title: Transcriptome sequencing of mung bean (Vigna radiate L.) genes and the identification of EST-SSR markers.
abstract: Mung bean (Vigna radiate (L.) Wilczek) is an important traditional food legume crop, with high economic and nutritional value. It is widely grown in China and other Asian countries. Despite its importance, genomic information is currently unavailable for this crop plant species or some of its close relatives in the Vigna genus. In this study, more than 103 million high quality cDNA sequence reads were obtained from mung bean using Illumina paired-end sequencing technology. The processed reads were assembled into 48,693 unigenes with an average length of 874 bp. Of these unigenes, 25,820 (53.0%) and 23,235 (47.7%) showed significant similarity to proteins in the NCBI non-redundant protein and nucleotide sequence databases, respectively. Furthermore, 19,242 (39.5%) could be classified into gene ontology categories, 18,316 (37.6%) into Swiss-Prot categories and 10,918 (22.4%) into KOG database categories (E-value < 1.0E-5). A total of 6,585 (8.3%) were mapped onto 244 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway database. Among the unigenes, 10,053 sequences contained a unique simple sequence repeat (SSR), and 2,303 sequences contained more than one SSR together in the same expressed sequence tag (EST). A total of 13,134 EST-SSRs were identified as potential molecular markers, with mono-nucleotide A/T repeats being the most abundant motif class and G/C repeats being rare. In this SSR analysis, we found five main repeat motifs: AG/CT (30.8%), GAA/TTC (12.6%), AAAT/ATTT (6.8%), AAAAT/ATTTT (6.2%) and AAAAAT/ATTTTT (1.9%). A total of 200 SSR loci were randomly selected for validation by PCR amplification as EST-SSR markers. Of these, 66 marker primer pairs produced reproducible amplicons that were polymorphic among 31 mung bean accessions selected from diverse geographical locations. The large number of SSR-containing sequences found in this study will be valuable for the construction of a high-resolution genetic linkage maps, association or comparative mapping and genetic analyses of various Vigna species.
authors.affiliation: The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Honglin
authors.initials: H
authors.lastname: Chen
authors.affiliation: The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Lixia
authors.initials: L
authors.lastname: Wang
authors.affiliation: The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Suhua
authors.initials: S
authors.lastname: Wang
authors.affiliation: CSIRO Plant Industry, Queensland Bioscience Precinct, Queensland, Australia.
authors.forename: Chunji
authors.initials: C
authors.lastname: Liu
authors.affiliation: Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, Tennessee, United States of America.
authors.forename: Matthew Wohlgemuth
authors.initials: MW
authors.lastname: Blair
authors.affiliation: The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Xuzhen
authors.initials: X
authors.lastname: Cheng
mesh_terms: D002874:Chromosome Mapping; D020224:Expressed Sequence Tags / Q000378:metabolism*; D007887:Fabaceae / Q000235:genetics* / Q000254:growth & development; D020869:Gene Expression Profiling; D017343:Genes, Plant / Q000235:genetics*; D005819:Genetic Markers / Q000235:genetics*; D018895:Microsatellite Repeats / Q000235:genetics*; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D011110:Polymorphism, Genetic; D017423:Sequence Analysis, RNA
chemical_list: D005819:Genetic Markers
references.citation: Nat Rev Genet. 2009 Jan;10(1):57-63
references.pmid: 19015660
references.citation: J Sci Food Agric. 2013 Jun;93(8):1805-13
references.pmid: 23426879
references.citation: Lett Appl Microbiol. 2000 Dec;31(6):421-6
references.pmid: 11123549
references.citation: Theor Appl Genet. 1992 Sep;84(7-8):839-44
references.pmid: 24201484
references.citation: Community Genet. 2006;9(1):55-61
references.pmid: 16490960
references.citation: Theor Appl Genet. 2008 Aug;117(4):629-40
references.pmid: 18548226
references.citation: Genome. 2010 Jul;53(7):508-23
references.pmid: 20616873
references.citation: Genome. 2009 Sep;52(9):772-82
references.pmid: 19935925
references.citation: Plant Biotechnol J. 2012 Aug;10(6):690-702
references.pmid: 22672127
references.citation: DNA Res. 2011 Feb;18(1):53-63
references.pmid: 21217129
references.citation: Nucleic Acids Res. 2012 Nov 1;40(20):10084-97
references.pmid: 22965124
references.citation: BMC Plant Biol. 2011;11:171
references.pmid: 22118559
references.citation: Theor Appl Genet. 2009 Feb;118(3):591-608
references.pmid: 19020854
references.citation: Nat Protoc. 2013 Aug;8(8):1494-512
references.pmid: 23845962
references.citation: BMC Plant Biol. 2009;9:100
references.pmid: 19646251
references.citation: BMC Plant Biol. 2011;11:50
references.pmid: 21426554
references.citation: J Integr Plant Biol. 2011 Jan;53(1):63-73
references.pmid: 21205180
references.citation: BMC Genomics. 2013;14:490
references.pmid: 23870214
references.citation: Bioinformatics. 2005 Sep 15;21(18):3674-6
references.pmid: 16081474
references.citation: DNA Res. 2010 Feb;17(1):11-22
references.pmid: 20007682
references.citation: IEEE/ACM Trans Comput Biol Bioinform. 2004 Jul-Sep;1(3):116-29
references.pmid: 17048387
references.citation: BMC Genomics. 2010;11:383
references.pmid: 20565764
references.citation: Theor Appl Genet. 2004 Mar;108(5):903-13
references.pmid: 14624337
references.citation: Nat Methods. 2010 Sep;7(9):709-15
references.pmid: 20711195
references.citation: Mol Ecol Resour. 2014 May;14(3):569-77
references.pmid: 24286608
references.citation: PLoS One. 2014;9(8):e104990
references.pmid: 25153330
references.citation: Theor Appl Genet. 2008 Dec;118(1):91-103
references.pmid: 18784914
references.citation: Theor Appl Genet. 2013 Aug;126(8):2017-27
references.pmid: 23674132
references.citation: Mol Biol Rep. 2012 Sep;39(9):9047-57
references.pmid: 22744420
references.citation: Theor Appl Genet. 2003 Feb;106(3):411-22
references.pmid: 12589540
references.citation: BMC Genomics. 2005;6:23
references.pmid: 15720707
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: BMC Plant Biol. 2011;11:17
references.pmid: 21251263
references.citation: Mol Gen Genet. 1998 May;258(4):378-84
references.pmid: 9648742