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Ma X, Wang W, Cai L, Xiao M, He F, Liu Z, Chen D, Wang Y, Shen L, Gu Y. Analysis of the microbial diversity in takin ( Budorcas taxicolor) feces. Front Microbiol 2023; 14:1303085. [PMID: 38188576 PMCID: PMC10768053 DOI: 10.3389/fmicb.2023.1303085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024] Open
Abstract
Introduction The intestinal tract of animals is a complex and dynamic microecosystem that is inextricably linked to the health of the host organism. Takin (Budorcas taxicolor) is a threatened species, and its gut microbiome is poorly understood. Therefore, this study aimed to analyze the microbial community structure and potential pathogens of takin. Methods Takin fecal samples were collected from five sites in a nature reserve to ensure the uniformity of sample collection, determine the effects of different geographical locations on gut microbes, and analyze the differences in microbial communities between sites. Subsequently, high-throughput 16S rDNA gene sequencing was performed to analyze the microbial diversity and potential pathogens in the gut; the findings were verified by isolating and culturing bacteria and metagenomic sequencing. Results and discussion The takin gut microflora consisted mainly of four phyla: Firmicutes (69.72%), Bacteroidota (13.55%), Proteobacteria (9.02%), and Verrucomicrobiota (3.77%), representing 96.07% of all microorganisms. The main genera were UCG-005 (20.25%), UCG-010_unclassified (12.35%), Firmicus_unclassified (4.03%), and Rumino coccsea_unclassified (3.49%), while the main species were assigned to Bacteria_unclassified. Potential pathogens were also detected, which could be used as a reference for the protection of takin. Pseudomonas presented the highest abundance at Shuichiping and may represent the main pathogen responsible for the death of takin at the site. This study provides an important reference for investigating the composition of the bacterial community in the intestine of takin.
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Affiliation(s)
- Xiaoping Ma
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Weichen Wang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Lijun Cai
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Management Office of Tangjiahe National Nature Reserve, Qingchuan, China
| | - Mei Xiao
- Management Office of Tangjiahe National Nature Reserve, Qingchuan, China
| | - Fang He
- Management Office of Tangjiahe National Nature Reserve, Qingchuan, China
| | - Zhen Liu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dong Chen
- Sichuan Provincial Center for Animal Disease Prevention and Control, Chengdu, China
| | - Ya Wang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Limin Shen
- Management Office of Tangjiahe National Nature Reserve, Qingchuan, China
| | - Yu Gu
- College of Life Sciences, Sichuan Agricultural University, Chengdu, China
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Li A, Yang Q, Li R, Dai X, Cai K, Lei Y, Jia K, Jiang Y, Zan L. Chromosome-level genome assembly for takin (Budorcas taxicolor) provides insights into its taxonomic status and genetic diversity. Mol Ecol 2023; 32:1323-1334. [PMID: 35467052 DOI: 10.1111/mec.16483] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/29/2022] [Accepted: 04/17/2022] [Indexed: 11/29/2022]
Abstract
The takin (Budorcas taxicolor) is one of the largest bovid herbivores in the subfamily Caprinae. The takin is at high risk of extinction, but its taxonomic status and genetic diversity remain unclear. In this study, we constructed the first reference genome of Bu. 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, which were anchored onto 25+XY chromosomes. We found that the takin was more closely related to muskox than to other Caprinae species. Compared to the common ancestral karyotype of bovidae (2n = 60), we found the takin (2n = 52) experienced four chromosome fusions and one large translocation. Furthermore, we resequenced nine golden takins from the main distribution area, the Qinling Mountains, and identified 3.3 million single nucleotide polymorphisms. The genetic diversity of takin was very low (θπ = 0.00028 and heterozygosity =0.00038), among the lowest detected in domestic and wild mammals. Takin genomes showed a high inbreeding coefficient (FROH =0.217), suggesting severe inbreeding depression. The demographic history showed 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 their evolution.
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Affiliation(s)
- Anning Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Qimeng Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Center for Ruminant Genetic and Evolution, Northwest A&F University, Yangling, Shaanxi, China
| | - Ran Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Center for Ruminant Genetic and Evolution, Northwest A&F University, Yangling, Shaanxi, China
| | - Xuelei Dai
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Center for Ruminant Genetic and Evolution, Northwest A&F University, Yangling, Shaanxi, China
| | - Keli Cai
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yinghu Lei
- Research Center for the Qinling Giant Panda (Shaanxi Rare Wildlife Rescue Base), Shaanxi Academy of Forestry Sciences, Zhouzhi, Shaanxi, China
| | - Kangsheng Jia
- Research Center for the Qinling Giant Panda (Shaanxi Rare Wildlife Rescue Base), Shaanxi Academy of Forestry Sciences, Zhouzhi, Shaanxi, China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Center for Ruminant Genetic and Evolution, Northwest A&F University, Yangling, Shaanxi, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Research Center for the Qinling Giant Panda (Shaanxi Rare Wildlife Rescue Base), Shaanxi Academy of Forestry Sciences, Zhouzhi, Shaanxi, China
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Qiu J, Guo R, Li Y, Zhang Y, Jia K, Lei Y, Zan L, Li A. De Novo Transcriptome Assembly, Functional Annotation and SSR Marker Discovery of Qinling Takin ( Budorcas taxicolor bedfordi). Animals (Basel) 2021; 11:2366. [PMID: 34438823 PMCID: PMC8388659 DOI: 10.3390/ani11082366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/08/2021] [Accepted: 08/09/2021] [Indexed: 11/17/2022] Open
Abstract
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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Affiliation(s)
- Ju Qiu
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (J.Q.); (R.G.); (Y.L.); (Y.Z.); (L.Z.)
| | - Rui Guo
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (J.Q.); (R.G.); (Y.L.); (Y.Z.); (L.Z.)
| | - Yidan Li
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (J.Q.); (R.G.); (Y.L.); (Y.Z.); (L.Z.)
| | - Yuyao Zhang
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (J.Q.); (R.G.); (Y.L.); (Y.Z.); (L.Z.)
| | - Kangsheng Jia
- Research Center for the Qinling Giant Panda (Shaanxi Rare Wildlife Rescue Base), Shaanxi Academy of Forestry, Xi'an 710402, China; (K.J.); (Y.L.)
| | - Yinghu Lei
- Research Center for the Qinling Giant Panda (Shaanxi Rare Wildlife Rescue Base), Shaanxi Academy of Forestry, Xi'an 710402, China; (K.J.); (Y.L.)
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (J.Q.); (R.G.); (Y.L.); (Y.Z.); (L.Z.)
- Research Center for the Qinling Giant Panda (Shaanxi Rare Wildlife Rescue Base), Shaanxi Academy of Forestry, Xi'an 710402, China; (K.J.); (Y.L.)
| | - Anning Li
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (J.Q.); (R.G.); (Y.L.); (Y.Z.); (L.Z.)
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Marinkovich M, Wisner ER, Brenner DJ. DISTAL LIMB SWELLING AND PERIOSTEAL PRODUCTIVE REACTION IN PERIPARTURIENT SICHUAN TAKIN ( BUDORCAS TAXICOLOR TIBETANA): FIVE CASES OF PRESUMPTIVE HYPERTROPHIC OSTEOPATHY. J Zoo Wildl Med 2019; 50:437-46. [PMID: 31260211 DOI: 10.1638/2018-0174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2019] [Indexed: 11/21/2022] Open
Abstract
Hypertrophic osteopathy, a syndrome characterized by painful distal limb swelling and proliferative periosteal reaction, primarily involves the metacarpal and metatarsal bones and phalanges. Lesions are often bilaterally symmetric and typically affect all four limbs. Hypertrophic osteopathy is frequently associated with primary intrathoracic disease, though this condition has also been reported secondary to intra-abdominal and intrapelvic disease and associated with pregnancy in both people and horses. Over a 20-yr period, five adult female Sichuan takin (Budorcas taxicolor tibetana), with 13 total pregnancies, were evaluated because of lameness and distal limb swelling. These clinical signs were observed between 2 and 32 days (mean = 19 days) prior to parturition (gestation period in takin approximately 200-240 days) and resolved in all animals following parturition. Lameness and limb swelling resolved between 8 and 168 days (median = 15 days) after parturition. Sixteen radiographic examinations, from four of the individuals, documented proliferative periosteal reaction, primarily of the metacarpal bones, metatarsal bones, and phalanges. The clinical progression, resolution of signs, and radiographic features in these cases are consistent with hypertrophic osteopathy, secondary to pregnancy. This is the first report describing presumptive hypertrophic osteopathy in takin.
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