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Buthasane W, Shotelersuk V, Chetruengchai W, Srichomthong C, Assawapitaksakul A, Tangphatsornruang S, Pootakham W, Sonthirod C, Tongsima S, Wangkumhang P, Wilantho A, Thongphakdee A, Sanannu S, Poksawat C, Nipanunt T, Kasorndorkbua C, Koepfli KP, Pukazhenthi BS, Suriyaphol P, Wongsurawat T, Jenjaroenpun P, Suriyaphol G. Comprehensive genome assembly reveals genetic diversity and carcass consumption insights in critically endangered Asian king vultures. Sci Rep 2024; 14:9455. [PMID: 38658744 PMCID: PMC11043450 DOI: 10.1038/s41598-024-59990-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 04/17/2024] [Indexed: 04/26/2024] Open
Abstract
The Asian king vulture (AKV), a vital forest scavenger, is facing globally critical endangerment. This study aimed to construct a reference genome to unveil the mechanisms underlying its scavenger abilities and to assess the genetic relatedness of the captive population in Thailand. A reference genome of a female AKV was assembled from sequencing reads obtained from both PacBio long-read and MGI short-read sequencing platforms. Comparative genomics with New World vultures (NWVs) and other birds in the Family Accipitridae revealed unique gene families in AKV associated with retroviral genome integration and feather keratin, contrasting with NWVs' genes related to olfactory reception. Expanded gene families in AKV were linked to inflammatory response, iron regulation and spermatogenesis. Positively selected genes included those associated with anti-apoptosis, immune response and muscle cell development, shedding light on adaptations for carcass consumption and high-altitude soaring. Using restriction site-associated DNA sequencing (RADseq)-based genome-wide single nucleotide polymorphisms (SNPs), genetic relatedness and inbreeding status of five captive AKVs were determined, revealing high genomic inbreeding in two females. In conclusion, the AKV reference genome was established, providing insights into its unique characteristics. Additionally, the potential of RADseq-based genome-wide SNPs for selecting AKV breeders was demonstrated.
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Affiliation(s)
- Wannapol Buthasane
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Henri Dunant Road, Pathumwan, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Wanna Chetruengchai
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Henri Dunant Road, Pathumwan, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Henri Dunant Road, Pathumwan, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Adjima Assawapitaksakul
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Henri Dunant Road, Pathumwan, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Sissades Tongsima
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Pongsakorn Wangkumhang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Alisa Wilantho
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Ampika Thongphakdee
- Animal Conservation and Research Institute, The Zoological Park Organization of Thailand under the Royal Patronage of H.M. The King, Bangkok, 10300, Thailand
| | - Saowaphang Sanannu
- Animal Conservation and Research Institute, The Zoological Park Organization of Thailand under the Royal Patronage of H.M. The King, Bangkok, 10300, Thailand
| | - Chaianan Poksawat
- Animal Conservation and Research Institute, The Zoological Park Organization of Thailand under the Royal Patronage of H.M. The King, Bangkok, 10300, Thailand
| | - Tarasak Nipanunt
- Huai Kha Khaeng Wildlife Breeding Center, Department of National Parks, Wildlife and Plant Conservation, Uthai Thani, 61160, Thailand
| | - Chaiyan Kasorndorkbua
- Laboratory of Raptor Research and Conservation Medicine, Department of Pathology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, 10900, Thailand
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, 22630, USA
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA, 22630, USA
| | - Budhan S Pukazhenthi
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA, 22630, USA
| | - Prapat Suriyaphol
- Division of Medical Bioinformatics, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Thidathip Wongsurawat
- Division of Medical Bioinformatics, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Piroon Jenjaroenpun
- Division of Medical Bioinformatics, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Gunnaporn Suriyaphol
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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Adawaren EO, Labuschagne C, Abera A, Naidoo V. A premature stop codon in the CYP2C19 gene may explain the unexpected sensitivity of vultures to diclofenac toxicity. Toxicol Appl Pharmacol 2024; 482:116771. [PMID: 38013149 DOI: 10.1016/j.taap.2023.116771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 11/29/2023]
Abstract
The unintended environmental exposure of vultures to diclofenac has resulted in the deaths of millions of old-world vultures on the Asian subcontinent. While toxicity has been since associated with a long half-life of elimination and zero order metabolism, the actual constraint in biotransformation is yet to be clarified. For this study we evaluated if the evident zero order metabolism could be due to defects in the CYP2C9/2C19 enzyme system. For this, using whole genome sequencing and de-novo transcriptome alignment, the vulture CYP2C19 open reading frame was identified through Splign analysis. The result sequence analysis revealed the presence of a premature stop codon on intron 7 of the identified open reading frame. Even if the stop codon was not present, amino acid residue analysis tended to suggest that the enzyme would be lower in activity than the equivalent human enzyme, with differences present at sites 105, 286 and 289. The defect was also conserved across the eight non-related vultures tested. From these results, we conclude that the sensitivity of the old-world vultures to diclofenac is due to the non-expression of a viable CYP2C19 enzyme system. This is not too dissimilar to the effects seen in certain people with a similar defective enzyme.
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Affiliation(s)
- Emmanuel Oluwasegun Adawaren
- Department of Paraclinical Science, Faculty of Veterinary Science, University of Pretoria, Gauteng, South Africa
| | - Christiaan Labuschagne
- Iqaba Biotechnical Industries (Pty), 525 Justice Mahomed St, Muckleneuk, 0002 Pretoria, Gauteng, South Africa
| | - Aron Abera
- Iqaba Biotechnical Industries (Pty), 525 Justice Mahomed St, Muckleneuk, 0002 Pretoria, Gauteng, South Africa
| | - Vinny Naidoo
- Department of Paraclinical Science, Faculty of Veterinary Science, University of Pretoria, Gauteng, South Africa.
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3
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Hu L, Long J, Lin Y, Gu Z, Su H, Dong X, Lin Z, Xiao Q, Batbayar N, Bold B, Deutschová L, Ganusevich S, Sokolov V, Sokolov A, Patel HR, Waters PD, Graves JAM, Dixon A, Pan S, Zhan X. Arctic introgression and chromatin regulation facilitated rapid Qinghai-Tibet Plateau colonization by an avian predator. Nat Commun 2022; 13:6413. [PMID: 36302769 PMCID: PMC9613686 DOI: 10.1038/s41467-022-34138-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 10/14/2022] [Indexed: 12/25/2022] Open
Abstract
The Qinghai-Tibet Plateau (QTP), possesses a climate as cold as that of the Arctic, and also presents uniquely low oxygen concentrations and intense ultraviolet (UV) radiation. QTP animals have adapted to these extreme conditions, but whether they obtained genetic variations from the Arctic during cold adaptation, and how genomic mutations in non-coding regions regulate gene expression under hypoxia and intense UV environment, remain largely unknown. Here, we assemble a high-quality saker falcon genome and resequence populations across Eurasia. We identify female-biased hybridization with Arctic gyrfalcons in the last glacial maximum, that endowed eastern sakers with alleles conveying larger body size and changes in fat metabolism, predisposing their QTP cold adaptation. We discover that QTP hypoxia and UV adaptations mainly involve independent changes in non-coding genomic variants. Our study highlights key roles of gene flow from Arctic relatives during QTP hypothermia adaptation, and cis-regulatory elements during hypoxic response and UV protection.
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Affiliation(s)
- Li Hu
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Juan Long
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Yi Lin
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Zhongru Gu
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China
| | - Han Su
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Xuemin Dong
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Zhenzhen Lin
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China
| | - Qian Xiao
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China ,grid.20513.350000 0004 1789 9964Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, 100875 Beijing, China
| | - Nyambayar Batbayar
- Wildlife Science and Conservation Center, Union Building B-802, Ulaanbaatar, 14210 Mongolia
| | - Batbayar Bold
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China ,Wildlife Science and Conservation Center, Union Building B-802, Ulaanbaatar, 14210 Mongolia
| | - Lucia Deutschová
- grid.455051.0Raptor Protection of Slovakia, Trhová 54, SK-841 01, Bratislava, Slovakia
| | - Sergey Ganusevich
- Wild Animal Rescue Centre, Krasnostudencheskiy pr., 21-45, Moscow, 125422 Russia
| | - Vasiliy Sokolov
- grid.426536.00000 0004 1760 306XInstitute of Plant and Animal Ecology, Ural Division Russian Academy of Sciences, 202-8 Marta Street, Ekaterinburg, 620144 Russia
| | - Aleksandr Sokolov
- Arctic Research Station of the Institute of Plant and Animal Ecology, Ural Division Russian Academy of Sciences, 21 Zelenaya Gorka, Labytnangi, Yamalo-Nenetski District 629400 Russia
| | - Hardip R. Patel
- grid.1001.00000 0001 2180 7477The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601 Australia
| | - Paul D. Waters
- grid.1005.40000 0004 4902 0432School of Biotechnology and Biomolecular Science, Faculty of Science, UNSW Sydney, Sydney, NSW 2052 Australia
| | | | - Andrew Dixon
- Emirates Falconers’ Club, Al Mamoura Building (A), P.O. Box 47716, Muroor Road, Abu Dhabi, UAE ,grid.511767.30000 0004 5895 0922International Wildlife Consultants, P.O. Box 19, Carmarthen, SA33 5YL UK
| | - Shengkai Pan
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China
| | - Xiangjiang Zhan
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China ,grid.9227.e0000000119573309Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223 China
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