32 species validation of a new Illumina paired-end approach for the development of microsatellites

Abstract

Development and optimization of novel species-specific microsatellites, or simple sequence repeats (SSRs) remains an important step for studies in ecology, evolution, and behavior. Numerous approaches exist for identifying new SSRs that vary widely in terms of both time and cost investments. A recent approach of using paired-end Illumina sequence data in conjunction with the bioinformatics pipeline, PAL_FINDER, has the potential to substantially reduce the cost and labor investment while also improving efficiency. However, it does not appear that the approach has been widely adopted, perhaps due to concerns over its broad applicability across taxa. Therefore, to validate the utility of the approach we developed SSRs for 32 species representing 30 families, 25 orders, 11 classes, and six phyla and optimized SSRs for 13 of the species. Overall the IPE method worked extremely well and we identified 1000s of SSRs for all species (mean = 128,485), with 17% of loci being potentially amplifiable loci, and 25% of these met our most stringent criteria designed to that avoid SSRs associated with repetitive elements. Approximately 61% of screened primers yielded strong amplification of a single locus.

Genetic assignment to stock of stranded common bottlenose dolphins in southeastern Louisiana after the Deepwater Horizon oil spill

“…The power to detect differentiation and the accuracy of assignment tests are both directly related to the number of informative loci. To improve assignment tests results, we screened an additional 66 microsatellite loci and ultimately identified and optimized an additional 22 loci, 14 identified from screening the common bottlenose dolphin genome through Illumina 454 sequencing (see Lance et al 2013) and 8 optimized from loci previously identified in other cetacean species. See Text S1 in the Supplement for description of methods to identify and optimize these additional loci.…”

The mitochondrial genome of the Arizona Snowfly Mesocapnia arizonensis (Plecoptera, Capniidae)

“…It inhabits mountain streams that can dry out in the summer months (Baumann & Gaufin, 1969). The data were generated by Lance et al (2013) for microsatellite marker development. The data were generated by Lance et al (2013) for microsatellite marker development.…”

“…For mitochondrial genome assembly HiSeq data from the NCBI SRA database was used (Accession ID: SRR1145748). Additional information about DNA extraction and sequencing are provided in Lance et al (2013). Additional information about DNA extraction and sequencing are provided in Lance et al (2013).…”

Efficient development of highly polymorphic microsatellite markers based on polymorphic repeats in transcriptome sequences of multiple individuals

“…Although many recent studies have been published on microsatellite marker development in which such sequences are mined (e.g. Cardoso et al 2013;Lance et al 2013), most studies do not make use of the full potential of the sequencing data in combination with multiple genotypes to predict the most polymorphic microsatellite markers. To our knowledge, only the recent study by Hoffman and Nichols (2011) utilized a similar approach to our study to identify polymorphic microsatellite markers from 454 sequences of the Antarctic fur seal (Arctocephalus gazella).…”