ArticleScientific reports2013
Combining next-generation sequencing and online databases for microsatellite development in non-model organisms.
Article in Scientific reports, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Novel Microsatellite Loci, Cross-Species Validation of Multiplex Assays, and By-Catch Mitochondrial Genomes onInsects · 2023Article
- De novo assembly, transcriptome characterization and marker discovery in Indian major carp, Labeo rohita through pyrosequencing.Genetica · 2022Article
- Isolation and characterization of microsatellite markers for the threatened African endemic tree speciesEcology and evolution · 2020Article
- Microsatellite development from genome skimming and transcriptome sequencing: comparison of strategies and lessons from frog species.BMC genomics · 2018Article
- Characterization of microsatellite primers in the endangered orchidApplications in plant sciences · 2017Article
- Development of microsatellite markers using Illumina MiSeq sequencing to characterizeApplications in plant sciences · 2017Article
- High-throughput sequencing and graph-based cluster analysis facilitate microsatellite development from a highly complex genome.Ecology and evolution · 2016Article
- Microsatellite markers for the notothenioid fish Lepidonotothen nudifrons and two congeneric species.BMC research notes · 2016Article
- Developing informative microsatellite markers for non-model species using reference mapping against a model species' genome.Scientific reports · 2016Article
- A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum.Scientific reports · 2016Article
- Article
- RAD-QTL Mapping Reveals Both Genome-Level Parallelism and Different Genetic Architecture Underlying the Evolution of Body Shape in Lake Whitefish (Coregonus clupeaformis) Species Pairs.G3 (Bethesda, Md.) · 2015Article
- Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing (NGS) is revolutionising marker development and the rapidly increasing amount of transcriptomes published across a wide variety of taxa is providing valuable sequence databases for the identification of genetic markers without the need to generate new sequences. Microsatellites are still the most important source of polymorphic markers in ecology and evolution. Motivated by our long-term interest in the adaptive radiation of a non-model species complex of whitefishes (Coregonus spp.), in this study, we focus on microsatellite characterisation and multiplex optimisation using transcriptome sequences generated by Illumina® and Roche-454, as well as online databases of Expressed Sequence Tags (EST) for the study of whitefish evolution and demographic history. We identified and optimised 40 polymorphic loci in multiplex PCR reactions and validated the robustness of our analyses by testing several population genetics and phylogeographic predictions using 494 fish from five lakes and 2 distinct ecotypes.
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