title: Transcriptome characterization and SSR discovery in large-scale loach Paramisgurnus dabryanus (Cobitidae, Cypriniformes).
abstract: The large-scale loach (Paramisgurnus dabryanus, Cypriniformes) is a bottom-dwelling freshwater species of fish found mainly in eastern Asia. The natural germplasm resources of this important aquaculture species has been recently threatened due to overfishing and artificial propagation. The objective of this study is to obtain the first functional genomic resource and candidate molecular markers for future conservation and breeding research. Illumina paired-end sequencing generated over one hundred million reads that resulted in 71,887 assembled transcripts, with an average length of 1465bp. 42,093 (58.56%) protein-coding sequences were predicted; and 43,837 transcripts had significant matches to NCBI nonredundant protein (Nr) database. 29,389 and 14,419 transcripts were assigned into gene ontology (GO) categories and Eukaryotic Orthologous Groups (KOG), respectively. 22,102 (31.14%) transcripts were mapped to 302 KEGG pathways. In addition, 15,106 candidate SSR markers were identified, with 11,037 pairs of PCR primers designed. 400 primers pairs of SSR selected randomly were validated, of which 364 (91%) pairs of primers were able to produce PCR products. Further test with 41 loci and 20 large-scale loach specimens collected from the four largest lakes in China showed that 36 (87.8%) loci were polymorphic. The transcriptomic profile and SSR repertoire obtained in this study will facilitate population genetic studies and selective breeding of large-scale loach in the future.
authors.affiliation: School of Biology and Basic Medical Sciences, Soochow University, 199 Renai Road, Suzhou, Jiangsu 215123, PR China.
authors.forename: Caijuan
authors.initials: C
authors.lastname: Li
authors.affiliation: School of Biology and Basic Medical Sciences, Soochow University, 199 Renai Road, Suzhou, Jiangsu 215123, PR China. Electronic address: lingqf@suda.edu.cn.
authors.forename: Qufei
authors.initials: Q
authors.lastname: Ling
authors.affiliation: School of Biology and Basic Medical Sciences, Soochow University, 199 Renai Road, Suzhou, Jiangsu 215123, PR China.
authors.forename: Chen
authors.initials: C
authors.lastname: Ge
authors.affiliation: School of Biology and Basic Medical Sciences, Soochow University, 199 Renai Road, Suzhou, Jiangsu 215123, PR China.
authors.forename: Zhuqing
authors.initials: Z
authors.lastname: Ye
authors.affiliation: School of Biology and Basic Medical Sciences, Soochow University, 199 Renai Road, Suzhou, Jiangsu 215123, PR China.
authors.forename: Xiaofei
authors.initials: X
authors.lastname: Han
mesh_terms: D000818:Animals; D001483:Base Sequence; D003531:Cypriniformes / Q000235:genetics*; D005260:Female; D005787:Gene Frequency; D063990:Gene Ontology; D008297:Male; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA; D059467:Transcriptome
keywords: Illumina sequencing; Paramisgurnus dabryanus; SSR markers; Transcriptome analysis