Rapid development of microsatellites for the endangered Neotropical catfish Conorhynchus conirostris using a modest amount of 454 shot-gun pyrosequencing

A set of 13 polymorphic microsatellites were developed using a next generation sequencing approach for the endangered Neotropical catfish Conorhynchus conirostris. Using only 1/16 of a shot-gun pyrosequencing reaction, we were able to obtain 3,796 sequences containing putative microsatellites motifs. Out of 20 selected loci for further optimization, 13 loci were successfully geno-typed in 25 specimens from a locality in the Sao Francisco River, Southeast Brazil. All microsatellite loci were polymorphic, with 4-18 alleles per locus (mean = 10.5) and generally high values of heterozygosity (mean = 0.796). These polymorphic markers will be a valuable tool for captive breeding and stoking programs and for analyses of population connectivity and genetic structure in this endangered Neotropical catfish.