Fast sequence-based microsatellite genotyping development workflow.
HapSTR
Haplotype sequence
SNPSTR
SSR-GBS
SSR-seq
Sequence-based microsatellite genotyping
Journal
PeerJ
ISSN: 2167-8359
Titre abrégé: PeerJ
Pays: United States
ID NLM: 101603425
Informations de publication
Date de publication:
2020
2020
Historique:
received:
03
01
2020
accepted:
08
04
2020
entrez:
16
5
2020
pubmed:
16
5
2020
medline:
16
5
2020
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 32411534
doi: 10.7717/peerj.9085
pii: 9085
pmc: PMC7204839
doi:
Types de publication
Journal Article
Langues
eng
Pagination
e9085Informations de copyright
©2020 Lepais et al.
Déclaration de conflit d'intérêts
The authors declare there are no competing interests.
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