Data from: High-throughput microsatellite genotyping in ecology: improved accuracy, efficiency, standardization and success with low-quantity and degraded DNA
Microsatellite markers have played a major role in ecological, evolutionary and conservation research during the past 20 years. However, technical constrains related to the use of capillary electrophoresis and a recent technological revolution that has impacted other marker types have brought to que...
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fttriple:oai:gotriple.eu:50|dedup_wf_001::f0b393b59c349b8b6730ae77c4bdbb2f 2023-05-15T18:42:15+02:00 Data from: High-throughput microsatellite genotyping in ecology: improved accuracy, efficiency, standardization and success with low-quantity and degraded DNA De Barba, Marta Miquel, Christian Lobreaux, Stephane Quenette, Pierre Yves Swenson, Jon E. Taberlet, Pierre 2016-08-10 https://doi.org/10.5061/dryad.18tg7 undefined unknown http://dx.doi.org/10.5061/dryad.18tg7 https://dx.doi.org/10.5061/dryad.18tg7 lic_creative-commons oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:94898 10.5061/dryad.18tg7 oai:easy.dans.knaw.nl:easy-dataset:94898 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f re3data_____::r3d100000044 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c Life sciences medicine and health care faecal DNA Ursus arctos individual identification parentage analysis high-throughput sequencing short tandem repeat (STR) envir psy Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2016 fttriple https://doi.org/10.5061/dryad.18tg7 2023-01-22T17:42:06Z Microsatellite markers have played a major role in ecological, evolutionary and conservation research during the past 20 years. However, technical constrains related to the use of capillary electrophoresis and a recent technological revolution that has impacted other marker types have brought to question the continued use of microsatellites for certain applications. We present a study for improving microsatellite genotyping in ecology using high-throughput sequencing (HTS). This approach entails selection of short markers suitable for HTS, sequencing PCR-amplified microsatellites on an Illumina platform and bioinformatic treatment of the sequence data to obtain multilocus genotypes. It takes advantage of the fact that HTS gives direct access to microsatellite sequences, allowing unambiguous allele identification and enabling automation of the genotyping process through bioinformatics. In addition, the massive parallel sequencing abilities expand the information content of single experimental runs far beyond capillary electrophoresis. We illustrated the method by genotyping brown bear samples amplified with a multiplex PCR of 13 new microsatellite markers and a sex marker. HTS of microsatellites provided accurate individual identification and parentage assignment and resulted in a significant improvement of genotyping success (84%) of faecal degraded DNA and costs reduction compared to capillary electrophoresis. The HTS approach holds vast potential for improving success, accuracy, efficiency and standardization of microsatellite genotyping in ecological and conservation applications, especially those that rely on profiling of low-quantity/quality DNA and on the construction of genetic databases. We discuss and give perspectives for the implementation of the method in the light of the challenges encountered in wildlife studies. Readmeobitools_scriptScripts to filter raw sequence data and perform conversion to tableR_python_scriptsR and python scripts to extract genotypes from tabular data ... Dataset Ursus arctos Unknown |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
unknown |
topic |
Life sciences medicine and health care faecal DNA Ursus arctos individual identification parentage analysis high-throughput sequencing short tandem repeat (STR) envir psy |
spellingShingle |
Life sciences medicine and health care faecal DNA Ursus arctos individual identification parentage analysis high-throughput sequencing short tandem repeat (STR) envir psy De Barba, Marta Miquel, Christian Lobreaux, Stephane Quenette, Pierre Yves Swenson, Jon E. Taberlet, Pierre Data from: High-throughput microsatellite genotyping in ecology: improved accuracy, efficiency, standardization and success with low-quantity and degraded DNA |
topic_facet |
Life sciences medicine and health care faecal DNA Ursus arctos individual identification parentage analysis high-throughput sequencing short tandem repeat (STR) envir psy |
description |
Microsatellite markers have played a major role in ecological, evolutionary and conservation research during the past 20 years. However, technical constrains related to the use of capillary electrophoresis and a recent technological revolution that has impacted other marker types have brought to question the continued use of microsatellites for certain applications. We present a study for improving microsatellite genotyping in ecology using high-throughput sequencing (HTS). This approach entails selection of short markers suitable for HTS, sequencing PCR-amplified microsatellites on an Illumina platform and bioinformatic treatment of the sequence data to obtain multilocus genotypes. It takes advantage of the fact that HTS gives direct access to microsatellite sequences, allowing unambiguous allele identification and enabling automation of the genotyping process through bioinformatics. In addition, the massive parallel sequencing abilities expand the information content of single experimental runs far beyond capillary electrophoresis. We illustrated the method by genotyping brown bear samples amplified with a multiplex PCR of 13 new microsatellite markers and a sex marker. HTS of microsatellites provided accurate individual identification and parentage assignment and resulted in a significant improvement of genotyping success (84%) of faecal degraded DNA and costs reduction compared to capillary electrophoresis. The HTS approach holds vast potential for improving success, accuracy, efficiency and standardization of microsatellite genotyping in ecological and conservation applications, especially those that rely on profiling of low-quantity/quality DNA and on the construction of genetic databases. We discuss and give perspectives for the implementation of the method in the light of the challenges encountered in wildlife studies. Readmeobitools_scriptScripts to filter raw sequence data and perform conversion to tableR_python_scriptsR and python scripts to extract genotypes from tabular data ... |
format |
Dataset |
author |
De Barba, Marta Miquel, Christian Lobreaux, Stephane Quenette, Pierre Yves Swenson, Jon E. Taberlet, Pierre |
author_facet |
De Barba, Marta Miquel, Christian Lobreaux, Stephane Quenette, Pierre Yves Swenson, Jon E. Taberlet, Pierre |
author_sort |
De Barba, Marta |
title |
Data from: High-throughput microsatellite genotyping in ecology: improved accuracy, efficiency, standardization and success with low-quantity and degraded DNA |
title_short |
Data from: High-throughput microsatellite genotyping in ecology: improved accuracy, efficiency, standardization and success with low-quantity and degraded DNA |
title_full |
Data from: High-throughput microsatellite genotyping in ecology: improved accuracy, efficiency, standardization and success with low-quantity and degraded DNA |
title_fullStr |
Data from: High-throughput microsatellite genotyping in ecology: improved accuracy, efficiency, standardization and success with low-quantity and degraded DNA |
title_full_unstemmed |
Data from: High-throughput microsatellite genotyping in ecology: improved accuracy, efficiency, standardization and success with low-quantity and degraded DNA |
title_sort |
data from: high-throughput microsatellite genotyping in ecology: improved accuracy, efficiency, standardization and success with low-quantity and degraded dna |
publishDate |
2016 |
url |
https://doi.org/10.5061/dryad.18tg7 |
genre |
Ursus arctos |
genre_facet |
Ursus arctos |
op_source |
oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:94898 10.5061/dryad.18tg7 oai:easy.dans.knaw.nl:easy-dataset:94898 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f re3data_____::r3d100000044 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c |
op_relation |
http://dx.doi.org/10.5061/dryad.18tg7 https://dx.doi.org/10.5061/dryad.18tg7 |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.18tg7 |
_version_ |
1766231887068528640 |