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Adeola AC, Luka PD, Jiang XX, Cai ZF, Oluwole OO, Shi X, Oladele BM, Olorungbounmi TO, Boladuro B, Omotosho O, Okoro VMO, Dawuda PM, Olaogun SC, Sanke OJ, Xie HB, Bishop RP, Han J, Li J, Zhang YP, Peng MS. Target capture sequencing for the first Nigerian genotype I ASFV genome. Microb Genom 2023; 9:mgen001069. [PMID: 37489884 PMCID: PMC10438811 DOI: 10.1099/mgen.0.001069] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/20/2023] [Indexed: 07/26/2023] Open
Abstract
African swine fever (ASF) is a contagious viral disease that affects domestic pigs and wild boars, causing significant economic losses globally. After the first Nigerian outbreak in 1997, there have been frequent reports of ASF in pig-producing regions in the country. To facilitate control, it is important to understand the genotype and phylogenetic relationship of ASF viruses (ASFVs). Recent genetic analysis of Nigerian ASFV isolates has revealed the presence of both genotypes I and II; this is based on analysis of a few selected genes. Phylogenetic analysis of ASFV whole genomes highlights virus origins and evolution in greater depth. However, there is currently no information on the ASFV genome from Nigerian isolates. Two ASFV-positive samples were detected during a random survey of 150 Nigerian indigenous pig samples collected in 2016. We assembled near-complete genomes of the two ASFV-positive samples using in-solution hybrid capture sequencing. The genome-wide phylogenetic tree assigned these two genomes into p72 genotype I, particularly close to the virulent Benin 97/1 strain. The two ASFVs share 99.94 and 99.92 % genomic sequence identity to Benin97/1. This provides insight into the origin and relationship of ASFV strains from Nigeria and Italy. The study reports for the first time the determination of near-complete genomes of ASFV using in-solution hybrid capture sequencing, which represents an important advance in understanding the global evolutionary landscape of ASFVs.
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Affiliation(s)
- Adeniyi C. Adeola
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China
- Sino‐Africa Joint Research Center, Chinese Academy of Sciences, Kunming, PR China
- Centre for Biotechnology Research, Bayero University, Kano, Nigeria
| | - Pam D. Luka
- National Veterinary Research Institute, Vom, Nigeria
| | - Xiang-Xiang Jiang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China
- College of Life Sciences, Anhui Normal University, Wuhu, PR China
| | - Zheng-Fei Cai
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, PR China
| | - Olufunke O. Oluwole
- Institute of Agricultural Research and Training, Obafemi Awolowo University, Ibadan, Nigeria
| | - Xian Shi
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, PR China
| | - Bukola M. Oladele
- Institute of Agricultural Research and Training, Obafemi Awolowo University, Ibadan, Nigeria
| | | | - Bamidele Boladuro
- Institute of Agricultural Research and Training, Obafemi Awolowo University, Ibadan, Nigeria
| | - Oladipo Omotosho
- Department of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Victor M. O. Okoro
- Department of Animal Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
| | - Philip M. Dawuda
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture Makurdi, Makurdi, Nigeria
| | - Sunday C. Olaogun
- Department of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oscar J. Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria
| | - Hai-Bing Xie
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China
| | | | - Jianlin Han
- International Livestock Research Institute (ILRI), Nairobi, Kenya
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science Chinese Academy of Agricultural Sciences(CAAS), Beijing, PR China
| | - Jianbo Li
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China
- Sino‐Africa Joint Research Center, Chinese Academy of Sciences, Kunming, PR China
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, PR China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, PR China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China
- Sino‐Africa Joint Research Center, Chinese Academy of Sciences, Kunming, PR China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, PR China
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Adeola AC, Oluwole OO, Oladele BM, Olorungbounmi TO, Boladuro B, Olaogun SC, Nneji LM, Sanke OJ, Dawuda PM, Omitogun OG, Frantz L, Murphy RW, Xie HB, Peng MS, Zhang YP. Analysis of the genetic variation in mitochondrial DNA, Y-chromosome sequences, and MC1R sheds light on the ancestry of Nigerian indigenous pigs. Genet Sel Evol 2017. [PMID: 28651519 PMCID: PMC5485568 DOI: 10.1186/s12711-017-0326-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background The history of pig populations in Africa remains controversial due to insufficient evidence from archaeological and genetic data. Previously, a Western ancestry for West African pigs was reported based on loci that are involved in the determination of coat color. We investigated the genetic diversity of Nigerian indigenous pigs (NIP) by simultaneously analyzing variation in mitochondrial DNA (mtDNA), Y-chromosome sequence and the melanocortin receptor 1 (MC1R) gene. Results Median-joining network analysis of mtDNA D-loop sequences from 201 NIP and previously characterized loci clustered NIP with populations from the West (Europe/North Africa) and East/Southeast Asia. Analysis of partial sequences of the Y-chromosome in 57 Nigerian boars clustered NIP into lineage HY1. Finally, analysis of MC1R in 90 NIP resulted in seven haplotypes, among which the European wild boar haplotype was carried by one individual and the European dominant black by most of the other individuals (93%). The five remaining unique haplotypes differed by a single synonymous substitution from European wild type, European dominant black and Asian dominant black haplotypes. Conclusions Our results demonstrate a European and East/Southeast Asian ancestry for NIP. Analyses of MC1R provide further evidence. Additional genetic analyses and archaeological studies may provide further insights into the history of African pig breeds. Our findings provide a valuable resource for future studies on whole-genome analyses of African pigs. Electronic supplementary material The online version of this article (doi:10.1186/s12711-017-0326-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Olufunke O Oluwole
- Institute of Agricultural Research and Training, Obafemi Awolowo University, Ibadan, Nigeria
| | - Bukola M Oladele
- Institute of Agricultural Research and Training, Obafemi Awolowo University, Ibadan, Nigeria
| | | | - Bamidele Boladuro
- Institute of Agricultural Research and Training, Obafemi Awolowo University, Ibadan, Nigeria
| | - Sunday C Olaogun
- Department of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Lotanna M Nneji
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria
| | - Philip M Dawuda
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture Makurdi, Makurdi, Nigeria
| | - Ofelia G Omitogun
- Department of Animal Sciences, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Laurent Frantz
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology, University of Oxford, Oxford, UK.,School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Canada
| | - Hai-Bing Xie
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. .,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. .,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China. .,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.
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