title: Development and characterization of genic SSR markers from low depth genome sequence of Clarias batrachus (magur).
abstract: Indian magur (Clarias batrachus) is an important freshwater catfish, which is listed as endangered under A3cde+4acde ver. 3.1 categories by the IUCN (2015) due to decreasing population trend. Microsatellites or short sequence repeats (SSRs) tagged to genes have been utilized as gene marker. In the present study, 31,814 SSRs of C. batrachus (magur) were identified using microsatellite identification tool programme from the next generation sequencing data generated on Roche 454 and Ion Torrent platforms. A bioinformatics pipeline, with stringent criteria resulted in selection of 1672 microsatellite loci falling in the genic region. Initially, a total of 30 loci were selected for primer development; and of these 14 were successfully amplified and five were found to be polymorphic in 30 individuals of C. batrachus (magur). The observed as well as expected heterozygosity ranged from 0.038 to 0.526 and 0.434 to 0.784, respectively, and the number of observed alleles ranged from three to five. The study reported the application of next generation sequencing technologies for rapid development of microsatellite loci in Indian catfish species, C. batrachus (magur).
authors.affiliation: Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow 226 002, India.basdeo.scientist@gmail.com.
authors.forename: Shreya
authors.initials: S
authors.lastname: Srivastava
authors.forename: Basdeo
authors.initials: B
authors.lastname: Kushwaha
authors.forename: Jyoti
authors.initials: J
authors.lastname: Prakash
authors.forename: Ravindra
authors.initials: R
authors.lastname: Kumar
authors.forename: N S
authors.initials: NS
authors.lastname: Nagpure
authors.forename: Suyash
authors.initials: S
authors.lastname: Agarwal
authors.forename: Manmohan
authors.initials: M
authors.lastname: Pandey
authors.forename: P
authors.initials: P
authors.lastname: Das
authors.forename: C G
authors.initials: CG
authors.lastname: Joshi
authors.forename: J K
authors.initials: JK
authors.lastname: Jena
mesh_terms: D000483:Alleles; D000818:Animals; D002397:Catfishes / Q000235:genetics*; D002874:Chromosome Mapping; D002875:Chromosomes / Q000737:chemistry*; D019295:Computational Biology / Q000379:methods; D017931:DNA Primers / Q000138:chemical synthesis; D056727:Endangered Species; D063990:Gene Ontology; D056426:Genetic Loci; D005819:Genetic Markers; D016678:Genome; D006579:Heterozygote; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D011110:Polymorphism, Genetic
chemical_list: D017931:DNA Primers; D005819:Genetic Markers