Third-Generation Sequencing Reveals the Adaptive Role of the Epigenome in Three Deep-Sea Polychaetes

Abstract

The roles of DNA methylation in invertebrates are poorly characterised, and critical data are missing for the phylum Annelida. We fill this knowledge gap by conducting the first genome-wide survey of DNA methylation in the deep-sea polychaetes dominant in deep-sea vents and seeps: Paraescarpia echinospica, Ridgeia piscesae and Paralvinella palmiformis. DNA methylation calls were inferred from Oxford Nanopore sequencing after assembling high-quality genomes of these animals. The genomes of these worms encode all the key enzymes of the DNA methylation metabolism and possess a mosaic methylome similar to that of other invertebrates. Transcriptomic data of these polychaetes support the hypotheses that gene body methylation strengthens the expression of housekeeping genes and that promoter methylation acts as a silencing mechanism but not the hypothesis that DNA methylation suppress the activity of transposable elements. The conserved epigenetic profiles of genes responsible for maintaining homeostasis under extreme hydrostatic pressure suggest DNA methylation plays an important adaptive role in these worms.

Chromosome-scale genome assembly and gene annotation of the hydrothermal vent annelidAlvinella pompejanayield insight into animal evolution in extreme environments

“…A variety of deep-sea vent invertebrates have recently had their genomes sequenced, including the mussel Bathymodiolus platifrons [90], the clam Archivesica marissinica [97], the scaly-footed snail Chrysomallon squamiferum [98], the snail Gigantopelta aegis [99]; among annelids, the scale worm Branchipolynoe longqiensis, several siboglinids and the alvinellid Paralvinella palmiformis [25]; among cnidarians, the deep sea anemones Alvinactis idsseensis sp. Nov. [100] and Actinernus sp.…”

“…Recently, a fragmented whole genome sequence of Alvinella pompejana was analysed together with its transcriptome to explore the genomic patterns in the diversification of A. pompejana and the closely related A. caudata [24]. A sub-chromosome level genome of Paralvinella palmiformis has been reported and analysed within the context of an epigenome study, without extensive study of its protein coding gene set [25]. Here we report a chromosome level genome assembly of Alvinella pompejana .…”

Adaptive Evolution of Marine Organisms: A Bibliometric Analysis Based on CiteSpace

“…These findings are likely attributed to geographic barriers, constrained diffusion capacity and diverse pressures imposed by deep-sea environments [45]. Similarly, Perez et al (2023) [46] discovered that gene methylation in deep-sea polychaetes contributes to the expression of housekeeping gene, thereby facilitating their adaptation to the deep-sea environment. Notably, DNA methylation played a significant role in this adaptive process.…”