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Genome-Wide Identification and Analysis of Variants in Domestic and Wild Bactrian Camels Using Whole-Genome Sequencing Data

The population size of Bactrian camels is smaller than dromedary, and they are distributed in cold and mountain regions and are also at the risk of extinction in some countries such as Iran. To identify and investigate the genome-wide variations, whole-genome sequencing of two Iranian Bactrian camel...

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Autores principales: Hedayat-Evrigh, Nemat, Khalkhali-Evrigh, Reza, Bakhtiarizadeh, Mohammad Reza
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7381958/
https://www.ncbi.nlm.nih.gov/pubmed/32724789
http://dx.doi.org/10.1155/2020/2430846
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author Hedayat-Evrigh, Nemat
Khalkhali-Evrigh, Reza
Bakhtiarizadeh, Mohammad Reza
author_facet Hedayat-Evrigh, Nemat
Khalkhali-Evrigh, Reza
Bakhtiarizadeh, Mohammad Reza
author_sort Hedayat-Evrigh, Nemat
collection PubMed
description The population size of Bactrian camels is smaller than dromedary, and they are distributed in cold and mountain regions and are also at the risk of extinction in some countries such as Iran. To identify and investigate the genome-wide variations, whole-genome sequencing of two Iranian Bactrian camels were performed with 37.4- and 42.6-fold coverage for the first time. Along with Iranian Bactrian camels, sequencing data from two Mongolian domestic and two wild Bactrian camels deposited in the NCBI were reanalyzed. The analysis eventuated to the identification of 4,908,998, 4,485,725, and 4,706,654 SNPs for Iranian, Mongolian domestic, and wild Bactrian camels, respectively. Also, INDEL variations ranged from 358,311 to 533,188 in all six camels. Results of variants annotation in all samples revealed that more than 88 percent of SNPs and INDELs were located in the intergenic and intronic regions. We found that 800,530 SNPs were common among all studied camels, containing 4,046 missense variants that affected 2,428 genes. Investigation of common genes among all camels containing the missense SNPs showed that there are 98 zinc finger and 4 fertility-related genes (ZP1, ZP2, ZP4, and ZPBP) in this set.
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spelling pubmed-73819582020-07-27 Genome-Wide Identification and Analysis of Variants in Domestic and Wild Bactrian Camels Using Whole-Genome Sequencing Data Hedayat-Evrigh, Nemat Khalkhali-Evrigh, Reza Bakhtiarizadeh, Mohammad Reza Int J Genomics Research Article The population size of Bactrian camels is smaller than dromedary, and they are distributed in cold and mountain regions and are also at the risk of extinction in some countries such as Iran. To identify and investigate the genome-wide variations, whole-genome sequencing of two Iranian Bactrian camels were performed with 37.4- and 42.6-fold coverage for the first time. Along with Iranian Bactrian camels, sequencing data from two Mongolian domestic and two wild Bactrian camels deposited in the NCBI were reanalyzed. The analysis eventuated to the identification of 4,908,998, 4,485,725, and 4,706,654 SNPs for Iranian, Mongolian domestic, and wild Bactrian camels, respectively. Also, INDEL variations ranged from 358,311 to 533,188 in all six camels. Results of variants annotation in all samples revealed that more than 88 percent of SNPs and INDELs were located in the intergenic and intronic regions. We found that 800,530 SNPs were common among all studied camels, containing 4,046 missense variants that affected 2,428 genes. Investigation of common genes among all camels containing the missense SNPs showed that there are 98 zinc finger and 4 fertility-related genes (ZP1, ZP2, ZP4, and ZPBP) in this set. Hindawi 2020-07-15 /pmc/articles/PMC7381958/ /pubmed/32724789 http://dx.doi.org/10.1155/2020/2430846 Text en Copyright © 2020 Nemat Hedayat-Evrigh et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Hedayat-Evrigh, Nemat
Khalkhali-Evrigh, Reza
Bakhtiarizadeh, Mohammad Reza
Genome-Wide Identification and Analysis of Variants in Domestic and Wild Bactrian Camels Using Whole-Genome Sequencing Data
title Genome-Wide Identification and Analysis of Variants in Domestic and Wild Bactrian Camels Using Whole-Genome Sequencing Data
title_full Genome-Wide Identification and Analysis of Variants in Domestic and Wild Bactrian Camels Using Whole-Genome Sequencing Data
title_fullStr Genome-Wide Identification and Analysis of Variants in Domestic and Wild Bactrian Camels Using Whole-Genome Sequencing Data
title_full_unstemmed Genome-Wide Identification and Analysis of Variants in Domestic and Wild Bactrian Camels Using Whole-Genome Sequencing Data
title_short Genome-Wide Identification and Analysis of Variants in Domestic and Wild Bactrian Camels Using Whole-Genome Sequencing Data
title_sort genome-wide identification and analysis of variants in domestic and wild bactrian camels using whole-genome sequencing data
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7381958/
https://www.ncbi.nlm.nih.gov/pubmed/32724789
http://dx.doi.org/10.1155/2020/2430846
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