ArticlePeerJ2020
Fast sequence-based microsatellite genotyping development workflow.
Article in PeerJ, 2020. 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.
- Bridging the gap between legacy polymerase chain reaction-based microsatellite data with high-throughput sequencing data for conservation genomics.The Journal of heredity · 2026Article
- Article
- Complementary Evidence From Historical and Contemporary Gene Dispersal Reveals Contrasting Population Dynamics in a Tropical Tree Species.Evolutionary applications · 2026Article
- Article
- Birth-Death Dynamics of Microsatellites: Mechanistic Insights from Orthologous Loci in Felidae.Genes · 2025Article
- First Assembly of a Draft Genome of the Critically Endangered Northern Muriqui (Ecology and evolution · 2025Article
- Genetic diversity and fine-scale spatial genetic structure of European beech populations along an elevational gradient.Heredity · 2025Article
- Restricted Dispersal in the Late Successional Forest Tree SpeciesEcology and evolution · 2025Article
- Genetic Conservation and Population Management of Non-Human Primates: Parentage Determination Using Seven Microsatellite-Based Multiplexes.Ecology and evolution · 2025Article
- Genome-Wide Microsatellites inAnimals : an open access journal from MDPI · 2024Article
- Genetic diversity and population structure of Botryosphaeria dothidea and Neofusicoccum parvum on English walnut (Juglans regia L.) in France.Scientific reports · 2024Article
- Article
- Contrasts in riverscape patterns of intraspecific genetic variation in a diverse Neotropical fish community of high conservation value.Heredity · 2023Article
- The effect of the 7R allele at the DRD4 locus on risk tolerance is independent of background risk in Senegalese fishermen.Scientific reports · 2023Article
- Article
- A Pipeline for the Development of Microsatellite Markers using Next Generation Sequencing Data.Current genomics · 2022Article
- Development of SSR Databases Available for Both NGS and Capillary Electrophoresis in Apple, Pear and Tea.Plants (Basel, Switzerland) · 2021Article
- Article
- An integrated strategy for target SSR genotyping with toleration of nucleotide variations in the SSRs and flanking regions.BMC bioinformatics · 2021Article
- Mismatch Between Specific and Genetic Diversity in an Evergreen Broadleaf Forest in Southeast China: A Study Case of 10.24 ha Forest Dynamics Plot of Huangshan.Frontiers in plant science · 2021Article
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Application of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown to remove many of the limitations of electrophoresis-based methods and to refine inference of population genetic diversity and structure. We present here a streamlined SSRseq development workflow that includes microsatellite development, multiplexed marker amplification and sequencing, and automated bioinformatics data analysis. We illustrate its application to five groups of species across phyla (fungi, plant, insect and fish) with different levels of genomic resource availability. We found that relying on previously developed microsatellite assay is not optimal and leads to a resulting low number of reliable locus being genotyped. In contrast, de novo ad hoc primer designs gives highly multiplexed microsatellite assays that can be sequenced to produce high quality genotypes for 20-40 loci. We highlight critical upfront development factors to consider for effective SSRseq setup in a wide range of situations. Sequence analysis accounting for all linked polymorphisms along the sequence quickly generates a powerful multi-allelic haplotype-based genotypic dataset, calling to new theoretical and analytical frameworks to extract more information from multi-nucleotide polymorphism marker systems.
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