Linkage Disequilibrium-Based Inference of Genome Homology and Chromosomal Rearrangements Between Species
Autor(a) principal: | |
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Data de Publicação: | 2020 |
Outros Autores: | , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1534/g3.120.401090 http://hdl.handle.net/11449/199126 |
Resumo: | The aim of this study was to analyze the genomic homology between cattle (Bos taurus) and buffaloes (Bubalus bubalis) and to propose a rearrangement of the buffalo genome through linkage disequilibrium analyses of buffalo SNP markers referenced in the cattle genome assembly and also compare it to the buffalo genome assembly. A panel of bovine SNPs (single nucleotide polymorphisms) was used for hierarchical, non-hierarchical and admixture cluster analyses. Thus, the linkage disequilibrium information between markers of a specific panel of buffalo was used to infer chromosomal rearrangement. Haplotype diversity and imputation accuracy of the submetacentric chromosomes were also analyzed. The genomic homology between the species enabled us to use the bovine genome assembly to recreate a buffalo genomic reference by rearranging the submetacentric chromosomes. The centromere of the submetacentric chromosomes exhibited high linkage disequilibrium and low haplotype diversity. It allowed hypothesizing about chromosome evolution. It indicated that buffalo submetacentric chromosomes are a centric fusion of ancestral acrocentric chromosomes. The chronology of fusions was also suggested. Moreover, a linear regression between buffalo and cattle rearranged assembly and the imputation accuracy indicated that the rearrangement of the chromosomes was adequate. When using the bovine reference genome assembly, the rearrangement of the buffalo submetacentric chromosomes could be done by SNP BTA (chromosome of Bos taurus) calculations: shorter BTA (shorter arm of buffalo chromosome) was given as [(shorter BTA length - SNP position in shorter BTA)] and larger BTA length as [shorter BTA length + (larger BTA length - SNP position in larger BTA)]. Finally, the proposed linkage disequilibrium-based method can be applied to elucidate other chromosomal rearrangement events in other species with the possibility of better understanding the evolutionary relationship between their genomes. |
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Repositório Institucional da UNESP |
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Linkage Disequilibrium-Based Inference of Genome Homology and Chromosomal Rearrangements Between SpeciesBuffaloCattleChromosome EvolutionGenome AssemblyGenotype ImputationHaplotype DiversitySNPThe aim of this study was to analyze the genomic homology between cattle (Bos taurus) and buffaloes (Bubalus bubalis) and to propose a rearrangement of the buffalo genome through linkage disequilibrium analyses of buffalo SNP markers referenced in the cattle genome assembly and also compare it to the buffalo genome assembly. A panel of bovine SNPs (single nucleotide polymorphisms) was used for hierarchical, non-hierarchical and admixture cluster analyses. Thus, the linkage disequilibrium information between markers of a specific panel of buffalo was used to infer chromosomal rearrangement. Haplotype diversity and imputation accuracy of the submetacentric chromosomes were also analyzed. The genomic homology between the species enabled us to use the bovine genome assembly to recreate a buffalo genomic reference by rearranging the submetacentric chromosomes. The centromere of the submetacentric chromosomes exhibited high linkage disequilibrium and low haplotype diversity. It allowed hypothesizing about chromosome evolution. It indicated that buffalo submetacentric chromosomes are a centric fusion of ancestral acrocentric chromosomes. The chronology of fusions was also suggested. Moreover, a linear regression between buffalo and cattle rearranged assembly and the imputation accuracy indicated that the rearrangement of the chromosomes was adequate. When using the bovine reference genome assembly, the rearrangement of the buffalo submetacentric chromosomes could be done by SNP BTA (chromosome of Bos taurus) calculations: shorter BTA (shorter arm of buffalo chromosome) was given as [(shorter BTA length - SNP position in shorter BTA)] and larger BTA length as [shorter BTA length + (larger BTA length - SNP position in larger BTA)]. Finally, the proposed linkage disequilibrium-based method can be applied to elucidate other chromosomal rearrangement events in other species with the possibility of better understanding the evolutionary relationship between their genomes.Departamento de ZootecniaDepartment of Animal and Avian Sciences University of Maryland, College ParkDepartamento de Ciências Exatas Universidade Estadual Paulista (Unesp)Instituto Federal Goiano, Campus Rio VerdeDepartamento de Ciências Exatas Universidade Estadual Paulista (Unesp)University of MarylandUniversidade Estadual Paulista (Unesp)Instituto Federal Goianode Abreu Santos, Daniel JordanFerreira de Camargo, Gregório MiguelCardoso, Diercles FranciscoBuzanskas, Marcos Eli [UNESP]Aspilcueta-Borquis, Rusbel RaulHurtado-Lugo, Naudin Alejandrode Araújo Neto, Francisco RibeiroGalvão de Albuquerque, LúciaMa, LiTonhati, Humberto2020-12-12T01:31:26Z2020-12-12T01:31:26Z2020-07-07info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article2327-2343http://dx.doi.org/10.1534/g3.120.401090G3 (Bethesda, Md.), v. 10, n. 7, p. 2327-2343, 2020.2160-1836http://hdl.handle.net/11449/19912610.1534/g3.120.4010902-s2.0-85088207894Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengG3 (Bethesda, Md.)info:eu-repo/semantics/openAccess2021-10-23T03:21:13Zoai:repositorio.unesp.br:11449/199126Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T14:05:37.737808Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Linkage Disequilibrium-Based Inference of Genome Homology and Chromosomal Rearrangements Between Species |
title |
Linkage Disequilibrium-Based Inference of Genome Homology and Chromosomal Rearrangements Between Species |
spellingShingle |
Linkage Disequilibrium-Based Inference of Genome Homology and Chromosomal Rearrangements Between Species de Abreu Santos, Daniel Jordan Buffalo Cattle Chromosome Evolution Genome Assembly Genotype Imputation Haplotype Diversity SNP |
title_short |
Linkage Disequilibrium-Based Inference of Genome Homology and Chromosomal Rearrangements Between Species |
title_full |
Linkage Disequilibrium-Based Inference of Genome Homology and Chromosomal Rearrangements Between Species |
title_fullStr |
Linkage Disequilibrium-Based Inference of Genome Homology and Chromosomal Rearrangements Between Species |
title_full_unstemmed |
Linkage Disequilibrium-Based Inference of Genome Homology and Chromosomal Rearrangements Between Species |
title_sort |
Linkage Disequilibrium-Based Inference of Genome Homology and Chromosomal Rearrangements Between Species |
author |
de Abreu Santos, Daniel Jordan |
author_facet |
de Abreu Santos, Daniel Jordan Ferreira de Camargo, Gregório Miguel Cardoso, Diercles Francisco Buzanskas, Marcos Eli [UNESP] Aspilcueta-Borquis, Rusbel Raul Hurtado-Lugo, Naudin Alejandro de Araújo Neto, Francisco Ribeiro Galvão de Albuquerque, Lúcia Ma, Li Tonhati, Humberto |
author_role |
author |
author2 |
Ferreira de Camargo, Gregório Miguel Cardoso, Diercles Francisco Buzanskas, Marcos Eli [UNESP] Aspilcueta-Borquis, Rusbel Raul Hurtado-Lugo, Naudin Alejandro de Araújo Neto, Francisco Ribeiro Galvão de Albuquerque, Lúcia Ma, Li Tonhati, Humberto |
author2_role |
author author author author author author author author author |
dc.contributor.none.fl_str_mv |
University of Maryland Universidade Estadual Paulista (Unesp) Instituto Federal Goiano |
dc.contributor.author.fl_str_mv |
de Abreu Santos, Daniel Jordan Ferreira de Camargo, Gregório Miguel Cardoso, Diercles Francisco Buzanskas, Marcos Eli [UNESP] Aspilcueta-Borquis, Rusbel Raul Hurtado-Lugo, Naudin Alejandro de Araújo Neto, Francisco Ribeiro Galvão de Albuquerque, Lúcia Ma, Li Tonhati, Humberto |
dc.subject.por.fl_str_mv |
Buffalo Cattle Chromosome Evolution Genome Assembly Genotype Imputation Haplotype Diversity SNP |
topic |
Buffalo Cattle Chromosome Evolution Genome Assembly Genotype Imputation Haplotype Diversity SNP |
description |
The aim of this study was to analyze the genomic homology between cattle (Bos taurus) and buffaloes (Bubalus bubalis) and to propose a rearrangement of the buffalo genome through linkage disequilibrium analyses of buffalo SNP markers referenced in the cattle genome assembly and also compare it to the buffalo genome assembly. A panel of bovine SNPs (single nucleotide polymorphisms) was used for hierarchical, non-hierarchical and admixture cluster analyses. Thus, the linkage disequilibrium information between markers of a specific panel of buffalo was used to infer chromosomal rearrangement. Haplotype diversity and imputation accuracy of the submetacentric chromosomes were also analyzed. The genomic homology between the species enabled us to use the bovine genome assembly to recreate a buffalo genomic reference by rearranging the submetacentric chromosomes. The centromere of the submetacentric chromosomes exhibited high linkage disequilibrium and low haplotype diversity. It allowed hypothesizing about chromosome evolution. It indicated that buffalo submetacentric chromosomes are a centric fusion of ancestral acrocentric chromosomes. The chronology of fusions was also suggested. Moreover, a linear regression between buffalo and cattle rearranged assembly and the imputation accuracy indicated that the rearrangement of the chromosomes was adequate. When using the bovine reference genome assembly, the rearrangement of the buffalo submetacentric chromosomes could be done by SNP BTA (chromosome of Bos taurus) calculations: shorter BTA (shorter arm of buffalo chromosome) was given as [(shorter BTA length - SNP position in shorter BTA)] and larger BTA length as [shorter BTA length + (larger BTA length - SNP position in larger BTA)]. Finally, the proposed linkage disequilibrium-based method can be applied to elucidate other chromosomal rearrangement events in other species with the possibility of better understanding the evolutionary relationship between their genomes. |
publishDate |
2020 |
dc.date.none.fl_str_mv |
2020-12-12T01:31:26Z 2020-12-12T01:31:26Z 2020-07-07 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1534/g3.120.401090 G3 (Bethesda, Md.), v. 10, n. 7, p. 2327-2343, 2020. 2160-1836 http://hdl.handle.net/11449/199126 10.1534/g3.120.401090 2-s2.0-85088207894 |
url |
http://dx.doi.org/10.1534/g3.120.401090 http://hdl.handle.net/11449/199126 |
identifier_str_mv |
G3 (Bethesda, Md.), v. 10, n. 7, p. 2327-2343, 2020. 2160-1836 10.1534/g3.120.401090 2-s2.0-85088207894 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
G3 (Bethesda, Md.) |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
2327-2343 |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1808128314341064704 |