Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing
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TL;DR: This study uses high-throughput genomic sequencing technology to produce millions of base pairs of short fragment reads, which were screened with bioinformatics toolsets to identify primers that amplify polymorphic microsatellite loci.
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Abstract: Microsatellites are the genetic markers of choice for many population genetic studies, but must be isolated de novo using recombinant approaches where prior genetic data are lacking. Here we utilized high-throughput genomic sequencing technology to produce millions of base pairs of short fragment reads, which were screened with bioinformatics toolsets to identify primers that amplify polymorphic microsatellite loci. Using this approach we isolated 13 polymorphic microsatellites for the blue duck (Hymenolaimus malacorhynchos), a species for which limited genetic data were available. Our genomic approach eliminates recombinant genetic steps, significantly reducing the time and cost requirements of marker development compared with traditional approaches. While this application of genomic sequencing may seem obvious to many, this study is, to the best of our knowledge, the first attempt to describe the use of genomic sequencing for the development of microsatellite markers in a non-model organism or indeed any organism.
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Citations
32 species validation of a new Illumina paired-end approach for the development of microsatellites
Stacey L. Lance,Cara N. Love,Schyler O. Nunziata,Jason R. O’Bryhim,David E. Scott,R. Wesley Flynn,Kenneth L. Jones +6 more
TL;DR: Overall the IPE method worked extremely well and 1000s of SSRs were identified for all species, with 17% of loci being potentially amplifiable loci, and 25% of these met the most stringent criteria designed to that avoid SSRs associated with repetitive elements.
First Evidence of Inbreeding, Relatedness and Chaotic Genetic Patchiness in the Holoplanktonic Jellyfish Pelagia noctiluca (Scyphozoa, Cnidaria)
Giorgio Aglieri,Chiara Papetti,Lorenzo Zane,Giacomo Milisenda,Ferdinando Boero,Stefano Piraino +5 more
TL;DR: The results suggest that despite its extreme dispersal potential, P. noctiluca does not maintain a single homogenous population, but rather these jellyfish appear to have intra-bloom localized recruitment and/or individual cohesiveness, whereby siblings more likely swarm together as a single group and remain close after spawning events.
Analysis of microsatellites from transcriptome sequences of Phytophthora capsici and applications for population studies.
TL;DR: The authors' findings highlight the usefulness of these 12 microsatellites to characterize the population structure of P. capsici and potential transferability to closely-related Phytophthora spp.
DNA Based Techniques for Studying Genetic Diversity
Ahmed L. Abdel-Mawgood
- 24 Feb 2012
TL;DR: Both Genetic diversity and fingerprinting studies are done using molecular markers and are the unambiguous identification of an individual (based on the presence or absence of alleles at different markers) or a population ( based on frequencies of allele of the markers).
Rapid Development of Microsatellite Markers with 454 Pyrosequencing in a Vulnerable Fish, the Mottled Skate, Raja pulchra
TL;DR: The mottled skate, Raja pulchra, is an economically valuable fish, however, due to a severe population decline, it is listed as a vulnerable species by the International Union for Conservation of Nature and microsatellite markers were developed using 454 pyrosequencing.
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