The State of Squamate Genomics: Past, Present, and Future of Genome Research in the Most Speciose Terrestrial Vertebrate Order
Squamates include more than 11,000 extant species of lizards, snakes, and amphisbaenians, and display a dazzling diversity of phenotypes across their over 200-million-year evolutionary history on Earth. Here, we introduce and define squamates (Order Squamata) and review the history and promise of ge...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-07-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/7/1387 |
| _version_ | 1797589149237116928 |
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| author | Simone M. Gable Jasmine M. Mendez Nicholas A. Bushroe Adam Wilson Michael I. Byars Marc Tollis |
| author_facet | Simone M. Gable Jasmine M. Mendez Nicholas A. Bushroe Adam Wilson Michael I. Byars Marc Tollis |
| author_sort | Simone M. Gable |
| collection | DOAJ |
| description | Squamates include more than 11,000 extant species of lizards, snakes, and amphisbaenians, and display a dazzling diversity of phenotypes across their over 200-million-year evolutionary history on Earth. Here, we introduce and define squamates (Order Squamata) and review the history and promise of genomic investigations into the patterns and processes governing squamate evolution, given recent technological advances in DNA sequencing, genome assembly, and evolutionary analysis. We survey the most recently available whole genome assemblies for squamates, including the taxonomic distribution of available squamate genomes, and assess their quality metrics and usefulness for research. We then focus on disagreements in squamate phylogenetic inference, how methods of high-throughput phylogenomics affect these inferences, and demonstrate the promise of whole genomes to settle or sustain persistent phylogenetic arguments for squamates. We review the role transposable elements play in vertebrate evolution, methods of transposable element annotation and analysis, and further demonstrate that through the understanding of the diversity, abundance, and activity of transposable elements in squamate genomes, squamates can be an ideal model for the evolution of genome size and structure in vertebrates. We discuss how squamate genomes can contribute to other areas of biological research such as venom systems, studies of phenotypic evolution, and sex determination. Because they represent more than 30% of the living species of amniote, squamates deserve a genome consortium on par with recent efforts for other amniotes (i.e., mammals and birds) that aim to sequence most of the extant families in a clade. |
| first_indexed | 2024-03-11T01:02:17Z |
| format | Article |
| id | doaj.art-0cf3d4b52909415289d9701978defae8 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T01:02:17Z |
| publishDate | 2023-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-0cf3d4b52909415289d9701978defae82023-11-18T19:29:42ZengMDPI AGGenes2073-44252023-07-01147138710.3390/genes14071387The State of Squamate Genomics: Past, Present, and Future of Genome Research in the Most Speciose Terrestrial Vertebrate OrderSimone M. Gable0Jasmine M. Mendez1Nicholas A. Bushroe2Adam Wilson3Michael I. Byars4Marc Tollis5School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USASchool of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USASchool of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USASchool of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USASchool of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USASchool of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USASquamates include more than 11,000 extant species of lizards, snakes, and amphisbaenians, and display a dazzling diversity of phenotypes across their over 200-million-year evolutionary history on Earth. Here, we introduce and define squamates (Order Squamata) and review the history and promise of genomic investigations into the patterns and processes governing squamate evolution, given recent technological advances in DNA sequencing, genome assembly, and evolutionary analysis. We survey the most recently available whole genome assemblies for squamates, including the taxonomic distribution of available squamate genomes, and assess their quality metrics and usefulness for research. We then focus on disagreements in squamate phylogenetic inference, how methods of high-throughput phylogenomics affect these inferences, and demonstrate the promise of whole genomes to settle or sustain persistent phylogenetic arguments for squamates. We review the role transposable elements play in vertebrate evolution, methods of transposable element annotation and analysis, and further demonstrate that through the understanding of the diversity, abundance, and activity of transposable elements in squamate genomes, squamates can be an ideal model for the evolution of genome size and structure in vertebrates. We discuss how squamate genomes can contribute to other areas of biological research such as venom systems, studies of phenotypic evolution, and sex determination. Because they represent more than 30% of the living species of amniote, squamates deserve a genome consortium on par with recent efforts for other amniotes (i.e., mammals and birds) that aim to sequence most of the extant families in a clade.https://www.mdpi.com/2073-4425/14/7/1387squamatesgenome sequencinggenome assemblyphylogenomicstransposable elements |
| spellingShingle | Simone M. Gable Jasmine M. Mendez Nicholas A. Bushroe Adam Wilson Michael I. Byars Marc Tollis The State of Squamate Genomics: Past, Present, and Future of Genome Research in the Most Speciose Terrestrial Vertebrate Order Genes squamates genome sequencing genome assembly phylogenomics transposable elements |
| title | The State of Squamate Genomics: Past, Present, and Future of Genome Research in the Most Speciose Terrestrial Vertebrate Order |
| title_full | The State of Squamate Genomics: Past, Present, and Future of Genome Research in the Most Speciose Terrestrial Vertebrate Order |
| title_fullStr | The State of Squamate Genomics: Past, Present, and Future of Genome Research in the Most Speciose Terrestrial Vertebrate Order |
| title_full_unstemmed | The State of Squamate Genomics: Past, Present, and Future of Genome Research in the Most Speciose Terrestrial Vertebrate Order |
| title_short | The State of Squamate Genomics: Past, Present, and Future of Genome Research in the Most Speciose Terrestrial Vertebrate Order |
| title_sort | state of squamate genomics past present and future of genome research in the most speciose terrestrial vertebrate order |
| topic | squamates genome sequencing genome assembly phylogenomics transposable elements |
| url | https://www.mdpi.com/2073-4425/14/7/1387 |
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