Chromosome-level Genome Assembly for Takin (Budorcas taxicolor) Provides Insights into Its Taxonomic Status and Genetic Diversity
The takin (Budorcas taxicolor) is one of the largest bovid herbivores across caprinae subfamily. The takin is at high risk of extinction, however, its taxonomic status is still unclear. In this study, we constructed the first reference genome of B. taxicolor using PacBio long High-Fidelity reads and...
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2022
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crwinnower:10.22541/au.164275202.25941291/v1 2024-06-02T08:10:29+00:00 Chromosome-level Genome Assembly for Takin (Budorcas taxicolor) Provides Insights into Its Taxonomic Status and Genetic Diversity Li, Anning Yang, Qimeng Li, Ran Dai, Xuelei Cai, Keli Lei, Yinghu Jia, Kangsheng Jiang, Yu Zan, Linsen 2022 http://dx.doi.org/10.22541/au.164275202.25941291/v1 unknown Authorea, Inc. posted-content 2022 crwinnower https://doi.org/10.22541/au.164275202.25941291/v1 2024-05-07T14:19:27Z The takin (Budorcas taxicolor) is one of the largest bovid herbivores across caprinae subfamily. The takin is at high risk of extinction, however, its taxonomic status is still unclear. In this study, we constructed the first reference genome of B. taxicolor using PacBio long High-Fidelity reads and Hi-C technology. The assembled genome is ~2.95 Gb with a contig N50 of 68.05 Mb and a scaffold N50 of 101.27 Mb, which were anchored onto 25+XY chromosomes. Compared to the common ancestral karyotype of bovidae (2n=60), we found the takin (2n=52) experienced four chromosome fusions and one large translocation. We also found that the takin was most closely related to muskox, not other caprinae species. Further, we re-sequenced nine golden takins from the main distribution area, Qinling Mountains, and identified 3.3 million SNPs. The genetic diversity of takin was very low (θπ=0.00028 and heterozygosity=0.00038), which was among the lowest detected in the domestic and wild mammals. We also found takin genomes showed high inbreeding coefficient (FROH=0.217) suggesting severe inbreeding depression. The genome analysis show that the effective population size of takins declined significantly from ~100,000 years ago. Our results provide valuable information for protection of takins and insights into its evolution. Other/Unknown Material muskox The Winnower |
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The takin (Budorcas taxicolor) is one of the largest bovid herbivores across caprinae subfamily. The takin is at high risk of extinction, however, its taxonomic status is still unclear. In this study, we constructed the first reference genome of B. taxicolor using PacBio long High-Fidelity reads and Hi-C technology. The assembled genome is ~2.95 Gb with a contig N50 of 68.05 Mb and a scaffold N50 of 101.27 Mb, which were anchored onto 25+XY chromosomes. Compared to the common ancestral karyotype of bovidae (2n=60), we found the takin (2n=52) experienced four chromosome fusions and one large translocation. We also found that the takin was most closely related to muskox, not other caprinae species. Further, we re-sequenced nine golden takins from the main distribution area, Qinling Mountains, and identified 3.3 million SNPs. The genetic diversity of takin was very low (θπ=0.00028 and heterozygosity=0.00038), which was among the lowest detected in the domestic and wild mammals. We also found takin genomes showed high inbreeding coefficient (FROH=0.217) suggesting severe inbreeding depression. The genome analysis show that the effective population size of takins declined significantly from ~100,000 years ago. Our results provide valuable information for protection of takins and insights into its evolution. |
format |
Other/Unknown Material |
author |
Li, Anning Yang, Qimeng Li, Ran Dai, Xuelei Cai, Keli Lei, Yinghu Jia, Kangsheng Jiang, Yu Zan, Linsen |
spellingShingle |
Li, Anning Yang, Qimeng Li, Ran Dai, Xuelei Cai, Keli Lei, Yinghu Jia, Kangsheng Jiang, Yu Zan, Linsen Chromosome-level Genome Assembly for Takin (Budorcas taxicolor) Provides Insights into Its Taxonomic Status and Genetic Diversity |
author_facet |
Li, Anning Yang, Qimeng Li, Ran Dai, Xuelei Cai, Keli Lei, Yinghu Jia, Kangsheng Jiang, Yu Zan, Linsen |
author_sort |
Li, Anning |
title |
Chromosome-level Genome Assembly for Takin (Budorcas taxicolor) Provides Insights into Its Taxonomic Status and Genetic Diversity |
title_short |
Chromosome-level Genome Assembly for Takin (Budorcas taxicolor) Provides Insights into Its Taxonomic Status and Genetic Diversity |
title_full |
Chromosome-level Genome Assembly for Takin (Budorcas taxicolor) Provides Insights into Its Taxonomic Status and Genetic Diversity |
title_fullStr |
Chromosome-level Genome Assembly for Takin (Budorcas taxicolor) Provides Insights into Its Taxonomic Status and Genetic Diversity |
title_full_unstemmed |
Chromosome-level Genome Assembly for Takin (Budorcas taxicolor) Provides Insights into Its Taxonomic Status and Genetic Diversity |
title_sort |
chromosome-level genome assembly for takin (budorcas taxicolor) provides insights into its taxonomic status and genetic diversity |
publisher |
Authorea, Inc. |
publishDate |
2022 |
url |
http://dx.doi.org/10.22541/au.164275202.25941291/v1 |
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muskox |
genre_facet |
muskox |
op_doi |
https://doi.org/10.22541/au.164275202.25941291/v1 |
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1800756360928821248 |