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Linkage Disequilibrium-Based Inference of Genome Homology and Chromosomal Rearrangements Between Species

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 th...

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Autores principales: de Abreu Santos, Daniel Jordan, Ferreira de Camargo, Gregório Miguel, Cardoso, Diercles Francisco, Buzanskas, Marcos Eli, Aspilcueta-Borquis, Rusbel Raul, Hurtado-Lugo, Naudin Alejandro, de Araújo Neto, Francisco Ribeiro, Galvão de Albuquerque, Lúcia, Ma, Li, Tonhati, Humberto
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Genetics Society of America 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7341147/
https://www.ncbi.nlm.nih.gov/pubmed/32434754
http://dx.doi.org/10.1534/g3.120.401090
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author de Abreu Santos, Daniel Jordan
Ferreira de Camargo, Gregório Miguel
Cardoso, Diercles Francisco
Buzanskas, Marcos Eli
Aspilcueta-Borquis, Rusbel Raul
Hurtado-Lugo, Naudin Alejandro
de Araújo Neto, Francisco Ribeiro
Galvão de Albuquerque, Lúcia
Ma, Li
Tonhati, Humberto
author_facet de Abreu Santos, Daniel Jordan
Ferreira de Camargo, Gregório Miguel
Cardoso, Diercles Francisco
Buzanskas, Marcos Eli
Aspilcueta-Borquis, Rusbel Raul
Hurtado-Lugo, Naudin Alejandro
de Araújo Neto, Francisco Ribeiro
Galvão de Albuquerque, Lúcia
Ma, Li
Tonhati, Humberto
author_sort de Abreu Santos, Daniel Jordan
collection PubMed
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.
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spelling pubmed-73411472020-07-21 Linkage Disequilibrium-Based Inference of Genome Homology and Chromosomal Rearrangements Between Species de Abreu Santos, Daniel Jordan Ferreira de Camargo, Gregório Miguel Cardoso, Diercles Francisco Buzanskas, Marcos Eli Aspilcueta-Borquis, Rusbel Raul Hurtado-Lugo, Naudin Alejandro de Araújo Neto, Francisco Ribeiro Galvão de Albuquerque, Lúcia Ma, Li Tonhati, Humberto G3 (Bethesda) Investigations 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. Genetics Society of America 2020-05-20 /pmc/articles/PMC7341147/ /pubmed/32434754 http://dx.doi.org/10.1534/g3.120.401090 Text en Copyright © 2020 Jordan de Abreu Santos et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Investigations
de Abreu Santos, Daniel Jordan
Ferreira de Camargo, Gregório Miguel
Cardoso, Diercles Francisco
Buzanskas, Marcos Eli
Aspilcueta-Borquis, Rusbel Raul
Hurtado-Lugo, Naudin Alejandro
de Araújo Neto, Francisco Ribeiro
Galvão de Albuquerque, Lúcia
Ma, Li
Tonhati, Humberto
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
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_short 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
topic Investigations
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7341147/
https://www.ncbi.nlm.nih.gov/pubmed/32434754
http://dx.doi.org/10.1534/g3.120.401090
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