title: Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (L.) Wilczek).
abstract: BACKGROUND
  Mungbean is an important economical crop in Asia. However, genomic research has lagged behind other crop species due to the lack of polymorphic DNA markers found in this crop. The objective of this work is to develop and characterize microsatellite or simple sequence repeat (SSR) markers from genome shotgun sequencing of mungbean.
  
  
  RESULTS
  We have generated and characterized a total of 470,024 genome shotgun sequences covering 100.5 Mb of the mungbean (Vigna radiata (L.) Wilczek) genome using 454 sequencing technology. We identified 1,493 SSR motifs that could be used as potential molecular markers. Among 192 tested primer pairs in 17 mungbean accessions, 60 loci revealed polymorphism with polymorphic information content (PIC) values ranging from 0.0555 to 0.6907 with an average of 0.2594. Majority of microsatellite markers were transferable in Vigna species, whereas transferability rates were only 22.90% and 24.43% in Phaseolus vulgaris and Glycine max, respectively. We also used 16 SSR loci to evaluate phylogenetic relationship of 35 genotypes of the Asian Vigna group. The genome survey sequences were further analyzed to search for gene content. The evidence suggested 1,542 gene fragments have been sequence tagged, that fell within intersected existing gene models and shared sequence homology with other proteins in the database. Furthermore, potential microRNAs that could regulate developmental stages and environmental responses were discovered from this dataset.
  
  
  CONCLUSIONS
  In this report, we provided evidence of generating remarkable levels of diverse microsatellite markers and gene content from high throughput genome shotgun sequencing of the mungbean genomic DNA. The markers could be used in germplasm analysis, accessing genetic diversity and linkage mapping of mungbean.
authors.affiliation: National Center for Genetic Engineering and Biotechnology, 113 Phaholyothin Rd,, Klong 1, Klong Luang, Pathumthani 12120, Thailand. somvong.tra@biotec.or.th.
authors.forename: Sithichoke
authors.initials: S
authors.lastname: Tangphatsornruang
authors.forename: Prakit
authors.initials: P
authors.lastname: Somta
authors.forename: Pichahpuk
authors.initials: P
authors.lastname: Uthaipaisanwong
authors.forename: Juntima
authors.initials: J
authors.lastname: Chanprasert
authors.forename: Duangjai
authors.initials: D
authors.lastname: Sangsrakru
authors.forename: Worapa
authors.initials: W
authors.lastname: Seehalak
authors.forename: Warunee
authors.initials: W
authors.lastname: Sommanas
authors.forename: Somvong
authors.initials: S
authors.lastname: Tragoonrung
authors.forename: Peerasak
authors.initials: P
authors.lastname: Srinives
mesh_terms: D018744:DNA, Plant / Q000235:genetics; D020224:Expressed Sequence Tags; D007887:Fabaceae / Q000235:genetics*; D018745:Genome, Plant; D035683:MicroRNAs / Q000235:genetics; D018895:Microsatellite Repeats; D016366:Open Reading Frames; D010802:Phylogeny; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D018744:DNA, Plant; D035683:MicroRNAs