Data from: High-throughput microsatellite marker development in two sparid species and verification of their transferability in the family Sparidae
Reid, Kerry, University of Pretoria
Hoareau, Thierry B., University of Pretoria
Bloomer, Paulette, University of Pretoria
Published Feb 24, 2012 on Dryad.
Cite this dataset
Reid, Kerry; Hoareau, Thierry B.; Bloomer, Paulette (2012). Data from: High-throughput microsatellite marker development in two sparid species and verification of their transferability in the family Sparidae [Dataset]. Dryad. https://doi.org/10.5061/dryad.320kb06t
Recently, 454 sequencing has emerged as a popular method for isolating microsatellites owing to cost-effectiveness and time saving. In this study, repeat-enriched libraries from two southern African endemic sparids (Pachymetopon blochii and Lithognathus lithognathus) were 454 GS-FLX sequenced. From these, 7370 sequences containing repeats (SCRs) were identified. A brief survey of 23 studies showed a significant difference between the number of SCRs when enrichment was performed first before 454 sequencing. We designed primers for 302 unique fragments containing more than five repeat units and suitable flanking regions. A fraction (<11%) of these loci were characterized with 18 polymorphic microsatellite loci (nine in each of the focal species) being described. Sanger sequencing of alleles confirmed that size variation was because of differences in the number of tandem repeats. However, a case of homoplasy and sequencing errors in the 454 sequencing were identified. These newly developed and four previously isolated loci were successfully used to identify polymorphic markers in nine other economically important species, representative of sparid diversity. The combination of newly developed markers with data from previous sparid cross-species studies showed a significant negative correlation between genetic divergence to focal species and microsatellite transferability. The high level of transferability we described (48% amplification success and 32% polymorphism) suggests that the 302 microsatellite loci identified represent an excellent resource for future studies on sparids. Microsatellite marker development should commonly include tests of transferability to reduce costs and increase feasibility of population genetics studies in nonmodel organisms.
DRYAD genotypic data for two focal species
File 1 Genotypic data for two focal species: Excel spreadsheet of genotypic data for 50 individuals each of two focal sparid species for the developed microsatellite markers in these species. There are nine microsatellite markers for Pachymetopon blochii and nine for Lithognathus lithognathus. The program GeneMarker was used to score the alleles.
DRYAD location information of species
File 2 Location information of species: Excel spreadsheet of specimens used and locations sampled for the microsatellite marker development and cross-species amplification study.
DRYAD primers and 454 sequences for additional sparid loci
File 3 Primers and 454 sequences for additional sparid loci: Excel spreadsheet of additional microsatellite markers identified in two focal sparid species from two repeat enrich libraries (using the FIASCO protocol) and a fraction of 454 sequencing. The table includes repeat type, primers, fragment size and the 454 sequences in FASTA format.