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SNiPloid: A Utility to Exploit High-Throughput SNP Data Derived from RNA-Seq in Allopolyploid Species
High-throughput sequencing is a common approach to discover SNP variants, especially in plant species. However, methods to analyze predicted SNPs are often optimized for diploid plant species whereas many crop species are allopolyploids and combine related but divergent subgenomes (homoeologous chro...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Hindawi Publishing Corporation
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791807/ https://www.ncbi.nlm.nih.gov/pubmed/24163691 http://dx.doi.org/10.1155/2013/890123 |
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author | Peralta, Marine Combes, Marie-Christine Cenci, Alberto Lashermes, Philippe Dereeper, Alexis |
author_facet | Peralta, Marine Combes, Marie-Christine Cenci, Alberto Lashermes, Philippe Dereeper, Alexis |
author_sort | Peralta, Marine |
collection | PubMed |
description | High-throughput sequencing is a common approach to discover SNP variants, especially in plant species. However, methods to analyze predicted SNPs are often optimized for diploid plant species whereas many crop species are allopolyploids and combine related but divergent subgenomes (homoeologous chromosome sets). We created a software tool, SNiPloid, that exploits and interprets putative SNPs in the context of allopolyploidy by comparing SNPs from an allopolyploid with those obtained in its modern-day diploid progenitors. SNiPloid can compare SNPs obtained from a sample to estimate the subgenome contribution to the transcriptome or SNPs obtained from two polyploid accessions to search for SNP divergence. |
format | Online Article Text |
id | pubmed-3791807 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Hindawi Publishing Corporation |
record_format | MEDLINE/PubMed |
spelling | pubmed-37918072013-10-27 SNiPloid: A Utility to Exploit High-Throughput SNP Data Derived from RNA-Seq in Allopolyploid Species Peralta, Marine Combes, Marie-Christine Cenci, Alberto Lashermes, Philippe Dereeper, Alexis Int J Plant Genomics Methodology Report High-throughput sequencing is a common approach to discover SNP variants, especially in plant species. However, methods to analyze predicted SNPs are often optimized for diploid plant species whereas many crop species are allopolyploids and combine related but divergent subgenomes (homoeologous chromosome sets). We created a software tool, SNiPloid, that exploits and interprets putative SNPs in the context of allopolyploidy by comparing SNPs from an allopolyploid with those obtained in its modern-day diploid progenitors. SNiPloid can compare SNPs obtained from a sample to estimate the subgenome contribution to the transcriptome or SNPs obtained from two polyploid accessions to search for SNP divergence. Hindawi Publishing Corporation 2013 2013-09-12 /pmc/articles/PMC3791807/ /pubmed/24163691 http://dx.doi.org/10.1155/2013/890123 Text en Copyright © 2013 Marine Peralta et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methodology Report Peralta, Marine Combes, Marie-Christine Cenci, Alberto Lashermes, Philippe Dereeper, Alexis SNiPloid: A Utility to Exploit High-Throughput SNP Data Derived from RNA-Seq in Allopolyploid Species |
title | SNiPloid: A Utility to Exploit High-Throughput SNP Data Derived from RNA-Seq in Allopolyploid Species |
title_full | SNiPloid: A Utility to Exploit High-Throughput SNP Data Derived from RNA-Seq in Allopolyploid Species |
title_fullStr | SNiPloid: A Utility to Exploit High-Throughput SNP Data Derived from RNA-Seq in Allopolyploid Species |
title_full_unstemmed | SNiPloid: A Utility to Exploit High-Throughput SNP Data Derived from RNA-Seq in Allopolyploid Species |
title_short | SNiPloid: A Utility to Exploit High-Throughput SNP Data Derived from RNA-Seq in Allopolyploid Species |
title_sort | sniploid: a utility to exploit high-throughput snp data derived from rna-seq in allopolyploid species |
topic | Methodology Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791807/ https://www.ncbi.nlm.nih.gov/pubmed/24163691 http://dx.doi.org/10.1155/2013/890123 |
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