Complete mitochondrial genome of the golden takin (<i>Budorcas taxicolor bedfordi</i>)

Feng, Hui; Feng, Chengli; Wang, Lu; Huang, Yuan

doi:10.1080/23802359.2016.1149792

Cited by 7 publications

(13 citation statements)

References 6 publications

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“…1b). The PCGs region consisted of twelve heavy strands and one light strand as commonly found in other vertebrate species [24][25][26] . The PCGs region consisted of seven NADH dehydrogenases, three cytochrome c oxidases, two ATPases and one cytochrome b genes.…”

Section: Resultsmentioning

confidence: 99%

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Assembling mitogenome of Himalayan Black Bear (U. t. laniger) from low depth reads and its application in drawing phylogenetic inferences

Bit

Thakur

Singh

et al. 2021

Sci Rep

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The complete mitogenome of Himalayan black bear (Ursus thibetanus laniger) from Indian Himalayan region was assembled following the modified approach of mitochondrial baiting and mapping using the next-generation sequencing reads. The complete mitogenome was of 16,556 bp long, consisted of 37 genes that contained 13 protein-coding genes, 22 tRNAs, 2 rRNAs and 1 control region. The complete base composition was 31.33% A, 15.24% G, 25.45%C, and 27.98%T and gene arrangement was similar to the other sub-species of Asiatic black bear. The relative synonymous codon usage analysis revealed the maximum abundance of Isoleucine, Tyrosine, Leucine and Threonine. The assembled mitogenome of U. t. laniger exhibited 99% similarity with the mitogenomes of Himalayan black bear available from Nepal and Tibetan Plateau-Himalaya region. The findings of the present study has proven low depth sequencing data, adequate and highly efficient in rapid recovering the mitochondrial genome by overcoming the conventional strategies of obtaining long-range PCR and subsequently drawing phylogenetic inferences.

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Section: Resultsmentioning

confidence: 99%

“…The mtDNA ribosomal region is known to be highly conserved and widely used for phylogenies of higher and middle category level, such as phyla, family and genera 24 , 26 . The length of 12S rRNA and 16S rRNA genes was 966 bp and 12,582 bp, respectively.…”

Section: Resultsmentioning

confidence: 99%

Assembling mitogenome of Himalayan Black Bear (U. t. laniger) from low depth reads and its application in drawing phylogenetic inferences

Bit

Thakur

Singh

et al. 2021

Sci Rep

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“…For the Cytb gene sequence, it was found that the homolog of takin was the most closely related to sheep, followed by goat [8,9]. However, the homolog of takin was the most closely related to goat, followed by sheep for the mitochondrial genome sequence [10][11][12]. To reveal the taxonomic status of takins, further research, particularly genome-wide analysis, will be necessary.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

“…Based on the comparative morphology, previous studies have reported that takin was closely related to the Musk-Oxen (Ovibos moschatus) [5]. However, based on Cytochrome b (Cytb) or mtDNA sequences, different molecular analyses have suggested that it is closely related to Caprinae [6][7][8][9][10][11][12]. So far, apart from it belonging to the bovine family, its other taxonomic status is still unclear.…”

Section: Introductionmentioning

confidence: 99%

De Novo Transcriptome Assembly, Functional Annotation and SSR Marker Discovery of Qinling Takin (Budorcas taxicolor bedfordi)

Qiu

Guo

et al. 2021

Animals

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The takin (Budorcas taxicolor) is an endemic ruminant species belonging to the bovine family. The International Union for Conservation of Nature (IUCN) has listed it as an endangered and vulnerable species. However, little is known about its molecular characterization since it lacks a reference genome. This study used RNA sequencing followed by de novo assembly, annotation and simple sequence repeats (SSRs) prediction to assess the transcriptome of Qinling takin (Budorcas taxicolor bedfordi) muscles. In total, 21,648 unigenes with an N50 and mean length of 1388 bp and 817 bp, respectively, were successfully detected and annotated against the public databases (NR, GO, KEGG, and EggNOG). Furthermore, 6222 SSRs were identified using the MIcroSAtellite (MISA) identification tool software. Taken together, these findings will provide valuable information for genetic, genomic, and evolutionary studies on takin.

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“…However, the analysis of mitochondrial cytochrome b genes (Cytb ) sequences showed that muskox and takin were not close with each other but under convergent evolution (Groves andShields 1997, Ren et al 2012). Recently, based on the complete mitochondrial genome, takin was found to be closely related to goat (Capra hircus ) rather than sheep (Ovis aries ) (Feng et al 2016, Kumar et al 2019, Zhou et al 2019. In our previous study, takin was found to be closely related to sheep rather than goat according to the transcriptome analysis (Qiu et al 2021).…”

Section: Introductionmentioning

confidence: 88%

Chromosome-level Genome Assembly for Takin (Budorcas taxicolor) Provides Insights into Its Taxonomic Status and Genetic Diversity

Yang

et al. 2022

Preprint

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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.

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Complete mitochondrial genome of the golden takin (Budorcas taxicolor bedfordi)

Cited by 7 publications

References 6 publications

Assembling mitogenome of Himalayan Black Bear (U. t. laniger) from low depth reads and its application in drawing phylogenetic inferences

Assembling mitogenome of Himalayan Black Bear (U. t. laniger) from low depth reads and its application in drawing phylogenetic inferences

De Novo Transcriptome Assembly, Functional Annotation and SSR Marker Discovery of Qinling Takin (Budorcas taxicolor bedfordi)

Chromosome-level Genome Assembly for Takin (Budorcas taxicolor) Provides Insights into Its Taxonomic Status and Genetic Diversity

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