title: Rapid development of microsatellite markers for the endangered fish Schizothorax biddulphi (Günther) using next generation sequencing and cross-species amplification.
abstract: Tarim schizothoracin (Schizothorax biddulphi) is an endemic fish species native to the Tarim River system of Xinjiang and has been classified as an extremely endangered freshwater fish species in China. Here, we used a next generation sequencing platform  (ion torrent PGM&#8482;) to obtain a large number of microsatellites for S. biddulphi, for the first time. A total of 40577 contigs were assembled, which contained 1379 SSRs. In these SSRs, the number of dinucleotide repeats were the most frequent (77.08%) and AC repeats were the most frequently occurring microsatellite, followed by AG, AAT and AT. Fifty loci were randomly selected for primer development; of these, 38 loci were successfully amplified and 29 loci were polymorphic across panels of 30 individuals. The H(o) ranged from 0.15 to 0.83, and H(e) ranged from 0.15 to 0.85, with 3.5 alleles per locus on average. Cross-species utility indicated that 20 of these markers were successfully amplified in a related, also an endangered fish species, S. irregularis. This study suggests that PGM&#8482; sequencing is a rapid and cost-effective tool for developing microsatellite markers for  non-model species and the developed microsatellite markers in this study would be useful in Schizothorax genetic analysis.
authors.affiliation: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China. gaozexia@hotmail.com.
authors.forename: Wei
authors.initials: W
authors.lastname: Luo
authors.forename: Zhulan
authors.initials: Z
authors.lastname: Nie
authors.forename: Fanbin
authors.initials: F
authors.lastname: Zhan
authors.forename: Jie
authors.initials: J
authors.lastname: Wei
authors.forename: Weimin
authors.initials: W
authors.lastname: Wang
authors.forename: Zexia
authors.initials: Z
authors.lastname: Gao
mesh_terms: D000818:Animals; D056727:Endangered Species; D005399:Fishes / Q000235:genetics*; D005787:Gene Frequency; D056426:Genetic Loci; D005819:Genetic Markers; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats; D021141:Nucleic Acid Amplification Techniques; D059372:Nucleotide Motifs; D011110:Polymorphism, Genetic
chemical_list: D005819:Genetic Markers