ArticlePloS one2013
Microsatellites for next-generation ecologists: a post-sequencing bioinformatics pipeline.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Article
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- Transcriptome of the pygmy grasshopperPeerJ · 2023Article
- Genome survey sequencing and mining of genome-wide microsatellite markers in yellow-billed babbler (Heliyon · 2023Article
- Whole-Genome Survey and Microsatellite Marker Detection of Antarctic Crocodile Icefish,Animals : an open access journal from MDPI · 2022Article
- Evaluation of a new antimicrobial agent production (RSMM C3) by using metagenomics approaches from Egyptian marine biota.Biotechnology reports (Amsterdam, Netherlands) · 2022Article
- Population genetics of the freshwater fishPeerJ · 2020Article
- A behavioral and genetic study of multiple paternity in a polygamous marine invertebrate,PeerJ · 2019Article
- Microsatellite development from genome skimming and transcriptome sequencing: comparison of strategies and lessons from frog species.BMC genomics · 2018Article
- A biting commentary: Integrating tooth characters with molecular data doubles known species diversity in a lineage of sea slugs that consume "killer algae".Molecular phylogenetics and evolution · 2018Article
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- Article
- Development and characterization of genic SSR markers from low depth genome sequence of Clarias batrachus (magur).Journal of genetics · 2016Article
- De Novo Assembly and Characterization of the Transcriptome of Grasshopper Shirakiacris shirakii.International journal of molecular sciences · 2016Article
- Microsatellite markers for the notothenioid fish Lepidonotothen nudifrons and two congeneric species.BMC research notes · 2016Article
- Article
- Article
- De Novo Assembly and Characterization of Four Anthozoan (Phylum Cnidaria) Transcriptomes.G3 (Bethesda, Md.) · 2015Article
- Article
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microsatellites are the markers of choice for a variety of population genetic studies. The recent advent of next-generation pyrosequencing has drastically accelerated microsatellite locus discovery by providing a greater amount of DNA sequencing reads at lower costs compared to other techniques. However, laboratory testing of PCR primers targeting potential microsatellite markers remains time consuming and costly. Here we show how to reduce this workload by screening microsatellite loci via bioinformatic analyses prior to primer design. Our method emphasizes the importance of sequence quality, and we avoid loci associated with repetitive elements by screening with repetitive sequence databases available for a growing number of taxa. Testing with the Yellowstripe Goatfish Mulloidichthys flavolineatus and the marine planktonic copepod Pleuromamma xiphias we show higher success rate of primers selected by our pipeline in comparison to previous in silico microsatellite detection methodologies. Following the same pipeline, we discover and select microsatellite loci in nine additional species including fishes, sea stars, copepods and octopuses.
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