Second-Generation Linkage Maps for the Pacific Oyster Crassostrea gigas Reveal Errors in Assembly of Genome Scaffolds
Abstract The Pacific oyster Crassostrea gigas, a widely cultivated marine bivalve mollusc, is becoming a genetically and genomically enabled model for highly fecund marine metazoans with complex life-histories. A genome sequence is available for the Pacific oyster, as are first-generation, low-densi...
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Online Access: | http://dx.doi.org/10.1534/g3.115.019570 http://academic.oup.com/g3journal/article-pdf/5/10/2007/37214684/g3journal2007.pdf |
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croxfordunivpr:10.1534/g3.115.019570 2024-06-23T07:52:16+00:00 Second-Generation Linkage Maps for the Pacific Oyster Crassostrea gigas Reveal Errors in Assembly of Genome Scaffolds Hedgecock, Dennis Shin, Grace Gracey, Andrew Y Den Berg, David Van Samanta, Manoj P 2015 http://dx.doi.org/10.1534/g3.115.019570 http://academic.oup.com/g3journal/article-pdf/5/10/2007/37214684/g3journal2007.pdf en eng Oxford University Press (OUP) https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model G3 Genes|Genomes|Genetics volume 5, issue 10, page 2007-2019 ISSN 2160-1836 journal-article 2015 croxfordunivpr https://doi.org/10.1534/g3.115.019570 2024-06-11T04:21:18Z Abstract The Pacific oyster Crassostrea gigas, a widely cultivated marine bivalve mollusc, is becoming a genetically and genomically enabled model for highly fecund marine metazoans with complex life-histories. A genome sequence is available for the Pacific oyster, as are first-generation, low-density, linkage and gene-centromere maps mostly constructed from microsatellite DNA markers. Here, higher density, second-generation, linkage maps are constructed from more than 1100 coding (exonic) single-nucleotide polymorphisms (SNPs), as well as 66 previously mapped microsatellite DNA markers, all typed in five families of Pacific oysters (nearly 172,000 genotypes). The map comprises 10 linkage groups, as expected, has an average total length of 588 cM, an average marker-spacing of 1.0 cM, and covers 86% of a genome estimated to be 616 cM. All but seven of the mapped SNPs map to 618 genome scaffolds; 260 scaffolds contain two or more mapped SNPs, but for 100 of these scaffolds (38.5%), the contained SNPs map to different linkage groups, suggesting widespread errors in scaffold assemblies. The 100 misassembled scaffolds are significantly longer than those that map to a single linkage group. On the genetic maps, marker orders and intermarker distances vary across families and mapping methods, owing to an abundance of markers segregating from only one parent, to widespread distortions of segregation ratios caused by early mortality, as previously observed for oysters, and to genotyping errors. Maps made from framework markers provide stronger support for marker orders and reasonable map lengths and are used to produce a consensus high-density linkage map containing 656 markers. Article in Journal/Newspaper Crassostrea gigas Pacific oyster Oxford University Press Pacific G3 Genes|Genomes|Genetics 5 10 2007 2019 |
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Open Polar |
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Oxford University Press |
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croxfordunivpr |
language |
English |
description |
Abstract The Pacific oyster Crassostrea gigas, a widely cultivated marine bivalve mollusc, is becoming a genetically and genomically enabled model for highly fecund marine metazoans with complex life-histories. A genome sequence is available for the Pacific oyster, as are first-generation, low-density, linkage and gene-centromere maps mostly constructed from microsatellite DNA markers. Here, higher density, second-generation, linkage maps are constructed from more than 1100 coding (exonic) single-nucleotide polymorphisms (SNPs), as well as 66 previously mapped microsatellite DNA markers, all typed in five families of Pacific oysters (nearly 172,000 genotypes). The map comprises 10 linkage groups, as expected, has an average total length of 588 cM, an average marker-spacing of 1.0 cM, and covers 86% of a genome estimated to be 616 cM. All but seven of the mapped SNPs map to 618 genome scaffolds; 260 scaffolds contain two or more mapped SNPs, but for 100 of these scaffolds (38.5%), the contained SNPs map to different linkage groups, suggesting widespread errors in scaffold assemblies. The 100 misassembled scaffolds are significantly longer than those that map to a single linkage group. On the genetic maps, marker orders and intermarker distances vary across families and mapping methods, owing to an abundance of markers segregating from only one parent, to widespread distortions of segregation ratios caused by early mortality, as previously observed for oysters, and to genotyping errors. Maps made from framework markers provide stronger support for marker orders and reasonable map lengths and are used to produce a consensus high-density linkage map containing 656 markers. |
format |
Article in Journal/Newspaper |
author |
Hedgecock, Dennis Shin, Grace Gracey, Andrew Y Den Berg, David Van Samanta, Manoj P |
spellingShingle |
Hedgecock, Dennis Shin, Grace Gracey, Andrew Y Den Berg, David Van Samanta, Manoj P Second-Generation Linkage Maps for the Pacific Oyster Crassostrea gigas Reveal Errors in Assembly of Genome Scaffolds |
author_facet |
Hedgecock, Dennis Shin, Grace Gracey, Andrew Y Den Berg, David Van Samanta, Manoj P |
author_sort |
Hedgecock, Dennis |
title |
Second-Generation Linkage Maps for the Pacific Oyster Crassostrea gigas Reveal Errors in Assembly of Genome Scaffolds |
title_short |
Second-Generation Linkage Maps for the Pacific Oyster Crassostrea gigas Reveal Errors in Assembly of Genome Scaffolds |
title_full |
Second-Generation Linkage Maps for the Pacific Oyster Crassostrea gigas Reveal Errors in Assembly of Genome Scaffolds |
title_fullStr |
Second-Generation Linkage Maps for the Pacific Oyster Crassostrea gigas Reveal Errors in Assembly of Genome Scaffolds |
title_full_unstemmed |
Second-Generation Linkage Maps for the Pacific Oyster Crassostrea gigas Reveal Errors in Assembly of Genome Scaffolds |
title_sort |
second-generation linkage maps for the pacific oyster crassostrea gigas reveal errors in assembly of genome scaffolds |
publisher |
Oxford University Press (OUP) |
publishDate |
2015 |
url |
http://dx.doi.org/10.1534/g3.115.019570 http://academic.oup.com/g3journal/article-pdf/5/10/2007/37214684/g3journal2007.pdf |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_source |
G3 Genes|Genomes|Genetics volume 5, issue 10, page 2007-2019 ISSN 2160-1836 |
op_rights |
https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model |
op_doi |
https://doi.org/10.1534/g3.115.019570 |
container_title |
G3 Genes|Genomes|Genetics |
container_volume |
5 |
container_issue |
10 |
container_start_page |
2007 |
op_container_end_page |
2019 |
_version_ |
1802643524412243968 |