1
|
Sun Y, Zeng Y, Rajput IR, Sanganyado E, Zheng R, Xie H, Li C, Tian Z, Huang Y, Yang L, Lin J, Li P, Liang B, Liu W. Interspecies differences in mammalian susceptibility to legacy POPs and trace metals using skin fibroblast cells. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 315:120358. [PMID: 36228850 DOI: 10.1016/j.envpol.2022.120358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/23/2022] [Accepted: 10/02/2022] [Indexed: 06/16/2023]
Abstract
The susceptibility to trace metals and legacy POPs is different between terrestrial and marine mammals. In this study, we established the first cell line from Indo-Pacific finless porpoises and compared the cellular responses of skin fibroblast cells from Pygmy killer whales, Pantropic spotted dolphins, Indo-Pacific finless porpoises, mice, and humans following exposure to copper, methylmercury, cadmium, PCB126, PCB153, and BDE47 to better understand the interspecies sensitivities of mammals to chemical pollutants. We conducted a risk assessment by comparing no-observed effect concentrations (NOEC), lowest-observed effect concentrations (LOEC), and half maximal effective concentrations (EC50) from cell viability assays and previously reported pollutant body burdens in mammals. Based on the in vitro data, Indo-Pacific finless porpoises were more sensitive to copper and methylmercury than other mammals. PCB153 exposure reduced cell viability in all mammals except humans, while PCB126 was more potent, with 13.33 μg/mL exposure reducing cell viability in all mammals. In contrast, BDE47 exposure reduced cell viability only in terrestrial mammals in addition to pantropic spotted dolphin. Based on the in vitro data and the natural context of metal concentrations, both methylmercury and cadmium posed a higher risk to cetaceans than human, while copper posed a lower risk to cetaceans. All three legacy POPs (PCB126, PCB153, and BDE47) posed minor risk to cetaceans for short-term exposure. This study demonstrated that a species-specific in vitro model may provide more accurate information on the potential risk of pollutants to mammals. However, due to the bioamplification of POPs and their potential impact on the endocrine system and immune system of cetaceans, risk assessment with long-term exposure with more in vitro models should be further studied.
Collapse
Affiliation(s)
- Yajing Sun
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou, Guangdong, 515063, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Ying Zeng
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou, Guangdong, 515063, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Imran Rashid Rajput
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou, Guangdong, 515063, China; Faculty of Veterinary and Animal Science, Department of Biotechnology, Lasbela University of Agriculture Water and Marine Science, 89250, Uthal, Balochistan, Pakistan
| | - Edmond Sanganyado
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou, Guangdong, 515063, China; Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne, NE2 4PB, UK
| | - Ruiqiang Zheng
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou, Guangdong, 515063, China; China Blue Sustainability Institute, Haikou, Hainan, 570208, China
| | - Huiying Xie
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou, Guangdong, 515063, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Chengzhang Li
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou, Guangdong, 515063, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Ziyao Tian
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou, Guangdong, 515063, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Ying Huang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou, Guangdong, 515063, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Liangliang Yang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou, Guangdong, 515063, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Jianqing Lin
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou, Guangdong, 515063, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Ping Li
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou, Guangdong, 515063, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Bo Liang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou, Guangdong, 515063, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
| | - Wenhua Liu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou, Guangdong, 515063, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| |
Collapse
|
2
|
The Landscape of Genome-Wide and Gender-Specific Microsatellites in Indo-Pacific Humpback Dolphin and Potential Applications in Cetacean Resource Investigation. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10060834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Microsatellites are one of the important genome characterizations that can be a valuable resource for variety identification, genetic diversity, phylogenetic analysis, as well as comparative and conservation genomics research. Here, we developed comprehensive microsatellites through genome-wide mining for the threatened cetacean Indo-Pacific humpback dolphin (Sousa chinensis). We found 87,757 microsatellites with 2–6 bp nucleotide motifs, showing that about 32.5 microsatellites per megabase comprises microsatellites sequences. Approximately 97.8% of the markers developed in this study were consistent with the published identified markers. About 75.3% microsatellites were with dinucleotide motifs, followed by tetranucleotide motifs (17.4%), sharing the same composition pattern as other cetaceans. The microsatellites were not evenly distributed in the S. chinensis genome, mainly in non-coding regions, with only about 0.5% of the markers located in coding regions. The microsatellite-containing genes were mainly functionally enriched in the methylation process, probably demonstrating the potential impacts of microsatellites on biological functions. Polymorphic microsatellites were developed between different genders of S. chinensis, which was expected to lay the foundation for genetic diversity investigation in cetaceans. The specific markers for a male Indo-Pacific humpback dolphin will provide comprehensive and representative male candidate markers for sex identification, providing a potential biomolecular tool for further analysis of population structure and social behavior of wild populations, population trend evaluation, and species conservation management.
Collapse
|
3
|
Dai Y, Sakornwimon W, Chantra R, Zhao L, Wu F, Aierken R, Kittiwattanawong K, Wang X. High genetic differentiation of Indo‐Pacific humpback dolphins (
Sousa chinensis
) along the Asian Coast of the Pacific Ocean. Ecol Evol 2022; 12:e8901. [PMID: 35571759 PMCID: PMC9077734 DOI: 10.1002/ece3.8901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 04/11/2022] [Accepted: 04/19/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Yufei Dai
- Laboratory of Marine Biology and Ecology Third Institute of Oceanography Ministry of Natural Resources Xiamen China
- Key Laboratory of Marine Ecological Conservation and Restoration Ministry of Natural Resources Xiamen China
- Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration Xiamen China
| | - Watchara Sakornwimon
- Marine and Coastal Resources Research Center The Central Gulf of Thailand Chumphon Thailand
| | - Rachawadee Chantra
- Marine and Coastal Resources Research Center The Upper Gulf of Thailand Samut Sakhon Thailand
| | - Liyuan Zhao
- Laboratory of Marine Biology and Ecology Third Institute of Oceanography Ministry of Natural Resources Xiamen China
- Key Laboratory of Marine Ecological Conservation and Restoration Ministry of Natural Resources Xiamen China
- Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration Xiamen China
| | - Fuxing Wu
- Laboratory of Marine Biology and Ecology Third Institute of Oceanography Ministry of Natural Resources Xiamen China
- Key Laboratory of Marine Ecological Conservation and Restoration Ministry of Natural Resources Xiamen China
- Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration Xiamen China
| | - Reyilamu Aierken
- Laboratory of Marine Biology and Ecology Third Institute of Oceanography Ministry of Natural Resources Xiamen China
| | | | - Xianyan Wang
- Laboratory of Marine Biology and Ecology Third Institute of Oceanography Ministry of Natural Resources Xiamen China
- Key Laboratory of Marine Ecological Conservation and Restoration Ministry of Natural Resources Xiamen China
- Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration Xiamen China
| |
Collapse
|
4
|
Chebii VJ, Mpolya EA, Muchadeyi FC, Domelevo Entfellner JB. Genomics of Adaptations in Ungulates. Animals (Basel) 2021; 11:1617. [PMID: 34072591 PMCID: PMC8230064 DOI: 10.3390/ani11061617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 11/16/2022] Open
Abstract
Ungulates are a group of hoofed animals that have long interacted with humans as essential sources of food, labor, clothing, and transportation. These consist of domesticated, feral, and wild species raised in a wide range of habitats and biomes. Given the diverse and extreme environments inhabited by ungulates, unique adaptive traits are fundamental for fitness. The documentation of genes that underlie their genomic signatures of selection is crucial in this regard. The increasing availability of advanced sequencing technologies has seen the rapid growth of ungulate genomic resources, which offers an exceptional opportunity to understand their adaptive evolution. Here, we summarize the current knowledge on evolutionary genetic signatures underlying the adaptations of ungulates to different habitats.
Collapse
Affiliation(s)
- Vivien J. Chebii
- School of Life Science and Bioengineering, Nelson Mandela Africa Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania;
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya;
| | - Emmanuel A. Mpolya
- School of Life Science and Bioengineering, Nelson Mandela Africa Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania;
| | - Farai C. Muchadeyi
- Agricultural Research Council Biotechnology Platform (ARC-BTP), Private Bag X5, Onderstepoort 0110, South Africa;
| | - Jean-Baka Domelevo Entfellner
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya;
| |
Collapse
|
5
|
Hung TH, So T, Sreng S, Thammavong B, Boounithiphonh C, Boshier DH, MacKay JJ. Reference transcriptomes and comparative analyses of six species in the threatened rosewood genus Dalbergia. Sci Rep 2020; 10:17749. [PMID: 33082403 PMCID: PMC7576600 DOI: 10.1038/s41598-020-74814-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 10/07/2020] [Indexed: 12/02/2022] Open
Abstract
Dalbergia is a pantropical genus with more than 250 species, many of which are highly threatened due to overexploitation for their rosewood timber, along with general deforestation. Many Dalbergia species have received international attention for conservation, but the lack of genomic resources for Dalbergia hinders evolutionary studies and conservation applications, which are important for adaptive management. This study produced the first reference transcriptomes for 6 Dalbergia species with different geographical origins and predicted ~ 32 to 49 K unique genes. We showed the utility of these transcriptomes by phylogenomic analyses with other Fabaceae species, estimating the divergence time of extant Dalbergia species to ~ 14.78 MYA. We detected over-representation in 13 Pfam terms including HSP, ALDH and ubiquitin families in Dalbergia. We also compared the gene families of geographically co-occurring D. cochinchinensis and D. oliveri and observed that more genes underwent positive selection and there were more diverged disease resistance proteins in the more widely distributed D. oliveri, consistent with reports that it occupies a wider ecological niche and has higher genetic diversity. We anticipate that the reference transcriptomes will facilitate future population genomics and gene-environment association studies on Dalbergia, as well as contributing to the genomic database where plants, particularly threatened ones, are currently underrepresented.
Collapse
Affiliation(s)
- Tin Hang Hung
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK.
| | - Thea So
- Institute of Forest and Wildlife Research and Development, Phnom Penh, Cambodia
| | - Syneath Sreng
- Institute of Forest and Wildlife Research and Development, Phnom Penh, Cambodia
| | - Bansa Thammavong
- Forest Research Center, National Agriculture and Forestry Research Institute, Vientiane, Lao PDR
| | - Chaloun Boounithiphonh
- Forest Research Center, National Agriculture and Forestry Research Institute, Vientiane, Lao PDR
| | - David H Boshier
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - John J MacKay
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK.
| |
Collapse
|
6
|
Zhang P, Zhao Y, Li C, Lin M, Dong L, Zhang R, Liu M, Li K, Zhang H, Liu X, Zhang Y, Yuan Y, Liu H, Seim I, Sun S, Du X, Chang Y, Li F, Liu S, Lee SMY, Wang K, Wang D, Wang X, McGowen MR, Jefferson TA, Olsen MT, Stiller J, Zhang G, Xu X, Yang H, Fan G, Liu X, Li S. An Indo-Pacific Humpback Dolphin Genome Reveals Insights into Chromosome Evolution and the Demography of a Vulnerable Species. iScience 2020; 23:101640. [PMID: 33103078 PMCID: PMC7569330 DOI: 10.1016/j.isci.2020.101640] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 08/25/2020] [Accepted: 09/30/2020] [Indexed: 01/12/2023] Open
Abstract
The Indo-Pacific humpback dolphin (Sousa chinensis) is a small inshore species of odontocete cetacean listed as Vulnerable on the IUCN Red List. Here, we report on the evolution of S. chinensis chromosomes from its cetruminant ancestor and elucidate the evolutionary history and population genetics of two neighboring S. chinensis populations. We found that breakpoints in ancestral chromosomes leading to S. chinensis could have affected the function of genes related to kidney filtration, body development, and immunity. Resequencing of individuals from two neighboring populations in the northwestern South China Sea, Leizhou Bay and Sanniang Bay, revealed genetic differentiation, low diversity, and small contemporary effective population sizes. Demographic analyses showed a marked decrease in the population size of the two investigated populations over the last ~4,000 years, possibly related to climatic oscillations. This study implies a high risk of extinction and strong conservation requirement for the Indo-Pacific humpback dolphin. Deducing chromosome evolution from ancestral Cetruminantia and ancestral Odontoceti Reconstructing the demographic history of Sousa chinensis Implying high risk of extinction and strong conservation requirement for S. chinensis
Collapse
Affiliation(s)
- Peijun Zhang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Yong Zhao
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Chang Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Mingli Lin
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China
| | - Lijun Dong
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China
| | - Rui Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Mingzhong Liu
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China
| | - Kuan Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China
| | - He Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Xiaochuan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Yaolei Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby 2800, Denmark
| | - Yuan Yuan
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Huan Liu
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
- Comparative and Endocrine Biology Laboratory, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane 4102, Australia
| | - Shuai Sun
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Xiao Du
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Yue Chang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Feida Li
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Shanshan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China
| | - Kun Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Ding Wang
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Xianyan Wang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian 361005, China
| | - Michael R. McGowen
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, Washington DC 20560, USA
| | | | - Morten Tange Olsen
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Øster Farimagsgade 5, Copenhagen 1353, Denmark
| | - Josefin Stiller
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
- China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong 518120, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Xun Xu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong 518120, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China
- Corresponding author
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- BGI-Fuyang, BGI-Shenzhen, Fuyang, Anhui 236009, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guandong 518083, China
- Corresponding author
| | - Songhai Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
- Tropical Marine Science Institute, National University of Singapore, Singapore 119227, Singapore
- Corresponding author
| |
Collapse
|
7
|
Whole Genome Sequencing of Chinese White Dolphin ( Sousa chinensis) for High-Throughput Screening of Antihypertensive Peptides. Mar Drugs 2019; 17:md17090504. [PMID: 31466310 PMCID: PMC6780146 DOI: 10.3390/md17090504] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/16/2019] [Accepted: 08/26/2019] [Indexed: 01/17/2023] Open
Abstract
Chinese white dolphin (Sousa chinensis), also known as the Indo-Pacific humpback dolphin, has been classified as “Vulnerable” on the IUCN Red List of Threatened Species. It is a special cetacean species that lives in tropical and subtropical nearshore waters, with significant differences from other cetaceans. Here, we sequenced and assembled a draft genome of the Chinese white dolphin with a total length of 2.3 Gb and annotation of 18,387 protein-coding genes. Genes from certain expanded families are potentially involved in DNA replication and repairing, suggesting that they may be related to adaptation of this marine mammal to nearshore environments. We also discovered that its historical population had undergone a remarkable bottleneck incident before the Mindel glaciation. In addition, a comparative genomic survey on antihypertensive peptides (AHTPs) among five representative mammals with various residential habitats (such as remarkable differences in exogenous ion concentrations and sea depth) revealed that these small bioactive peptides were highly conserved among these examined mammals, and they had the most abundant hits in collagen subunit proteins, especially for two putative AHTP peptides Gly-Leu-Pro (GLP) and Leu-Gly-Pro (LGP). Our genome assembly will be a valuable resource for further genetic researches on adaptive ecology and conservation biology of cetaceans, and for in-depth investigations into bioactive peptides in aquatic and terrestrial mammals for development of peptide-based drugs to treat various human cardiovascular diseases.
Collapse
|
8
|
Ming Y, Jian J, Yu X, Wang J, Liu W. The genome resources for conservation of Indo-Pacific humpback dolphin, Sousa chinensis. Sci Data 2019; 6:68. [PMID: 31118413 PMCID: PMC6531461 DOI: 10.1038/s41597-019-0078-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/16/2019] [Indexed: 11/24/2022] Open
Abstract
The Indo-Pacific humpback dolphin (Sousa chinensis), is a threatened marine mammal and belongs to the First Order of the National Key Protected Wild Aquatic Animals List in China. However, limited genomic information is available for studies of its population genetics and biological conservation. Here, we have assembled a genomic sequence of this species using a whole genome shotgun (WGS) sequencing strategy after a pilot low coverage genome survey. The total assembled genome size was 2.34 Gb: with a contig N50 of 67 kb and a scaffold N50 of 9 Mb (107.6-fold sequencing coverage). The S. chinensis genome contained 24,640 predicted protein-coding genes and had approximately 37% repeated sequences. The completeness of the genome assembly was evaluated by benchmarking universal single copy orthologous genes (BUSCOs): 94.3% of a total 4,104 expected mammalian genes were identified as complete, and 2.3% were identified as fragmented. This newly produced high-quality assembly and annotation of the genome will greatly promote the future studies of the genetic diversity, conservation and evolution. Design Type(s) | sequence assembly objective • sequence annotation objective | Measurement Type(s) | whole genome sequencing assay | Technology Type(s) | DNA sequencing | Factor Type(s) | | Sample Characteristic(s) | Sousa chinensis • skin of body |
Machine-accessible metadata file describing the reported data (ISA-Tab format)
Collapse
Affiliation(s)
- Yao Ming
- Marine Biology Institute, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Jianbo Jian
- Marine Biology Institute, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Xueying Yu
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou, Guangxi, 535011, P.R. China
| | - Jingzhen Wang
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou, Guangxi, 535011, P.R. China.
| | - Wenhua Liu
- Marine Biology Institute, Shantou University, Shantou, Guangdong, 515063, P.R. China.
| |
Collapse
|
9
|
The Singularity of Cetacea Behavior Parallels the Complete Inactivation of Melatonin Gene Modules. Genes (Basel) 2019; 10:genes10020121. [PMID: 30736361 PMCID: PMC6410235 DOI: 10.3390/genes10020121] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/01/2019] [Accepted: 02/01/2019] [Indexed: 12/26/2022] Open
Abstract
Melatonin, the hormone of darkness, is a peculiar molecule found in most living organisms. Emerging as a potent broad-spectrum antioxidant, melatonin was repurposed into extra roles such as the modulation of circadian and seasonal rhythmicity, affecting numerous aspects of physiology and behaviour, including sleep entrainment and locomotor activity. Interestingly, the pineal gland—the melatonin synthesising organ in vertebrates—was suggested to be absent or rudimentary in some mammalian lineages, including Cetacea. In Cetacea, pineal regression is paralleled by their unique bio-rhythmicity, as illustrated by the unihemispheric sleeping behaviour and long-term vigilance. Here, we examined the genes responsible for melatonin synthesis (Aanat and Asmt) and signalling (Mtnr1a and Mtnr1b) in 12 toothed and baleen whale genomes. Based on an ample genomic comparison, we deduce that melatonin-related gene modules are eroded in Cetacea.
Collapse
|