Cargando…
Rapid Development of Microsatellite Markers for the Endangered Fish Schizothorax biddulphi (Günther) Using Next Generation Sequencing and Cross-Species Amplification
Tarim schizothoracin (Schizothorax biddulphi) is an endemic fish species native to the Tarim River system of Xinjiang and has been classified as an extremely endangered freshwater fish species in China. Here, we used a next generation sequencing platform (ion torrent PGM™) to obtain a large number o...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Molecular Diversity Preservation International (MDPI)
2012
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3509620/ https://www.ncbi.nlm.nih.gov/pubmed/23203104 http://dx.doi.org/10.3390/ijms131114946 |
_version_ | 1782251369124593664 |
---|---|
author | Luo, Wei Nie, Zhulan Zhan, Fanbin Wei, Jie Wang, Weimin Gao, Zexia |
author_facet | Luo, Wei Nie, Zhulan Zhan, Fanbin Wei, Jie Wang, Weimin Gao, Zexia |
author_sort | Luo, Wei |
collection | PubMed |
description | Tarim schizothoracin (Schizothorax biddulphi) is an endemic fish species native to the Tarim River system of Xinjiang and has been classified as an extremely endangered freshwater fish species in China. Here, we used a next generation sequencing platform (ion torrent PGM™) to obtain a large number of microsatellites for S. biddulphi, for the first time. A total of 40577 contigs were assembled, which contained 1379 SSRs. In these SSRs, the number of dinucleotide repeats were the most frequent (77.08%) and AC repeats were the most frequently occurring microsatellite, followed by AG, AAT and AT. Fifty loci were randomly selected for primer development; of these, 38 loci were successfully amplified and 29 loci were polymorphic across panels of 30 individuals. The H(o) ranged from 0.15 to 0.83, and H(e) ranged from 0.15 to 0.85, with 3.5 alleles per locus on average. Cross-species utility indicated that 20 of these markers were successfully amplified in a related, also an endangered fish species, S. irregularis. This study suggests that PGM™ sequencing is a rapid and cost-effective tool for developing microsatellite markers for non-model species and the developed microsatellite markers in this study would be useful in Schizothorax genetic analysis. |
format | Online Article Text |
id | pubmed-3509620 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Molecular Diversity Preservation International (MDPI) |
record_format | MEDLINE/PubMed |
spelling | pubmed-35096202013-01-09 Rapid Development of Microsatellite Markers for the Endangered Fish Schizothorax biddulphi (Günther) Using Next Generation Sequencing and Cross-Species Amplification Luo, Wei Nie, Zhulan Zhan, Fanbin Wei, Jie Wang, Weimin Gao, Zexia Int J Mol Sci Article Tarim schizothoracin (Schizothorax biddulphi) is an endemic fish species native to the Tarim River system of Xinjiang and has been classified as an extremely endangered freshwater fish species in China. Here, we used a next generation sequencing platform (ion torrent PGM™) to obtain a large number of microsatellites for S. biddulphi, for the first time. A total of 40577 contigs were assembled, which contained 1379 SSRs. In these SSRs, the number of dinucleotide repeats were the most frequent (77.08%) and AC repeats were the most frequently occurring microsatellite, followed by AG, AAT and AT. Fifty loci were randomly selected for primer development; of these, 38 loci were successfully amplified and 29 loci were polymorphic across panels of 30 individuals. The H(o) ranged from 0.15 to 0.83, and H(e) ranged from 0.15 to 0.85, with 3.5 alleles per locus on average. Cross-species utility indicated that 20 of these markers were successfully amplified in a related, also an endangered fish species, S. irregularis. This study suggests that PGM™ sequencing is a rapid and cost-effective tool for developing microsatellite markers for non-model species and the developed microsatellite markers in this study would be useful in Schizothorax genetic analysis. Molecular Diversity Preservation International (MDPI) 2012-11-14 /pmc/articles/PMC3509620/ /pubmed/23203104 http://dx.doi.org/10.3390/ijms131114946 Text en © 2012 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland. http://creativecommons.org/licenses/by/3.0 This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0). |
spellingShingle | Article Luo, Wei Nie, Zhulan Zhan, Fanbin Wei, Jie Wang, Weimin Gao, Zexia Rapid Development of Microsatellite Markers for the Endangered Fish Schizothorax biddulphi (Günther) Using Next Generation Sequencing and Cross-Species Amplification |
title | Rapid Development of Microsatellite Markers for the Endangered Fish Schizothorax biddulphi (Günther) Using Next Generation Sequencing and Cross-Species Amplification |
title_full | Rapid Development of Microsatellite Markers for the Endangered Fish Schizothorax biddulphi (Günther) Using Next Generation Sequencing and Cross-Species Amplification |
title_fullStr | Rapid Development of Microsatellite Markers for the Endangered Fish Schizothorax biddulphi (Günther) Using Next Generation Sequencing and Cross-Species Amplification |
title_full_unstemmed | Rapid Development of Microsatellite Markers for the Endangered Fish Schizothorax biddulphi (Günther) Using Next Generation Sequencing and Cross-Species Amplification |
title_short | Rapid Development of Microsatellite Markers for the Endangered Fish Schizothorax biddulphi (Günther) Using Next Generation Sequencing and Cross-Species Amplification |
title_sort | rapid development of microsatellite markers for the endangered fish schizothorax biddulphi (günther) using next generation sequencing and cross-species amplification |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3509620/ https://www.ncbi.nlm.nih.gov/pubmed/23203104 http://dx.doi.org/10.3390/ijms131114946 |
work_keys_str_mv | AT luowei rapiddevelopmentofmicrosatellitemarkersfortheendangeredfishschizothoraxbiddulphiguntherusingnextgenerationsequencingandcrossspeciesamplification AT niezhulan rapiddevelopmentofmicrosatellitemarkersfortheendangeredfishschizothoraxbiddulphiguntherusingnextgenerationsequencingandcrossspeciesamplification AT zhanfanbin rapiddevelopmentofmicrosatellitemarkersfortheendangeredfishschizothoraxbiddulphiguntherusingnextgenerationsequencingandcrossspeciesamplification AT weijie rapiddevelopmentofmicrosatellitemarkersfortheendangeredfishschizothoraxbiddulphiguntherusingnextgenerationsequencingandcrossspeciesamplification AT wangweimin rapiddevelopmentofmicrosatellitemarkersfortheendangeredfishschizothoraxbiddulphiguntherusingnextgenerationsequencingandcrossspeciesamplification AT gaozexia rapiddevelopmentofmicrosatellitemarkersfortheendangeredfishschizothoraxbiddulphiguntherusingnextgenerationsequencingandcrossspeciesamplification |