New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae)
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...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-12-01
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| Series: | BMC Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12915-023-01772-2 |
| _version_ | 1797397752847532032 |
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| author | Alastair J. Ludington Jillian M. Hammond James Breen Ira W. Deveson Kate L. Sanders |
| author_facet | Alastair J. Ludington Jillian M. Hammond James Breen Ira W. Deveson Kate L. Sanders |
| author_sort | Alastair J. Ludington |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T01:15:39Z |
| format | Article |
| id | doaj.art-6cac2aa043084482ba199ed3e54d7e29 |
| institution | Directory Open Access Journal |
| issn | 1741-7007 |
| language | English |
| last_indexed | 2024-03-09T01:15:39Z |
| publishDate | 2023-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Biology |
| spelling | doaj.art-6cac2aa043084482ba199ed3e54d7e292023-12-10T12:31:39ZengBMCBMC Biology1741-70072023-12-0121112310.1186/s12915-023-01772-2New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae)Alastair J. Ludington0Jillian M. Hammond1James Breen2Ira W. Deveson3Kate L. Sanders4School of Biological Sciences, The University of AdelaideGenomics and Inherited Disease Program, Garvan Institute of Medical ResearchIndigenous Genomics, Telethon Kids InstituteGenomics and Inherited Disease Program, Garvan Institute of Medical ResearchSchool of Biological Sciences, The University of AdelaideAbstract 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.https://doi.org/10.1186/s12915-023-01772-2Chromosome-scale genomeSyntenyPositive selectionMarine adaptationSea snake |
| spellingShingle | Alastair J. Ludington Jillian M. Hammond James Breen Ira W. Deveson Kate L. Sanders New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae) BMC Biology Chromosome-scale genome Synteny Positive selection Marine adaptation Sea snake |
| title | New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae) |
| title_full | New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae) |
| title_fullStr | New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae) |
| title_full_unstemmed | New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae) |
| title_short | New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae) |
| title_sort | new chromosome scale genomes provide insights into marine adaptations of sea snakes hydrophis elapidae |
| topic | Chromosome-scale genome Synteny Positive selection Marine adaptation Sea snake |
| url | https://doi.org/10.1186/s12915-023-01772-2 |
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