS  PubMed  Google Scholar 

  • Rozen S. and Skaletsky H. 2000 Primer3 on the www for general users and for biologist programmers. Methods Mol. Boli. 132, 365–386.

    CAS  Google Scholar 

  • Sehrawat N., Bhat K. V., Kaga A., Tomooka N., Yadav M. and Jaiwal P. K. 2014 Development of new gene-specific markers associated with salt tolerance for mungbean (Vigna radiata L.Wilczek). Span. J. Agri. Res. 12, 732–741.

    Article  Google Scholar 

  • Severin A. J., Woody J. L., Bolon Y. T., Joseph B., Diers B. W., Farmer A. D. et al. 2010 RNA-seq atlas of Glycine max: a guide to the soybean transcriptome. BMC Plant Biol. 10, 160.

    Article  PubMed  PubMed Central  Google Scholar 

  • Somta P., Musch W., Kongsamai B., Chanprame S., Nakasathien S., Toojinda T. et al. 2008 New microsatellite markers isolated from mungbean (Vigna radiata (l.) Wilczek). Mol. Ecol. Resour. 8, 1155–1157.

    Article  CAS  PubMed  Google Scholar 

  • Tangphatsornruang S., Somta P., Uthaipaisanwong P., Chanprasert J., Sangsrakru D., Seehalak W. et al. 2009 Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (l.) Wilczek). BMC Plant Biol. 9, 137.

    Article  PubMed  PubMed Central  Google Scholar 

  • Tomooka N., Vaughan D. A., Moss H. and Maxted N. 2002 The Asian Vigna: genus Vigna subgenus ceratotropis genetic resources. Kluwer Academic Publishers, London, UK.

    Book  Google Scholar 

  • Wang Z., Li J., Luo Z., Huang L., Chen X., Fang B. et al. 2011 Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas). BMC Plant Biol. 11, 139.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wei W., Qi X., Wang L., Zhang Y., Hua W., Li D. et al. 2011 Characterization of the sesame (Sesamum indicum l.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics 12, 451.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu J., Wang L., Li L. and Wang S. 2014 De novo assembly of the common bean transcriptome using short reads for the discovery of drought-responsive genes. PLoS One 9, e109262.

    Article  PubMed  PubMed Central  Google Scholar 

  • Ye J., Fang L., Zheng H., Zhang Y., Chen J., Zhang Z. et al. 2006 Wego: a web tool for plotting go annotations. Nucleic Acids Res. 34, W293–W297.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yin D., Wang Y., Zhang X., Li H., Lu X., Zhang J. et al. 2013 De novo assembly of the peanut (Arachis hypogaea l.) seed transcriptome revealed candidate unigenes for oil accumulation pathways. PLoS One 8, e73767.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zalapa J. E., Cuevas H., Zhu H., Steffan S., Senalik D., Zeldin E. et al. 2012 Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences . Am. J. Bot. 99, 193–208.

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This research was supported by China Agriculture Research System (CARS-09), Funds for Young Scholar of Hebei Academy of Agricultural and Forestry Sciences (A2015060302) and Science and Technology Support Program of Hebei Province (14226303D).

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Authors and Affiliations

  1. Key Laboratory of Crop Genetics and Breeding of Hebei Province, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, China

    CHANGYOU LIU, BAOJIE FAN, ZHIMIN CAO, QIUZHU SU, YAN WANG, ZHIXIAO ZHANG & JING TIAN

  2. Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, 10011, China

    JING WU

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  1. CHANGYOU LIU
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Correspondence to JING TIAN.

Additional information

[Liu C., Fan B., Cao Z., Su Q., Wang Y., Zhang Z., Wu J. and Tian J. 2016 A deep sequencing analysis of transcriptomes and the development of EST-SSR markers in mungbean (Vigna radiata). J. Genet. 95, xx–xx]

Jing Tian designed the experiment. Changyou Liu carried out the RNA isolation and sequence data analyses, and drafted the manuscript. Jing Tian and Jing Wu assisted in manuscript preparation. Baojie Fan, Zhimin Cao, Qiuzhu Su, Yan Wang and Zhixiao Zhang prepared the plant materials and participated in RNA and DNA extraction and SSR experiment.

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LIU, C., FAN, B., CAO, Z. et al. A deep sequencing analysis of transcriptomes and the development of EST-SSR markers in mungbean (Vigna radiata). J Genet 95, 527–535 (2016). https://doi.org/10.1007/s12041-016-0663-9

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  • DOI: https://doi.org/10.1007/s12041-016-0663-9

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