The First Genome Survey of the Snail <i>Provanna glabra</i> Inhabiting Deep-Sea Hydrothermal Vents
The snail <i>P. glabra</i> is an endemic species in deep-sea chemosynthetic ecosystems of the Northwest Pacific Ocean. To obtain more genetic information on this species and provide the basis for subsequent whole-genome map construction, a genome survey was performed on this snail from t...
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MDPI AG
2023-10-01
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| Online Access: | https://www.mdpi.com/2076-2615/13/21/3313 |
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| author | Min Hui Yu Zhang Aiyang Wang Zhongli Sha |
| author_facet | Min Hui Yu Zhang Aiyang Wang Zhongli Sha |
| author_sort | Min Hui |
| collection | DOAJ |
| description | The snail <i>P. glabra</i> is an endemic species in deep-sea chemosynthetic ecosystems of the Northwest Pacific Ocean. To obtain more genetic information on this species and provide the basis for subsequent whole-genome map construction, a genome survey was performed on this snail from the hydrothermal vent of Okinawa Trough. The genomic size of <i>P. glabra</i> was estimated to be 1.44 Gb, with a heterozygosity of 1.91% and a repeated sequence content of 69.80%. Based on the sequencing data, a draft genome of 1.32 Gb was assembled. Transposal elements (TEs) accounted for 40.17% of the entire genome, with DNA transposons taking the highest proportion. It was found that most TEs were inserted in the genome recently. In the simple sequence repeats, the dinucleotide motif was the most enriched microsatellite type, accounting for 53% of microsatellites. A complete mitochondrial genome of <i>P. glabra</i> with a total length of 16,268 bp was assembled from the sequencing data. After comparison with the published mitochondrial genome of <i>Provanna</i> sp. from a methane seep, 331 potential single nucleotide polymorphism (SNP) sites were identified in protein-coding genes (PCGs). Except for the <i>cox1</i> gene, <i>nad2</i>, <i>nad4</i>, <i>nad5</i>, and <i>cob</i> genes are expected to be candidate markers for population genetic and phylogenetic studies of <i>P. glabra</i> and other deep-sea snails. Compared with shallow-water species, three mitochondrial genes of deep-sea gastropods exhibited a higher evolutionary rate, indicating strong selection operating on mitochondria of deep-sea species. This study provides insights into the genome characteristics of <i>P. glabra</i> and supplies genomic resources for further studies on the adaptive evolution of the snail in extreme deep-sea chemosynthetic environments. |
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| spelling | doaj.art-62c2a770d59a4656a15920a12a53663a2023-11-10T14:57:40ZengMDPI AGAnimals2076-26152023-10-011321331310.3390/ani13213313The First Genome Survey of the Snail <i>Provanna glabra</i> Inhabiting Deep-Sea Hydrothermal VentsMin Hui0Yu Zhang1Aiyang Wang2Zhongli Sha3Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, ChinaCollege of Marine Life Sciences, Ocean University of China, Qingdao 266100, ChinaDepartment of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, ChinaDepartment of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, ChinaThe snail <i>P. glabra</i> is an endemic species in deep-sea chemosynthetic ecosystems of the Northwest Pacific Ocean. To obtain more genetic information on this species and provide the basis for subsequent whole-genome map construction, a genome survey was performed on this snail from the hydrothermal vent of Okinawa Trough. The genomic size of <i>P. glabra</i> was estimated to be 1.44 Gb, with a heterozygosity of 1.91% and a repeated sequence content of 69.80%. Based on the sequencing data, a draft genome of 1.32 Gb was assembled. Transposal elements (TEs) accounted for 40.17% of the entire genome, with DNA transposons taking the highest proportion. It was found that most TEs were inserted in the genome recently. In the simple sequence repeats, the dinucleotide motif was the most enriched microsatellite type, accounting for 53% of microsatellites. A complete mitochondrial genome of <i>P. glabra</i> with a total length of 16,268 bp was assembled from the sequencing data. After comparison with the published mitochondrial genome of <i>Provanna</i> sp. from a methane seep, 331 potential single nucleotide polymorphism (SNP) sites were identified in protein-coding genes (PCGs). Except for the <i>cox1</i> gene, <i>nad2</i>, <i>nad4</i>, <i>nad5</i>, and <i>cob</i> genes are expected to be candidate markers for population genetic and phylogenetic studies of <i>P. glabra</i> and other deep-sea snails. Compared with shallow-water species, three mitochondrial genes of deep-sea gastropods exhibited a higher evolutionary rate, indicating strong selection operating on mitochondria of deep-sea species. This study provides insights into the genome characteristics of <i>P. glabra</i> and supplies genomic resources for further studies on the adaptive evolution of the snail in extreme deep-sea chemosynthetic environments.https://www.mdpi.com/2076-2615/13/21/3313deep-sea chemosynthetic ecosystemgenome sizemolecular markertransposal elementsphylogenetics |
| spellingShingle | Min Hui Yu Zhang Aiyang Wang Zhongli Sha The First Genome Survey of the Snail <i>Provanna glabra</i> Inhabiting Deep-Sea Hydrothermal Vents Animals deep-sea chemosynthetic ecosystem genome size molecular marker transposal elements phylogenetics |
| title | The First Genome Survey of the Snail <i>Provanna glabra</i> Inhabiting Deep-Sea Hydrothermal Vents |
| title_full | The First Genome Survey of the Snail <i>Provanna glabra</i> Inhabiting Deep-Sea Hydrothermal Vents |
| title_fullStr | The First Genome Survey of the Snail <i>Provanna glabra</i> Inhabiting Deep-Sea Hydrothermal Vents |
| title_full_unstemmed | The First Genome Survey of the Snail <i>Provanna glabra</i> Inhabiting Deep-Sea Hydrothermal Vents |
| title_short | The First Genome Survey of the Snail <i>Provanna glabra</i> Inhabiting Deep-Sea Hydrothermal Vents |
| title_sort | first genome survey of the snail i provanna glabra i inhabiting deep sea hydrothermal vents |
| topic | deep-sea chemosynthetic ecosystem genome size molecular marker transposal elements phylogenetics |
| url | https://www.mdpi.com/2076-2615/13/21/3313 |
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