The First Genome Survey of the Snail Provanna glabra Inhabiting Deep-Sea Hydrothermal Vents

SIMPLE SUMMARY: Due to limited reporting of genomic resources for deep-sea organisms, studies of their adaptive mechanisms for extreme environments have been hindered. A genome survey of the snail Provanna glabra, a representative species in deep-sea chemosynthetic ecosystem, was conducted based on Illumina sequencing. Genome size, repetitive elements, heterozygosity, and other genome features were estimated and characterized. A draft genome and a complete mitochondrial genome were assembled for P. glabra, and candidate molecular markers were identified. Phylogenetic analysis based on mitochondrial genes was performed. The results provide effective genome information for P. glabra and supply a basis for further high-quality genome map construction and biogeography study of this deep-sea chemosynthetic snail. ABSTRACT: The snail P. glabra 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 P. glabra 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 P. glabra with a total length of 16,268 bp was assembled from the sequencing data. After comparison with the published mitochondrial genome of Provanna sp. from a methane seep, 331 potential single nucleotide polymorphism (SNP) sites were identified in protein-coding genes (PCGs). Except for the cox1 gene, nad2, nad4, nad5, and cob genes are expected to be candidate markers for population genetic and phylogenetic studies of P. glabra 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 P. glabra and supplies genomic resources for further studies on the adaptive evolution of the snail in extreme deep-sea chemosynthetic environments.