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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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Jiménez R, Burgos M, Barrionuevo FJ. The Biology and Evolution of Fierce Females (Moles and Hyenas). Annu Rev Anim Biosci 2023; 11:141-162. [PMID: 36130099 DOI: 10.1146/annurev-animal-050622-043424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Talpid moles and spotted hyenas have become the paradigms of anatomical and behavioral female masculinization. Females of many mole species develop ovotestes that produce testosterone, show external genitalia that resemble that of males, and close their vaginal orifice after every estrus, and female spotted hyenas lack an external vaginal orifice and develop a pseudoscrotum and a large pseudopenis through which they urinate, mate, and give birth. We review current knowledge about several significant aspects of the biology and evolution of these females, including (a) their specific study methods; (b) their unique anatomical features, and how these peculiarities influence certain physiological functions; and (c) the role that steroid hormones as well as genetic and environmental factors may have in urogenital system development, aggressive behavior, and social dominance. Nevertheless, both mole and hyena females are exceptionally efficient mothers, so their peculiar genitalia should not call into question their femininity.
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Affiliation(s)
- Rafael Jiménez
- Department of Genetics, Institute of Biotechnology, and Center of Biomedical Research (CIBM), University of Granada, Armilla, Granada, Spain; , ,
| | - Miguel Burgos
- Department of Genetics, Institute of Biotechnology, and Center of Biomedical Research (CIBM), University of Granada, Armilla, Granada, Spain; , ,
| | - Francisco J Barrionuevo
- Department of Genetics, Institute of Biotechnology, and Center of Biomedical Research (CIBM), University of Granada, Armilla, Granada, Spain; , ,
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3
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Shao Y, Wang XB, Zhang ML, Liu Y, Wang S, Zhang BL, Yang MM, Yang MH, Jia T, Pu TC, Lu Y, Liu H, Xu Z, Li B, Liu N, Onsongo VM, Wu DD, Zhang CL, Ruan J, Li Y. Long-read genome sequencing provides molecular insights into scavenging and societal complexity in spotted hyena Crocuta crocuta. Mol Biol Evol 2022; 39:6509522. [PMID: 35038730 PMCID: PMC8890499 DOI: 10.1093/molbev/msac011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The spotted hyena (Crocuta crocuta) is a large and unique terrestrial carnivore. It is a particularly fascinating species due to its distinct phenotypic traits, especially its complex social structure and scavenging lifestyle, with associated high dietary exposure to microbial pathogens. However, the underlying molecular mechanisms related to these phenotypes remain elusive. Here, we sequenced and assembled a high-quality long-read genome of the spotted hyena, with a contig N50 length of ∼13.75 Mb. Based on comparative genomics, immunoglobulin family members (e.g., IGKV4-1) showed significant adaptive duplications in the spotted hyena and striped hyena. Furthermore, immune-related genes (e.g., CD8A, LAG3, and TLR3) experienced species-specific positive selection in the spotted hyena lineage. These results suggest that immune tolerance between the spotted hyena and closely related striped hyena has undergone adaptive divergence to cope with prolonged dietary exposure to microbial pathogens from scavenging. Furthermore, we provided the potential genetic insights underlying social complexity, hinting at social behavior and cognition. Specifically, the RECNE-associated genes (e.g., UGP2 and ACTR2) in the spotted hyena genome are involved in regulation of social communication. Taken together, our genomic analyses provide molecular insights into the scavenging lifestyle and societal complexity of spotted hyenas.
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Affiliation(s)
- Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Xiao-Bo Wang
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Mei-Ling Zhang
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Yan Liu
- Beijing Zoo, Beijing, 100044, China
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Min-Min Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | | | - Ting Jia
- Beijing Zoo, Beijing, 100044, China
| | | | - Yan Lu
- Beijing Zoo, Beijing, 100044, China
| | - He Liu
- Beijing Zoo, Beijing, 100044, China
| | - Zhe Xu
- Beijing Zoo, Beijing, 100044, China
| | - Bo Li
- Beijing Zoo, Beijing, 100044, China
| | - Ning Liu
- Beijing Zoo, Beijing, 100044, China
| | - Violet Magoma Onsongo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | | | - Jue Ruan
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yan Li
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
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Wagner F, Ruf I, Lehmann T, Hofmann R, Ortmann S, Schiffmann C, Hiller M, Stefen C, Stuckas H. Reconstruction of evolutionary changes in fat and toxin consumption reveals associations with gene losses in mammals: a case study for the lipase inhibitor PNLIPRP1 and the xenobiotic receptor NR1I3. J Evol Biol 2021; 35:225-239. [PMID: 34882899 DOI: 10.1111/jeb.13970] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 11/28/2022]
Abstract
The inactivation of ancestral protein-coding genes (gene loss) can be associated with phenotypic modifications. Within placental mammals, repeated losses of PNLIPRP1 (gene inhibiting fat digestion) occurred preferentially in strictly herbivorous species, while repeated NR1I3 losses (gene involved in detoxification) occurred preferentially in strictly carnivorous species. It was hypothesized that lower fat contents of herbivorous diets and lower toxin contents of carnivorous diets cause relaxed selection pressure on these genes resulting in the accumulation of mutations and ultimately to convergent gene losses. However, since herbivorous and carnivorous diets differ vastly in their composition, a fine-grained analysis is required for hypothesis testing. We generated a trait matrix recording diet and semi-quantitative estimates of fat and toxin consumption for 52 placental species. By including data from 31 fossil taxa, we reconstructed the ancestral diets in major lineages (grundplan reconstruction). We found support that PNLIPRP1 loss is primarily associated with low levels of fat intake and not simply with herbivory/carnivory. In particular, PNLIPRP1 loss also occurred in carnivorous lineages feeding on a fat-poor diet, suggesting that the loss of this gene may be beneficial for occupying ecological niches characterized by fat-poor food resources. Similarly, we demonstrated that carnivorous species are indeed less exposed to diet-related toxins suggesting that the loss of NR1I3 and related genes (NR1I2, UGT1A6) resulted from relaxed selection pressure. This study illustrates the need of detailed phenotype studies to obtain a deeper understanding of factors underlying gene losses and to progress in understanding genomic causes of phenotypic variation in mammals.
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Affiliation(s)
- F Wagner
- Senckenberg, Leibniz Institution for Biodiversity and Earth System Research, Senckenberg Natural History Collections Dresden, Königsbrücker Landstraße 159, 01109, Dresden, Germany
| | - I Ruf
- Senckenberg, Leibniz Institution for Biodiversity and Earth System Research, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Goethe-University, Department of Geosciences, Altenöferallee 1, 60438, Frankfurt am Main, Germany
| | - T Lehmann
- Senckenberg, Leibniz Institution for Biodiversity and Earth System Research, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - R Hofmann
- Senckenberg, Leibniz Institution for Biodiversity and Earth System Research, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Goethe-University, Department of Geosciences, Altenöferallee 1, 60438, Frankfurt am Main, Germany
| | - S Ortmann
- Leibniz Institut für Zoo- und Wildtierforschung, Abteilung für Evolutionäre Ökologie, Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
| | - C Schiffmann
- Leibniz Institut für Zoo- und Wildtierforschung, Abteilung für Evolutionäre Ökologie, Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
| | - M Hiller
- Senckenberg, Leibniz Institution for Biodiversity and Earth System Research, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, 01187, Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307, Dresden, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Goethe University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - C Stefen
- Senckenberg, Leibniz Institution for Biodiversity and Earth System Research, Senckenberg Natural History Collections Dresden, Königsbrücker Landstraße 159, 01109, Dresden, Germany
| | - H Stuckas
- Senckenberg, Leibniz Institution for Biodiversity and Earth System Research, Senckenberg Natural History Collections Dresden, Königsbrücker Landstraße 159, 01109, Dresden, Germany
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