Genome sequencing of deep-sea hydrothermal vent snails reveals adaptions to extreme environments

Abstract

Background The scaly-foot snail (Chrysomallon squamiferum) is highly adapted to deep-sea hydrothermal vents and has drawn much interest since its discovery. However, the limited information on its genome has impeded further related research and understanding of its adaptation to deep-sea hydrothermal vents. Findings Here, we report the whole-genome sequencing and assembly of the scaly-foot snail and another snail (Gigantopelta aegis), which inhabits similar environments. Using Oxford Nanopore Technology, 10X Genomics, and Hi-C technologies, we obtained a chromosome-level genome of C. squamiferum with an N50 size of 20.71 Mb. By constructing a phylogenetic tree, we found that these 2 deep-sea snails evolved independently of other snails. Their divergence from each other occurred ∼66.3 million years ago. Comparative genomic analysis showed that different snails have diverse genome sizes and repeat contents. Deep-sea snails have more DNA transposons and long terminal repeats but fewer long interspersed nuclear elements than other snails. Gene family analysis revealed that deep-sea snails experienced stronger selective pressures than freshwater snails, and gene families related to the nervous system, immune system, metabolism, DNA stability, antioxidation, and biomineralization were significantly expanded in scaly-foot snails. We also found 251 H-2 Class II histocompatibility antigen, A-U α chain-like (H2-Aal) genes, which exist uniquely in the Gigantopelta aegis genome. This finding is important for investigating the evolution of major histocompatibility complex (MHC) genes. Conclusion Our study provides new insights into deep-sea snail genomes and valuable resources for further studies.

Genomic Hotspots: Localized chromosome gene expansions identify lineage-specific innovations as targets for functional biodiversity and predictions of stress resilience

“…Although patterns of gene expansion are less striking, the Patella species have more TRPM genes than Aplysia and with more small-scale expansions of 1 or 2 genes (Figure 2C and 2D). The two hydrothermal vent gastropods, Chrysomallon squamiferum and Gigantopelta aegis , belong to the same family but they have adapted to the extreme heat stress independently(77–79). Their genomes show striking patterns of parallel expansion in TRPM genes, less so than expansions found in bivalves but much greater than expansions seen in the other gastropods and octopus (Figure 2C and 2D).…”

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

“…After correction, genome size was revised into 1.44 Gb with heterozygous rate and repetitive sequence rate of 1.91% and 69.80%, respectively (Figure 1b), indicating a complex genome. Compared with other snails from deep-sea chemosynthetic environments, such as Ifremeria nautilei (0.88 Gb), Alviniconcha hessleri (0.92 Gb), Chrysomallon squamiferum (~0.46 Gb), and Gigantopelta aegis (~1.29 Gb), P. glabra exhibited relative larger genome sizes, as well as high heterozygosity and repeat content [27,28]. Considering the function of repetitive elements in genome evolution [29], the accumulation of repetitive sequences might contribute to the genome size variation among P. glabra and other deep-sea snails.…”

Understanding Snail Mucus Biosynthesis and Shell Biomineralisation through Genomic Data Mining of the Reconstructed Carbohydrate and Glycan Metabolic Pathways of the Giant African Snail (Achatina fulica)

“…Snail genomic research has progressed considerably through the advancement of whole-genome sequencing technologies. These have resulted in an increased number of snail genomes being deposited in the NCBI genome database, i.e., Biomphalaria glabrata [ 27 ], Pomacea snails [ 28 ], A. fulica [ 29 ], Chrysomallon squamiferum [ 30 ], Achatina immaculata [ 31 ], Candidula unifasciata [ 32 ], and Cepaea nemoralis [ 33 ]. Genetic data analysis with various bioinformatic tools has uncovered several mysteries related to snails and their biological adaptations.…”

“…Genetic data analysis with various bioinformatic tools has uncovered several mysteries related to snails and their biological adaptations. For example, long-read and Hi-C data analysis showed more DNA transposons, long terminal repeats, and expansion of particular gene families in the scaly foot snail ( C. squamiferum ), which inhabits deep-sea hydrothermal vents [ 30 ]. A comparative genomic analysis of four ampullariid snails ( Lanistes nyassanus , P. canaliculata , P. maculata , and Marisa cornuarietis ) found the expansion of genes involved in cellulolysis and environmental sensing, which could facilitate their aggressively causing damage to agricultural plants [ 28 ].…”