Fast sequence-based microsatellite genotyping development workflow
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 workf...
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doaj-2d255e91bccc41b980b913b06993ae222020-11-25T03:00:31ZengPeerJ Inc.PeerJ2167-83592020-05-018e908510.7717/peerj.9085Fast sequence-based microsatellite genotyping development workflowOlivier Lepais0Emilie Chancerel1Christophe Boury2Franck Salin3Aurélie Manicki4Laura Taillebois5Cyril Dutech6Abdeldjalil Aissi7Cecile F.E. Bacles8Françoise Daverat9Sophie Launey10Erwan Guichoux11INRAE, Univ. Bordeaux, BIOGECO, Cestas, FranceINRAE, Univ. Bordeaux, BIOGECO, Cestas, FranceINRAE, Univ. Bordeaux, BIOGECO, Cestas, FranceINRAE, Univ. Bordeaux, BIOGECO, Cestas, FranceINRAE, Université de Pau et Pays de l’Adour, ECOBIOP, Saint-Peé-sur-Nivelle, FranceINRAE, Université de Pau et Pays de l’Adour, ECOBIOP, Saint-Peé-sur-Nivelle, FranceINRAE, Univ. Bordeaux, BIOGECO, Cestas, FranceLAPAPEZA, University of Batna 1 Hadj Lakhdar, Batna, AlgeriaINRAE, Université de Pau et Pays de l’Adour, ECOBIOP, Saint-Peé-sur-Nivelle, FranceINRAE, EABX, Cestas, FranceINRAE, Agrocampus Ouest, ESE, Ecology and Ecosystem Health, Rennes, FranceINRAE, Univ. Bordeaux, BIOGECO, Cestas, FranceApplication 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.https://peerj.com/articles/9085.pdfSequence-based microsatellite genotypingSSR-GBSSSR-seqHaplotype sequenceHapSTRSNPSTR |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Olivier Lepais Emilie Chancerel Christophe Boury Franck Salin Aurélie Manicki Laura Taillebois Cyril Dutech Abdeldjalil Aissi Cecile F.E. Bacles Françoise Daverat Sophie Launey Erwan Guichoux |
spellingShingle |
Olivier Lepais Emilie Chancerel Christophe Boury Franck Salin Aurélie Manicki Laura Taillebois Cyril Dutech Abdeldjalil Aissi Cecile F.E. Bacles Françoise Daverat Sophie Launey Erwan Guichoux Fast sequence-based microsatellite genotyping development workflow PeerJ Sequence-based microsatellite genotyping SSR-GBS SSR-seq Haplotype sequence HapSTR SNPSTR |
author_facet |
Olivier Lepais Emilie Chancerel Christophe Boury Franck Salin Aurélie Manicki Laura Taillebois Cyril Dutech Abdeldjalil Aissi Cecile F.E. Bacles Françoise Daverat Sophie Launey Erwan Guichoux |
author_sort |
Olivier Lepais |
title |
Fast sequence-based microsatellite genotyping development workflow |
title_short |
Fast sequence-based microsatellite genotyping development workflow |
title_full |
Fast sequence-based microsatellite genotyping development workflow |
title_fullStr |
Fast sequence-based microsatellite genotyping development workflow |
title_full_unstemmed |
Fast sequence-based microsatellite genotyping development workflow |
title_sort |
fast sequence-based microsatellite genotyping development workflow |
publisher |
PeerJ Inc. |
series |
PeerJ |
issn |
2167-8359 |
publishDate |
2020-05-01 |
description |
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. |
topic |
Sequence-based microsatellite genotyping SSR-GBS SSR-seq Haplotype sequence HapSTR SNPSTR |
url |
https://peerj.com/articles/9085.pdf |
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