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High-resolution autosomal radiation hybrid maps of the pig genome and their contribution to the genome sequence assembly

BACKGROUND: The release of the porcine genome sequence offers great perspectives for Pig genetics and genomics, and more generally will contribute to the understanding of mammalian genome biology and evolution. The process of producing a complete genome sequence of high quality, while facilitated by...

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Autores principales: Servin, Bertrand, Faraut, Thomas, Iannuccelli, Nathalie, Zelenika, Diana, Milan, Denis
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3499281/
https://www.ncbi.nlm.nih.gov/pubmed/23153393
http://dx.doi.org/10.1186/1471-2164-13-585
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author Servin, Bertrand
Faraut, Thomas
Iannuccelli, Nathalie
Zelenika, Diana
Milan, Denis
author_facet Servin, Bertrand
Faraut, Thomas
Iannuccelli, Nathalie
Zelenika, Diana
Milan, Denis
author_sort Servin, Bertrand
collection PubMed
description BACKGROUND: The release of the porcine genome sequence offers great perspectives for Pig genetics and genomics, and more generally will contribute to the understanding of mammalian genome biology and evolution. The process of producing a complete genome sequence of high quality, while facilitated by high-throughput sequencing technologies, remains a difficult task. The porcine genome was sequenced using a combination of a hierarchical shotgun strategy and data generated with whole genome shotgun. In addition to the BAC contig map used for the clone-by-clone approach, genomic mapping resources for the pig include two radiation hybrid (RH) panels at two different resolutions. These two panels have been used extensively for the physical mapping of pig genes and markers prior to the availability of the pig genome sequence. RESULTS: In order to contribute to the assembly of the pig genome, we genotyped the two radiation hybrid (RH) panels with a SNP array (the Illumina porcineSNP60 array) and produced high density physical RH maps for each pig autosome. We first present the methods developed to obtain high density RH maps with 38,379 SNPs from the SNP array genotyping. We then show how they were useful to identify problems in a draft of the pig genome assembly, and how the RH maps enabled the problems to be corrected in the porcine genome sequence. Finally, we used the RH maps to predict the position of 2,703 SNPs and 1,328 scaffolds currently unplaced on the porcine genome assembly. CONCLUSIONS: A complete process, from genotyping of a high density SNP array on RH panels, to the construction of genome-wide high density RH maps, and finally their exploitation for validating and improving a genome assembly is presented here. The study includes the cross-validation of RH based findings with independent information from genetic data and comparative mapping with the Human genome. Several additional resources are also provided, in particular the predicted genomic location of currently unplaced SNPs and associated scaffolds summing up to a total of 72 megabases, that can be useful for the exploitation of the pig genome assembly.
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spelling pubmed-34992812012-11-20 High-resolution autosomal radiation hybrid maps of the pig genome and their contribution to the genome sequence assembly Servin, Bertrand Faraut, Thomas Iannuccelli, Nathalie Zelenika, Diana Milan, Denis BMC Genomics Research Article BACKGROUND: The release of the porcine genome sequence offers great perspectives for Pig genetics and genomics, and more generally will contribute to the understanding of mammalian genome biology and evolution. The process of producing a complete genome sequence of high quality, while facilitated by high-throughput sequencing technologies, remains a difficult task. The porcine genome was sequenced using a combination of a hierarchical shotgun strategy and data generated with whole genome shotgun. In addition to the BAC contig map used for the clone-by-clone approach, genomic mapping resources for the pig include two radiation hybrid (RH) panels at two different resolutions. These two panels have been used extensively for the physical mapping of pig genes and markers prior to the availability of the pig genome sequence. RESULTS: In order to contribute to the assembly of the pig genome, we genotyped the two radiation hybrid (RH) panels with a SNP array (the Illumina porcineSNP60 array) and produced high density physical RH maps for each pig autosome. We first present the methods developed to obtain high density RH maps with 38,379 SNPs from the SNP array genotyping. We then show how they were useful to identify problems in a draft of the pig genome assembly, and how the RH maps enabled the problems to be corrected in the porcine genome sequence. Finally, we used the RH maps to predict the position of 2,703 SNPs and 1,328 scaffolds currently unplaced on the porcine genome assembly. CONCLUSIONS: A complete process, from genotyping of a high density SNP array on RH panels, to the construction of genome-wide high density RH maps, and finally their exploitation for validating and improving a genome assembly is presented here. The study includes the cross-validation of RH based findings with independent information from genetic data and comparative mapping with the Human genome. Several additional resources are also provided, in particular the predicted genomic location of currently unplaced SNPs and associated scaffolds summing up to a total of 72 megabases, that can be useful for the exploitation of the pig genome assembly. BioMed Central 2012-11-15 /pmc/articles/PMC3499281/ /pubmed/23153393 http://dx.doi.org/10.1186/1471-2164-13-585 Text en Copyright ©2012 Servin et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Servin, Bertrand
Faraut, Thomas
Iannuccelli, Nathalie
Zelenika, Diana
Milan, Denis
High-resolution autosomal radiation hybrid maps of the pig genome and their contribution to the genome sequence assembly
title High-resolution autosomal radiation hybrid maps of the pig genome and their contribution to the genome sequence assembly
title_full High-resolution autosomal radiation hybrid maps of the pig genome and their contribution to the genome sequence assembly
title_fullStr High-resolution autosomal radiation hybrid maps of the pig genome and their contribution to the genome sequence assembly
title_full_unstemmed High-resolution autosomal radiation hybrid maps of the pig genome and their contribution to the genome sequence assembly
title_short High-resolution autosomal radiation hybrid maps of the pig genome and their contribution to the genome sequence assembly
title_sort high-resolution autosomal radiation hybrid maps of the pig genome and their contribution to the genome sequence assembly
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3499281/
https://www.ncbi.nlm.nih.gov/pubmed/23153393
http://dx.doi.org/10.1186/1471-2164-13-585
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