High-Density Linkage Maps Based on Genotyping-by-Sequencing (GBS) Confirm a Chromosome-Level Genome Assembly and Reveal Variation in Recombination Rate for the Pacific Oyster Crassostrea gigas
Studies of linkage and linkage mapping have advanced genetic and biological knowledge for over 100 years. In addition to their growing role, today, in mapping phenotypes to genotypes, dense linkage maps can help to validate genome assemblies. Previously, we showed that 40% of scaffolds in the first...
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GENETICS SOCIETY AMERICA
2021
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Online Access: | http://hdl.handle.net/10498/24305 https://doi.org/10.1534/g3.120.401728 |
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ftunivcadiz:oai:rodin.uca.es:10498/24305 2023-05-15T15:57:50+02:00 High-Density Linkage Maps Based on Genotyping-by-Sequencing (GBS) Confirm a Chromosome-Level Genome Assembly and Reveal Variation in Recombination Rate for the Pacific Oyster Crassostrea gigas Yin, Xiaoshen Arias Pérez, Alberto Kitapci, Tevfik Hamdi Hedgecock, Dennis Biomedicina, Biotecnología y Salud Pública 2021-01-22T09:52:58Z application/pdf http://hdl.handle.net/10498/24305 https://doi.org/10.1534/g3.120.401728 eng eng GENETICS SOCIETY AMERICA 2160-1836 http://hdl.handle.net/10498/24305 doi:10.1534/g3.120.401728 Atribución 4.0 Internacional http://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess CC-BY G3 Genes|Genomes|Genetics, Volume 10, Issue 12, 1 December 2020, Pages 4691–4705 linkage mapping genotyping-by-sequencing genome assembly recombination rate Pacific oyster Crassostrea gigas info:eu-repo/semantics/article 2021 ftunivcadiz https://doi.org/10.1534/g3.120.401728 2023-02-24T07:58:57Z Studies of linkage and linkage mapping have advanced genetic and biological knowledge for over 100 years. In addition to their growing role, today, in mapping phenotypes to genotypes, dense linkage maps can help to validate genome assemblies. Previously, we showed that 40% of scaffolds in the first genome assembly for the Pacific oyster Crassostrea gigas were chimeric, containing single nucleotide polymorphisms (SNPs) mapping to different linkage groups. Here, we merge 14 linkage maps constructed of SNPs generated from genotyping-by-sequencing (GBS) methods with five, previously constructed linkage maps, to create a compendium of nearly 69 thousand SNPs mapped with high confidence. We use this compendium to assess a recently available, chromosome-level assembly of the C. gigas genome, mapping SNPs in 275 of 301 contigs and comparing the ordering of these contigs, by linkage, to their assembly by Hi-C sequencing methods. We find that, while 26% of contigs contain chimeric blocks of SNPs, i.e., adjacent SNPs mapping to different linkage groups than the majority of SNPs in their contig, these apparent misassemblies amount to only 0.08% of the genome sequence. Furthermore, nearly 90% of 275 contigs mapped by linkage and sequencing are assembled identically; inconsistencies between the two assemblies for the remaining 10% of contigs appear to result from insufficient linkage information. Thus, our compilation of linkage maps strongly supports this chromosome-level assembly of the oyster genome. Finally, we use this assembly to estimate, for the first time in a Lophotrochozoan, genome-wide recombination rates and causes of variation in this fundamental process. Article in Journal/Newspaper Crassostrea gigas Pacific oyster RODIN - Repositorio de Objetos de Docencia e Investigación de la Universidad de Cádiz Pacific G3 Genes|Genomes|Genetics 10 12 4691 4705 |
institution |
Open Polar |
collection |
RODIN - Repositorio de Objetos de Docencia e Investigación de la Universidad de Cádiz |
op_collection_id |
ftunivcadiz |
language |
English |
topic |
linkage mapping genotyping-by-sequencing genome assembly recombination rate Pacific oyster Crassostrea gigas |
spellingShingle |
linkage mapping genotyping-by-sequencing genome assembly recombination rate Pacific oyster Crassostrea gigas Yin, Xiaoshen Arias Pérez, Alberto Kitapci, Tevfik Hamdi Hedgecock, Dennis High-Density Linkage Maps Based on Genotyping-by-Sequencing (GBS) Confirm a Chromosome-Level Genome Assembly and Reveal Variation in Recombination Rate for the Pacific Oyster Crassostrea gigas |
topic_facet |
linkage mapping genotyping-by-sequencing genome assembly recombination rate Pacific oyster Crassostrea gigas |
description |
Studies of linkage and linkage mapping have advanced genetic and biological knowledge for over 100 years. In addition to their growing role, today, in mapping phenotypes to genotypes, dense linkage maps can help to validate genome assemblies. Previously, we showed that 40% of scaffolds in the first genome assembly for the Pacific oyster Crassostrea gigas were chimeric, containing single nucleotide polymorphisms (SNPs) mapping to different linkage groups. Here, we merge 14 linkage maps constructed of SNPs generated from genotyping-by-sequencing (GBS) methods with five, previously constructed linkage maps, to create a compendium of nearly 69 thousand SNPs mapped with high confidence. We use this compendium to assess a recently available, chromosome-level assembly of the C. gigas genome, mapping SNPs in 275 of 301 contigs and comparing the ordering of these contigs, by linkage, to their assembly by Hi-C sequencing methods. We find that, while 26% of contigs contain chimeric blocks of SNPs, i.e., adjacent SNPs mapping to different linkage groups than the majority of SNPs in their contig, these apparent misassemblies amount to only 0.08% of the genome sequence. Furthermore, nearly 90% of 275 contigs mapped by linkage and sequencing are assembled identically; inconsistencies between the two assemblies for the remaining 10% of contigs appear to result from insufficient linkage information. Thus, our compilation of linkage maps strongly supports this chromosome-level assembly of the oyster genome. Finally, we use this assembly to estimate, for the first time in a Lophotrochozoan, genome-wide recombination rates and causes of variation in this fundamental process. |
author2 |
Biomedicina, Biotecnología y Salud Pública |
format |
Article in Journal/Newspaper |
author |
Yin, Xiaoshen Arias Pérez, Alberto Kitapci, Tevfik Hamdi Hedgecock, Dennis |
author_facet |
Yin, Xiaoshen Arias Pérez, Alberto Kitapci, Tevfik Hamdi Hedgecock, Dennis |
author_sort |
Yin, Xiaoshen |
title |
High-Density Linkage Maps Based on Genotyping-by-Sequencing (GBS) Confirm a Chromosome-Level Genome Assembly and Reveal Variation in Recombination Rate for the Pacific Oyster Crassostrea gigas |
title_short |
High-Density Linkage Maps Based on Genotyping-by-Sequencing (GBS) Confirm a Chromosome-Level Genome Assembly and Reveal Variation in Recombination Rate for the Pacific Oyster Crassostrea gigas |
title_full |
High-Density Linkage Maps Based on Genotyping-by-Sequencing (GBS) Confirm a Chromosome-Level Genome Assembly and Reveal Variation in Recombination Rate for the Pacific Oyster Crassostrea gigas |
title_fullStr |
High-Density Linkage Maps Based on Genotyping-by-Sequencing (GBS) Confirm a Chromosome-Level Genome Assembly and Reveal Variation in Recombination Rate for the Pacific Oyster Crassostrea gigas |
title_full_unstemmed |
High-Density Linkage Maps Based on Genotyping-by-Sequencing (GBS) Confirm a Chromosome-Level Genome Assembly and Reveal Variation in Recombination Rate for the Pacific Oyster Crassostrea gigas |
title_sort |
high-density linkage maps based on genotyping-by-sequencing (gbs) confirm a chromosome-level genome assembly and reveal variation in recombination rate for the pacific oyster crassostrea gigas |
publisher |
GENETICS SOCIETY AMERICA |
publishDate |
2021 |
url |
http://hdl.handle.net/10498/24305 https://doi.org/10.1534/g3.120.401728 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_source |
G3 Genes|Genomes|Genetics, Volume 10, Issue 12, 1 December 2020, Pages 4691–4705 |
op_relation |
2160-1836 http://hdl.handle.net/10498/24305 doi:10.1534/g3.120.401728 |
op_rights |
Atribución 4.0 Internacional http://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1534/g3.120.401728 |
container_title |
G3 Genes|Genomes|Genetics |
container_volume |
10 |
container_issue |
12 |
container_start_page |
4691 |
op_container_end_page |
4705 |
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1766393530417152000 |