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

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.

Keywords: deep-sea chemosynthetic ecosystem; genome size; molecular marker; phylogenetics; transposal elements.

Figure 1

Sampling site and genome characteristics of P. glabra. (a) Map showing the sampling area of P. glabra. It is drawn by Ocean Data View (ODV) v.5.0. (b) K-mer (K = 17) analysis for the genome. (c) Correlation between GC content and sequencing depth of the assembled draft genome. The horizontal axis represents GC content, and the vertical axis represents sequencing depth. The red portion represents the denser area of points in this scatterplot. The rightmost plot shows the distribution of sequencing depth of contigs, with the horizontal coordinate representing the number of contigs. The topmost plot displays the distribution of GC content, with its vertical coordinate indicating the number of contigs. (d) Divergence rates of four TE types in P. glabra draft genome.

Figure 2

Statistics on microsatellite motifs in P. glabra draft genome. (a) Distribution of different microsatellite motif types. (b) Frequency of different dinucleotide and trinucleotide microsatellite motifs.

Figure 3

Mitochondrial genome map of P. glabra. Purple, pink, and green represent PCGs, tRNA genes, and rRNA, respectively. The control region is marked in yellow.

Figure 4

Phylogenetic tree and evolutionary rates of gastropod mitochondrial genes. (a) Phylogenetic tree of gastropods with Amphioctopus marginatus as outgroup. Bootstrap value is displayed on the branch. Red branches represent deep-sea gastropods. (b) Evolutionary rate comparison of mitochondrial genes between deep-sea lineage (Abyssochrysoidea) and shallow-water lineage (Tonnoidea, Conoidea, and Muricoidea). ω0 represents the dN/dS values of the shallow-water lineage, and ω1 represents the dN/dS values of the deep-sea lineage. ** indicates extremely significant difference with 0.001 < p-value < 0.01.