title: Screening potential SSR markers of the anadromous fish Coilia nasus by de novo transcriptome analysis using Illumina sequencing.
abstract: RNA-Seq technology has been widely applied to transcriptomics, genomics, molecular marker development, and functional gene studies. In the genome, microsatellites are simple sequence repeats (SSR) with a high degree of polymorphism that are used as DNA markers in many molecular genetic studies. Using traditional methods such as magnetic bead enrichment, only a few microsatellite markers have been isolated. Coilia nasus is an anadromous, small-to-moderately sized fish species that is famous as an important fishery resource. Here, we have identified a large number of microsatellites from the fish brains by using Illumina sequencing. About 20 million Illumina reads were assembled into 148,845 unigenes. A total of 13,038 SSR motifs were identified via analysis of 3,958,293,117 (3.96 Gb) nucleotides to produce a comprehensive transcript dataset for the C. nasus brain, including mono-, di-, tri-, tetra-, and penta-repeat motifs. The most abundant type of repeat motif was di-nucleotide (42.97%), followed by mono-nucleotide (38.86%), tri-nucleotide (16.21%), tetra-nucleotide (1.83%), and penta-nucleotide (0.05%) repeat units, which is similar to the results obtained in studies in other species. These data provide a base of sequence information to improve molecular-assisted markers to study C. nasus genetic diversity.
authors.affiliation: Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China.
authors.forename: D-A
authors.initials: DA
authors.lastname: Fang
authors.affiliation: Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.
authors.forename: Y-F
authors.initials: YF
authors.lastname: Zhou
authors.affiliation: Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.
authors.forename: J-R
authors.initials: JR
authors.lastname: Duan
authors.affiliation: Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.
authors.forename: M-Y
authors.initials: MY
authors.lastname: Zhang
authors.affiliation: Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.
authors.forename: D-P
authors.initials: DP
authors.lastname: Xu
authors.affiliation: Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.
authors.forename: K
authors.initials: K
authors.lastname: Liu
authors.affiliation: Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China.
authors.forename: P
authors.initials: P
authors.lastname: Xu
authors.affiliation: Key Lab of Freshwater Biodiversity Conservation Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China.
authors.forename: Q
authors.initials: Q
authors.lastname: Wei
mesh_terms: D000818:Animals; D020224:Expressed Sequence Tags; D005399:Fishes / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods; D005819:Genetic Markers / Q000235:genetics; D014644:Genetic Variation; D016678:Genome; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D011110:Polymorphism, Genetic; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome
chemical_list: D005819:Genetic Markers