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Chakraborty A, Bisht MS, Saxena R, Mahajan S, Pulikkan J, Sharma VK. Genome sequencing and de novo and reference-based genome assemblies of Bos indicus breeds. Genes Genomics 2023; 45:1399-1408. [PMID: 37231295 DOI: 10.1007/s13258-023-01401-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023]
Abstract
BACKGROUND Indian cattle breeds (Bos indicus) are known for their remarkable adaptability to hot and humid climates, higher nutritious quality of milk, better disease tolerance, and greater ability to perform in poor feed compared to taurine cattle (Bos taurus). Distinct phenotypic differences are observed among the B. indicus breeds; however, the whole genome sequences were unavailable for these indigenous breeds. OBJECTIVE We aimed to perform whole genome sequencing to construct the draft genome assemblies of four B. indicus breeds; Ongole, Kasargod Dwarf, Kasargod Kapila, and Vechur (the smallest cattle of the world). METHODS We sequenced the whole genomes using Illumina short-read technology, and constructed de novo and reference-based genome assemblies of these native B. indicus breeds for the first time. RESULTS The draft de novo genome assemblies of B. indicus breeds ranged from 1.98 to 3.42 Gbp. We also constructed the mitochondrial genome assemblies (~ 16.3 Kbp), and yet unavailable 18S rRNA marker gene sequences of these B. indicus breeds. The genome assemblies helped to identify the bovine genes related to distinct phenotypic characteristics and other biological processes for this species compared to B. taurus, which are plausibly responsible for providing better adaptive traits. We also identified the genes that showed sequence variation in dwarf and non-dwarf breeds of B. indicus compared to B. taurus. CONCLUSIONS The genome assemblies of these Indian cattle breeds, the 18S rRNA marker genes, and identification of the distinct genes in B. indicus breeds compared to B. taurus will help in future studies on these cattle species.
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Affiliation(s)
- Abhisek Chakraborty
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Manohar S Bisht
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Rituja Saxena
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Shruti Mahajan
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Joby Pulikkan
- Department of Genomic Science, Central University of Kerala, Kasaragod, India
| | - Vineet K Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India.
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Li G, Wei X, Chen S, Li R, Zhou S, Li W, Lin Y, Yosri M, Hanif Q, Ma Z. Characterization of whole mitogenome sequence of the Tongde yak ( Bos grunniens). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2498-2500. [PMID: 34377805 PMCID: PMC8330789 DOI: 10.1080/23802359.2021.1958082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Tongde County is located in the southeast of Qinghai Province, China, harboring rich yak genetic resources. In the present study, the complete mitochondrial genome (mitogenome) of the Tongde yak (Bos grunniens) was firstly sequenced using Illumina sequencing technique and the corresponding sequence characterization was identified. Our results showed that the mitogenome of Tongde yak is a circular molecule with 16,323 bp length consisting of 37 genes (13 protein-coding genes, 2 rRNA genes, 22 tRNA genes) and a non-coding control region (D-loop), which is consistent with most bovine species. The overall nucleotide composition was found as: A (33.72%), T (27.27%), C (25.80%), and G (13.21%), respectively, yielding a higher AT content (60.99%). The complete mitogenome sequence of Tongde yak would provide useful information for further studies on its genetic resource conservation and molecular breeding programmes in the future.
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Affiliation(s)
- Guangzhen Li
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China.,Key Laboratory of Plateau Livestock Genetic Resources Protection and Innovative Utilization, Xining, China
| | - Xudong Wei
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China.,Key Laboratory of Plateau Livestock Genetic Resources Protection and Innovative Utilization, Xining, China
| | - Shengmei Chen
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China.,Key Laboratory of Plateau Livestock Genetic Resources Protection and Innovative Utilization, Xining, China
| | - Ruizhe Li
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China.,Key Laboratory of Plateau Livestock Genetic Resources Protection and Innovative Utilization, Xining, China
| | - Sangjia Zhou
- Agriculture, Animal husbandry and Water Conservancy Bureau of Tongde County in Qinghai Province, Tongde, China
| | - Wenhao Li
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China.,Key Laboratory of Plateau Livestock Genetic Resources Protection and Innovative Utilization, Xining, China
| | - Yuan Lin
- Agriculture, Animal husbandry and Water Conservancy Bureau of Tongde County in Qinghai Province, Tongde, China
| | - Mohammed Yosri
- The Regional center for Mycology and Biotechnology, Al Azhar University, Cairo, Egypt
| | - QuratulAin Hanif
- Animal Genomics Lab, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Zhijie Ma
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China.,Key Laboratory of Plateau Livestock Genetic Resources Protection and Innovative Utilization, Xining, China
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Pacha AS, Nigam P, Pandav B, Mondol S. Sequencing and annotation of the endangered wild buffalo (Bubalus arnee) mitogenome for taxonomic assessment. Mol Biol Rep 2021; 48:1995-2003. [PMID: 33527322 DOI: 10.1007/s11033-021-06165-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 01/15/2021] [Indexed: 11/28/2022]
Abstract
The wild water buffalo (Bubalus arnee) is one of the most endangered and least studied large bovid in the Indian subcontinent. India retains 90% of the estimated global population of >4000 individuals as two fragmented populations in Assam and Chhattisgarh, both threatened by habitat loss and degradation, hunting, disease from livestock, and hybridization with the domestic buffalos. Small, fragmented population size and potential hybridisation pressures from co-occurring domestic buffalos are the major conservation challenges. For the first time, we sequenced the 16,357 bp long mitogenome of three opportunistically collected wild water buffalo samples from Assam (n = 1) and Chhattishgarh (n = 2). The annotated sequence has a base composition of 26.4% T, 26.6% C, 33.1% A and 13.9% G depicting an AT-rich mitogenome composition, including 13 protein-coding genes (11,361 bp), 22 transfer RNA (tRNA) (1514 bp), two ribosomal genes (2525 bp), and a non-coding control region (928 bp). The gene order is conserved with other bovid species. Comparative mitogenome analyses showed both populations are genetically similar but significantly different from domestic buffalo. We also identified structural differences in seven tRNA secondary structures between both species. The genetic distance between wild buffalo and other bovids varied between 0.103 and 0.122. Multiple Bayesian phylogenetic trees showed that both wild and domestic water buffalo formed sister clades which were paraphyletic to other potentially sympatric species of genus Bos. This study provides baseline information on wild buffalo mitogenome for further research on phylogeny, phylogeography and hybrid assessment and help conserving this endangered species.
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Affiliation(s)
| | - Parag Nigam
- Wildlife Institute of India, Chandrabani, Dehradun, 248001, India
| | - Bivash Pandav
- Wildlife Institute of India, Chandrabani, Dehradun, 248001, India
| | - Samrat Mondol
- Wildlife Institute of India, Chandrabani, Dehradun, 248001, India.
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Xia X, Huang G, Wang Z, Sun J, Wu Z, Chen N, Lei C, Hanif Q. Mitogenome Diversity and Maternal Origins of Guangxi Cattle Breeds. Animals (Basel) 2019; 10:E19. [PMID: 31861849 PMCID: PMC7022393 DOI: 10.3390/ani10010019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/14/2019] [Accepted: 12/18/2019] [Indexed: 01/16/2023] Open
Abstract
Guangxi Province is located in the southernmost region of China, adjacent to the hotspot that is considered to be the putative migratory corridor or domestication area for Chinese indicine cattle. Here, we investigated the evolutionary status of Guangxi native breeds, Longlin (n = 21), Nandan (n = 18), and Weizhou cattle (n = 17) using mitogenome sequencing. Our results show that Bos indicus sub-haplogroup I1a predominates in Guangxi cattle breeds. Population structure by multidimensional-scaling analysis significantly differentiates Weizhou from the other two breeds (Longlin and Nandan). Moreover, the mtDNA haplotype composition and FST values indicate that the formation of Longlin and Nandan breeds may have been affected by Indian indicine, whereas, Weizhou island might have preserved pure Chinese indicine cattle due to its geographical isolation. We speculate that following the initial entry of zebu into southern China, the subsequent introgression of Indian indicine may have influenced the matrilineal origin of local breeds in southwestern China.
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Affiliation(s)
- Xiaoting Xia
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China; (X.X.); (G.H.); (Z.W.); (J.S.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (N.C.); (C.L.)
| | - Guangyun Huang
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China; (X.X.); (G.H.); (Z.W.); (J.S.)
| | - Zihao Wang
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China; (X.X.); (G.H.); (Z.W.); (J.S.)
| | - Junli Sun
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China; (X.X.); (G.H.); (Z.W.); (J.S.)
| | - Zhuyue Wu
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China; (X.X.); (G.H.); (Z.W.); (J.S.)
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (N.C.); (C.L.)
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (N.C.); (C.L.)
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering, Pakistan Institute of Engineering and Applied Sciences, Faisalabad 577, Pakistan;
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Sharma A, Shandilya UK, Sodhi M, Mohanty AK, Jain P, Mukesh M. Evaluation of Milk Colostrum Derived Lactoferrin of Sahiwal ( Bos indicus) and Karan Fries (Cross-Bred) Cows for Its Anti-Cancerous Potential. Int J Mol Sci 2019; 20:E6318. [PMID: 31847364 PMCID: PMC6940737 DOI: 10.3390/ijms20246318] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/26/2019] [Accepted: 10/30/2019] [Indexed: 01/01/2023] Open
Abstract
Lactoferrin (Lf) is an iron-binding glycoprotein protein known to have immune-modulatory role and recently, its anticancerous effect against different cancer cell types was emphasized. In the present investigation, a comparative evaluation of anticancer potential of colostrum-derived lactoferrin from Indian native zebu cow (Sahiwal, SAC), crossbred (Karan Fries, KFC) and commercially available (C-Lf) lactoferrin from exotic cow using cellular models was made. A protocol was standardized successfully to purify Lf protein from colostrum of both breeds using HPLC and purity was confirmed by LC-MS. A standardized dose of 750 µg/mL Lf was used to treat two cell types MDA-MB-231 and MCF-7 with Lf from three different sources; SAC-Lf, KFC-Lf and C-Lf for 48 h and 72 h. Different cellular parameters including cytotoxicity, viability, apoptosis and cell proliferation were determined. Comparatively, Lf from commercial source (C-Lf) had maximum effect in both cell types followed by SAC-Lf and KFC-Lf. Further, transcriptional changes in genes associated with apoptosis (Bax and Bcl-2), tumor progression (p53, p21, CD44 and NF-κβ) and survival (survivin) were evaluated in Lf treatment. The overall results strongly emphasized to the fact that Lf purified from cow colostrum has the capacity to inhibit the in vitro growth of cancerous cell lines albeit to a varied extent.
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Affiliation(s)
- Ankita Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, India; (A.S.); (U.K.S.); (M.S.)
- University Institute of Engineering and Technology, Kurukshetra University, Kurukshetra 136118, India;
- Department of Animal Biosceinces, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Umesh K Shandilya
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, India; (A.S.); (U.K.S.); (M.S.)
- Department of Animal Biosceinces, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Monika Sodhi
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, India; (A.S.); (U.K.S.); (M.S.)
| | - Ashok K Mohanty
- ICAR-National Dairy Research Institute, Karnal, Haryana 132001, India;
| | - Pranay Jain
- University Institute of Engineering and Technology, Kurukshetra University, Kurukshetra 136118, India;
| | - Manishi Mukesh
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, India; (A.S.); (U.K.S.); (M.S.)
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Pramod RK, Velayutham D, P K S, P S B, Zachariah A, Zachariah A, B C, S S S, P G, Dhinoth Kumar B, Iype S, Gupta R, Santhosh S, Thomas G. Complete mitogenome reveals genetic divergence and phylogenetic relationships among Indian cattle ( Bos indicus) breeds. Anim Biotechnol 2018; 30:219-232. [PMID: 29938580 DOI: 10.1080/10495398.2018.1476376] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Indigenous cattle of India belong to the species, Bos indicus and they possess various adaptability and production traits. However, little is known about the genetic diversity and origin of these breeds. To investigate the status, we sequenced and analyzed the whole mitochondrial DNA (mtDNA) of seven Indian cattle breeds. In total, 49 single-nucleotide variants (SNVs) were identified among the seven breeds analyzed. We observed a common synonymous SNV in the COII gene (m.7583G > A) of all the breeds studied. The phylogenetic analysis and genetic distance estimation showed the close genetic relationship among the Indian cattle breeds, whereas distinct genetic differences were observed between Bos indicus and Bos taurus cattle. Our results indicate a common ancestor for European Zwergzebu breed and South Indian cattle. The estimated divergence time demonstrated that the Bos indicus and Bos taurus cattle lineages diverged 0.92 million years ago. Our study also demonstrates that ancestors of present zebu breeds originated in South and North India separately ∼30,000 to 20,000 years ago. In conclusion, the identified genetic variants and results of the phylogenetic analysis may provide baseline information to develop appropriate strategies for management and conservation of Indian cattle breeds.
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Affiliation(s)
| | | | - Sajesh P K
- a AgriGenome Labs Pvt. Ltd., Smart City Kochi , India
| | - Beena P S
- a AgriGenome Labs Pvt. Ltd., Smart City Kochi , India
| | | | - Arun Zachariah
- c Department of Forest and Wildlife , Wayanad , Kerala , India
| | - Chandramohan B
- d National Institute of Science Education and Research , Jatni , India
| | - Sujith S S
- a AgriGenome Labs Pvt. Ltd., Smart City Kochi , India
| | - Ganapathi P
- e Bargur Cattle Research Station, Tamil Nadu Veterinary Animal Sciences University , Chennai , India
| | | | | | - Ravi Gupta
- f Medgenome Labs Pvt. Ltd. , Narayana Health City , Bommasandra , Bengaluru , India
| | - Sam Santhosh
- g SciGenom Research Foundation , Cheruthuruthy , India
| | - George Thomas
- g SciGenom Research Foundation , Cheruthuruthy , India
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