Phylotaxonomic position of Tianzhu white yak (<i>Poephagus grunniens</i>) based on nucleotide sequences of multiple subunits of cytochrome<i>c</i>oxidase

The Chinese forest musk deer ( Moschus berezovskii ; FMD) is an artiodactyl mammal and is both economically valuable and highly endangered. To investigate the genetic mechanisms of musk secretion and adaptive immunity in FMD, we compared its genome to nine other artiodactyl genomes. Comparative genomics demonstrated that eight positively selected genes (PSGs) in FMD were annotated in three KEGG pathways that were related to metabolic and synthetic activity of musk, similar to previous transcriptome studies. Functional enrichment analysis indicated that many PSGs were involved in the regulation of immune system processes, implying important reorganization of the immune system in FMD. FMD-specific missense mutations were found in two PSGs ( MHC class II antigen DRA and ADA ) that were classified as deleterious by PolyPhen-2, possibly contributing to immune adaptation to infectious diseases. Functional assessment showed that the FMD-specific mutation enhanced the ADA activity, which was likely to strengthen the immune defense against pathogenic invasion. Single nucleotide polymorphism-based inference showed the recent demographic trajectory for FMD. Our data and findings provide valuable genomic resources not only for studying the genetic mechanisms of musk secretion and adaptive immunity, but also for facilitating more effective management of the captive breeding programs for this endangered species.

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“…mutus / Bu. bubalis ; 11.5–19.7 Ma for the emergence of Bovinae tribes) (Bai 2015; Tan et al. 2017).…”

Section: Methodsmentioning

confidence: 99%

Comparative Genomics Reveals the Genetic Mechanisms of Musk Secretion and Adaptive Immunity in Chinese Forest Musk Deer

Zhou

Zhang

Wen

et al. 2019

Genome Biology and Evolution

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“…; Wang et al . ; Bai ; Bai et al . ), the population size of Tianzhu white yak in those studies was not large enough (4–60 individuals) to reveal the real genetic diversity of Tianzhu white yak.…”

Section: Sample Information and Genetic Diversity Of Seven Groups In mentioning

confidence: 99%

Comprehensive investigation of nucleotide diverdity in yaks

Yue

Liang

Liang³

et al. 2016

Animal Genetics

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To understand the maternal genetic diversity of Tianzhu white yak better, we analyzed mtDNA D-loop sequences of 209 Tianzhu white yaks, which are from the central region of Tianzhu white yak habitat. Accordingly, a total of 45 haplotypes were identified in Tianzhu white yaks in this study, and 18 of them were unique. The nucleotide diversity and haplotype diversity of population studied were 0.024 ± 0.003 and 0.946 ± 0.007 respectively, revealing that Tianzhu white yak possess a relatively high genetic diversity. The phylogenetic analysis, combining D-loop sequences in this study with 533 previous published D-loop sequences of 13 yak breeds, indicated that Tianzhu white yaks fell mainly into haplogroup A and that a small portion belonged to haplogroups B, C, D and E. Moreover, six haplotypes of 20 individuals identified in Tianzhu white yak were in the taurine haplogroup, indicating hybridization between Bos taurus and Tianzhu white yaks. In summary, this study supplies a comprehensive maternal genetic pattern for Tianzhu white yak and provides a basic reference for future breeding programs to conserve the purebred Tianzhu white yak.

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“…The high-level diversity change in cattle/yak may be attributed to their highly diverged relationship (split from each other before 1.05–1.50 million years ago) (Qiu et al. 2012 ; Bai 2015 ). Interestingly, we found a significantly greater change in the genetic diversity (4.68 fold change in chicken, compared with 1.29 in pig, 1.11 in goat, 1.05 in sheep) between the pairs compared in bird than so in mammal.…”

Section: Resultsmentioning

confidence: 99%

Analysis of mitochondrial DNA sequence and copy number variation across five high-altitude species and their low-altitude relatives

Liu

Jin

Long

et al. 2018

Mitochondrial DNA Part B

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High-altitude inhospitable environments impose a formidable life challenge for the local animals. Training and exposure to high-altitude environments produce both distinct physiological and phenotypic characteristics. The mitochondrion, an organelle crucial for the energy production, plays an important role in hypoxia adaptation. In this study, we investigated the mitochondrial DNA (mtDNA) polymorphism and copy number variation between the population pairs from distinct altitudes across the multi-species. Higher mitochondrial DNA control region's genetic diversity is conspicuous in highaltitude animals versus low-altitude relatives. We also found an accordant decrease of mtDNA copy number in most of the tissues from high-altitude animals. Compared to mammals, chickens have significantly distinct mitogenomic characteristics, and more significant changes in the skeletal muscle mtDNA copy number between high-and low-altitude individuals. Our study catches a snapshot of the biological similarities and differences in the mitochondrial high-altitude acclimation across the species.

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Phylotaxonomic position of Tianzhu white yak (Poephagus grunniens) based on nucleotide sequences of multiple subunits of cytochromecoxidase

Cited by 6 publications

References 23 publications

Comparative Genomics Reveals the Genetic Mechanisms of Musk Secretion and Adaptive Immunity in Chinese Forest Musk Deer

Comparative Genomics Reveals the Genetic Mechanisms of Musk Secretion and Adaptive Immunity in Chinese Forest Musk Deer

Comprehensive investigation of nucleotide diverdity in yaks

Analysis of mitochondrial DNA sequence and copy number variation across five high-altitude species and their low-altitude relatives

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