1
|
Ludington AJ, Hammond JM, Breen J, Deveson IW, Sanders KL. New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae). BMC Biol 2023; 21:284. [PMID: 38066641 PMCID: PMC10709897 DOI: 10.1186/s12915-023-01772-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Sea snakes underwent a complete transition from land to sea within the last ~ 15 million years, yet they remain a conspicuous gap in molecular studies of marine adaptation in vertebrates. RESULTS Here, we generate four new annotated sea snake genomes, three of these at chromosome-scale (Hydrophis major, H. ornatus and H. curtus), and perform detailed comparative genomic analyses of sea snakes and their closest terrestrial relatives. Phylogenomic analyses highlight the possibility of near-simultaneous speciation at the root of Hydrophis, and synteny maps show intra-chromosomal variations that will be important targets for future adaptation and speciation genomic studies of this system. We then used a strict screen for positive selection in sea snakes (against a background of seven terrestrial snake genomes) to identify genes over-represented in hypoxia adaptation, sensory perception, immune response and morphological development. CONCLUSIONS We provide the best reference genomes currently available for the prolific and medically important elapid snake radiation. Our analyses highlight the phylogenetic complexity and conserved genome structure within Hydrophis. Positively selected marine-associated genes provide promising candidates for future, functional studies linking genetic signatures to the marine phenotypes of sea snakes and other vertebrates.
Collapse
Affiliation(s)
- Alastair J Ludington
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
| | - Jillian M Hammond
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, Australia
| | - James Breen
- Indigenous Genomics, Telethon Kids Institute, Adelaide, Australia
- John Curtin School of Medical Research, College of Health & Medicine, Australian National University, Canberra, Australia
| | - Ira W Deveson
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, Australia
- Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Kate L Sanders
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
- The South Australian Museum, Adelaide, Australia.
| |
Collapse
|
2
|
Hosseinian Yousefkhani SS, Yasser A, Naser M, Rezaie-Atagholipour M, Askari Hesni M, Yousefabadi F, Rastegar Pouyani E. Genetic diversity among sea snakes of the genus Hydrophis (Elapidae, Reptilia) in the Persian Gulf and Gulf of Oman. Zookeys 2023; 1158:121-131. [PMID: 37215695 PMCID: PMC10193271 DOI: 10.3897/zookeys.1158.101347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/01/2023] [Indexed: 05/24/2023] Open
Abstract
Sea snakes of the genus Hydrophis are important components of animal diversity in Iranian waters of the Persian Gulf and Gulf of Oman. Ten species of Hydrophis have been identified from the these waters and, in this study, genetic structure of seven species was compared with other populations in the eastern Indian Ocean and the West Pacific. We found that six species (H.platurus, H.cyanocinctus, H.spiralis, H.schistosus, H.gracilis, and H.lapemiodes) show high genetic similarity with conspecific populations in the Indian Ocean and Australia. However, H.curtus from southern Iran shows a high level of genetic differentiation from conspecific populations in Sri Lanka and Indonesia (0.6% and 6% genetic distance from Sri Lankan samples for 16S and COI gene fragments, respectively). Variation between Iranian and Southeast Asian populations may reflect new genetic lineages and suggest the need of further morphological evaluations to re-evaluate their taxonomic position.
Collapse
Affiliation(s)
| | - Amaal Yasser
- Marine Science Centre, University of Basrah, Basra, Iraq
- Australian Rivers Institute, Griffith University, 170 Kessels Road, Nathan, Queensland 4111, Australia
| | - Murtada Naser
- Marine Science Centre, University of Basrah, Basra, Iraq
- Australian Rivers Institute, Griffith University, 170 Kessels Road, Nathan, Queensland 4111, Australia
| | - Mohsen Rezaie-Atagholipour
- School of Environment and Science, Griffith University, 170 Kessels Road, Nathan, Queensland, 4111, Australia
| | - Majid Askari Hesni
- Qeshm Environmental Conservation Institute (QECI), Qeshm Island, Hormozgan Province, Iran
| | - Fariba Yousefabadi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman Province, Iran
| | | |
Collapse
|
3
|
Ludington AJ, Sanders KL. Demographic analyses of marine and terrestrial snakes (Elapidae) using whole genome sequences. Mol Ecol 2020; 30:545-554. [PMID: 33170980 DOI: 10.1111/mec.15726] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/13/2020] [Accepted: 11/03/2020] [Indexed: 11/27/2022]
Abstract
The question of whether spatial aspects of evolution differ in marine versus terrestrial realms has endured since Ernst Mayr's 1954 essay on marine speciation. Marine systems are often suggested to support larger and more highly connected populations, but quantitative comparisons with terrestrial systems have been lacking. Here, we compared the population histories of marine and terrestrial elapid snakes using the pairwise sequentially Markovian coalescent (PSMC) model to track historical fluctuations in species' effective population sizes (Ne ) from individual whole-genome sequences. To do this we generated a draft genome for the olive sea snake (Aiysurus laevis) and analysed this alongside six published elapid genomes and their sequence reads (marine species Hydrophis curtus, H. melanocephalus and Laticauda laticaudata; terrestrial species Pseudonaja textilis, Naja Naja and Notechis scutatus). Counter to the expectation that marine species should show higher overall Ne and less pronounced fluctuations in Ne , our analyses reveal demographic patterns that are highly variable among species and do not clearly correspond to major ecological divisions. At deeper time intervals, the four marine elapids appear to have experienced relatively stable Ne , while each terrestrial species shows a prominent upturn in Ne starting at ~4 million years ago (Ma) followed by an equally strong decline. However, over the last million years, all seven species show strong and divergent fluctuations. Estimates of Ne in the most recent intervals (~10 kya) are lowest in two of four marine species (H. melanocephalus and Laticauda), and do not correspond to contemporary range sizes in marine or terrestrial taxa.
Collapse
Affiliation(s)
- Alastair J Ludington
- School of Biological Science, The University of Adelaide, Adelaide, South Australia, Australia
| | - Kate L Sanders
- School of Biological Science, The University of Adelaide, Adelaide, South Australia, Australia
| |
Collapse
|
4
|
Wang B, Wang Q, Wang C, Wang B, Qiu L, Zou S, Zhang F, Liu G, Zhang L. A comparative analysis of the proteomes and biological activities of the venoms from two sea snakes, Hydrophis curtus and Hydrophis cyanocinctus, from Hainan, China. Toxicon 2020; 187:35-46. [PMID: 32871160 DOI: 10.1016/j.toxicon.2020.08.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/05/2020] [Accepted: 08/13/2020] [Indexed: 12/25/2022]
Abstract
We characterized and compared the venom protein profiles of Hydrophis curtus (synonyms: Lapemis hardwickii, Lapemis curtus and Hydrophis hardwickii) and Hydrophis cyanocinctus, the two representatives of medically important venomous sea snakes in Chinese waters using proteomic approaches. A total of 47 and 38 putative toxins were identified in H. curtus venom (HcuV) and H. cyanocinctus venom (HcyV), respectively, and these toxins could be grouped into 15 functional categories, mainly proteinases, phospholipases, three-finger toxins (3FTxs), lectins, protease inhibitors, ion channel inhibitors, cysteine-rich venom proteins (CRVPs) and snake venom metalloproteases (SVMPs). The constituent ratio of each toxin category varied between HcuV and HcyV with 3FTx (54% in HcuV/69% in HcyV) and PLA2 (38% in HcuV/22% in HcyV) unanimously ranked as the top two most abundant families. Both HcuV and HcyV exhibited relatively high lethality (LD50 values in mice of 0.34 μg/g and 0.24 μg/g, respectively), specific PLA2 activity and hemolytic activity. On the basis of several previous reports of HcuV and HcyV collected from other areas, these findings greatly expand our understanding of geographical variation and interspecies diversity of the two sea snake venoms and can provide a scientific basis for the development of specific sea snake antivenom in the future.
Collapse
Affiliation(s)
- Bo Wang
- Department of Marine Biomedicine and Polar Medicine, Naval Characteristic Medical Center, Naval Medical University, Shanghai, 200433, China
| | - Qianqian Wang
- Department of Marine Biomedicine and Polar Medicine, Naval Characteristic Medical Center, Naval Medical University, Shanghai, 200433, China
| | - Chao Wang
- Department of Marine Biomedicine and Polar Medicine, Naval Characteristic Medical Center, Naval Medical University, Shanghai, 200433, China
| | - Beilei Wang
- Department of Marine Biomedicine and Polar Medicine, Naval Characteristic Medical Center, Naval Medical University, Shanghai, 200433, China
| | - Leilei Qiu
- Department of Marine Biomedicine and Polar Medicine, Naval Characteristic Medical Center, Naval Medical University, Shanghai, 200433, China
| | - Shuaijun Zou
- Department of Marine Biomedicine and Polar Medicine, Naval Characteristic Medical Center, Naval Medical University, Shanghai, 200433, China
| | - Fuhai Zhang
- Department of Marine Biomedicine and Polar Medicine, Naval Characteristic Medical Center, Naval Medical University, Shanghai, 200433, China
| | - Guoyan Liu
- Department of Marine Biomedicine and Polar Medicine, Naval Characteristic Medical Center, Naval Medical University, Shanghai, 200433, China.
| | - Liming Zhang
- Department of Marine Biomedicine and Polar Medicine, Naval Characteristic Medical Center, Naval Medical University, Shanghai, 200433, China.
| |
Collapse
|
5
|
Nitschke CR, Hourston M, Udyawer V, Sanders KL. Rates of population differentiation and speciation are decoupled in sea snakes. Biol Lett 2018; 14:rsbl.2018.0563. [PMID: 30333264 DOI: 10.1098/rsbl.2018.0563] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/14/2018] [Indexed: 11/12/2022] Open
Abstract
Comparative phylogeography can inform many macroevolutionary questions, such as whether species diversification is limited by rates of geographical population differentiation. We examined the link between population genetic structure and species diversification in the fully aquatic sea snakes (Hydrophiinae) by comparing mitochondrial phylogeography across northern Australia in 16 species from two closely related clades that show contrasting diversification dynamics. Contrary to expectations from theory and several empirical studies, our results show that, at the geographical scale studied here, rates of population differentiation and speciation are not positively linked in sea snakes. The eight species sampled from the rapidly speciating Hydrophis clade have weak population differentiation that lacks geographical structure. By contrast, all eight sampled Aipysurus-Emydocephalus species show clear geographical patterns and many deep intraspecific splits, but have threefold slower speciation rates. Alternative factors, such as ecological specialization, species duration and geographical range size, may underlie rapid speciation in sea snakes.
Collapse
Affiliation(s)
- Charlotte R Nitschke
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Mathew Hourston
- The Department of Primary Industries and Regional Development, Perth, Western Australia, Australia
| | - Vinay Udyawer
- Australian Institute of Marine Science, Darwin, Northern Territory 0810, Australia
| | - Kate L Sanders
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| |
Collapse
|
6
|
Neale V, Sotillo J, Seymour JE, Wilson D. The Venom of the Spine-Bellied Sea Snake (Hydrophis curtus): Proteome, Toxin Diversity and Intraspecific Variation. Int J Mol Sci 2017; 18:ijms18122695. [PMID: 29231898 PMCID: PMC5751296 DOI: 10.3390/ijms18122695] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 11/26/2017] [Accepted: 11/27/2017] [Indexed: 11/19/2022] Open
Abstract
The spine-bellied sea snake (Hydrophis curtus) is known to cause human deaths, yet its venom composition has not yet been proteomically characterised. An in-depth proteomic analysis was performed on H. curtus venom from two different seasons, January and June, corresponding to adults and subadults, respectively. Venoms from adult and subadult H. curtus individuals were compared using reversed-phase high-performance liquid chromatography (RP-HPLC), matrix-assisted laser desorption ionisation-time of flight (MALDI-TOF) mass spectrometry and liquid chromatography electrospray ionisation mass spectrometry (LC-ESI-MS) to detect intraspecific variation, and the molecular weight data obtained with ESI-MS were used to assess toxin diversity. RP-HPLC and LC-ESI-MS/MS were used to characterise the venom proteome and estimate the relative abundances of protein families present. The most abundant protein family in January and June venoms is phospholipase A2 (PLA2: January 66.7%; June 54.5%), followed by three-finger toxins (3FTx: January 30.4%; June 40.4%) and a minor component of cysteine-rich secretory proteins (CRISP: January 2.5%; June 5%). Trace amounts of snake venom metalloproteinases (SVMP), C-type lectins and housekeeping and regulatory proteins were also found. Although the complexity of the venom is low by number of families present, each family contained a more diverse set of isoforms than previously reported, a finding that may have implications for the development of next-generation sea snake antivenoms. Intraspecific variability was shown to be minor with one obvious exception of a 14,157-Da protein that was present in some January (adult) venoms, but not at all in June (subadult) venoms. There is also a greater abundance of short-chain neurotoxins in June (subadult) venom compared with January (adult) venom. These differences potentially indicate the presence of seasonal, ontogenetic or sexual variation in H. curtus venom.
Collapse
Affiliation(s)
- Vanessa Neale
- College of Public Health, Medical and Veterinary Sciences, James Cook University, McGregor Road, Smithfield, Cairns 4878, Australia.
- Australian Institute of Tropical Health and Medicine (AITHM) and Centre for Biodiscovery and Molecular Development of Therapeutics (CBMDT), James Cook University, McGregor Road, Smithfield, Cairns 4878, Australia.
| | - Javier Sotillo
- Australian Institute of Tropical Health and Medicine (AITHM) and Centre for Biodiscovery and Molecular Development of Therapeutics (CBMDT), James Cook University, McGregor Road, Smithfield, Cairns 4878, Australia.
| | - Jamie E Seymour
- Australian Institute of Tropical Health and Medicine (AITHM) and Centre for Biodiscovery and Molecular Development of Therapeutics (CBMDT), James Cook University, McGregor Road, Smithfield, Cairns 4878, Australia.
| | - David Wilson
- Australian Institute of Tropical Health and Medicine (AITHM) and Centre for Biodiscovery and Molecular Development of Therapeutics (CBMDT), James Cook University, McGregor Road, Smithfield, Cairns 4878, Australia.
| |
Collapse
|