Rapid microsatellite marker development in the endangered neotropical freshwater turtle Podocnemis lewyana (Testudines: Podocnemididae) using 454 sequencing

Publication date: April 2015 Source:Biochemical Systematics and Ecology, Volume 59 Author(s): Adriana Restrepo , Vivian P. Páez , Angelly Vásquez , Juan M. Daza Using high throughput sequencing we obtained a large number of microsatellites from Podocnemis lewyana, an endemic turtle from northwestern South America. We used 454 Genome Sequence FLX platform of sheared genomic DNA from randomly sampling approximately 17% of the haploid genome. We identified 86,501 reads (8.1% of all reads) that contained our definition of microsatellite loci. AC and TC were the most abundant motifs in the P. lewyana genome. TGC and AAAC were most abundant tri and tetra-nucleotide motifs respectively. 72.7% of microsatellite reads had flanking sequence regions suitable for primer design and PCR amplification. We validated the identified potentially amplifiable loci (PAL) and tested for polymorphism by selecting 15 loci corresponding to tetranucleotides. Twelve loci showed polymorphism in eight individuals. These findings demonstrates that microsatellite detection using next-generation sequencing is an efficient way of getting a lot of loci for listed taxa and in turn will have a large impact on future genetic studies aiming to understand and implement conservation plans for this highly threatened freshwater turtle.

Source: Biochemical Systematics and Ecology - March 4, 2015 Category: Biochemistry Source Type: research