Genome and annotation files for Hediste diversicolor
Data files
Jun 11, 2026 version files 2 GB
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Hdiv_full_annotation.gtf
66.26 MB
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Hdiv_full_genome.fasta
960.94 MB
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Hdiv_NCBI_submitted_annotation.gff
10.93 MB
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Hdiv_NCBI_submitted_masked_genome.fasta
966.76 MB
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README.md
2.18 KB
Abstract
Infaunal bioturbators are central to estuarine and coastal ecosystem functioning. Studying species that appear tolerant of variable conditions can reveal the molecular pathways that underpin apparent resilience, and so provide a basis for comparison with more sensitive species. Here, we generated the first chromosome-level annotated genome for the marine ragworm Hediste diversicolor and used it to characterise pH sensing, signalling, and stress responses in two populations. One-hour low-pH exposure elicited acid-base regulatory responses in Ria Formosa (Portugal) ragworms, whereas Humber (UK) ragworms showed a broader response involving metabolism and oxidative-stress pathways. A future-ocean treatment additionally activated apoptosis and genome-maintenance. Abiotic stress cues from a low-pH-exposed predator altered sensory and extracellular matrix-related pathways, suggesting seawater acidification may disrupt chemically mediated interspecific interactions. Together, these results show that apparent tolerance in variable coastal habitats can involve both rapid molecular compensation while masking cellular damage, and that pH stress may alter chemical communication between species.
Dataset DOI: 10.5061/dryad.w9ghx3g4z
Description of the data and file structure
Hediste diversicolor used for genome sequencing originated from the Humber Estuary, United Kingdom (53.7144° N, 0.4458° W), and were subsequently maintained and bred in the laboratory at the University of Hull for two generations in an artificial seawater tank buffered to pH 8.2. In February 2021, four adult F2 worms were flash-frozen in liquid nitrogen and sequenced at Cantata Bio (formerly Dovetail Genomics, California) using PacBio long-read sequencing and Omni-C chromosome conformation capture. A combined assembly was generated and used as the reference genome for all downstream analyses. Gene prediction was performed with BRAKER2 using transcript evidence from nine H. diversicolor transcriptomes from the Ria Formosa population and protein evidence from Polychaeta entries in UniProt and OrthoDB. Annotation was further complemented by noncoding RNAs predicted with Infernal. Additional filtering and quality-control steps were applied to remove unlikely gene models. Full assembly, annotation, and quality-control procedures are described in the Supplementary Methods
Files and variables
File: Hdiv_NCBI_submitted_annotation.gff
Description: Annotation file submitted to NCBI after cleanup
File: Hdiv_full_annotation.gtf
Description: Full annotation file including sensory genes and noncoding RNAs
File: Hdiv_NCBI_submitted_masked_genome.fasta
Description: Masked genome submitted to NCBI in fasta format
File: Hdiv_full_genome.fasta
Description: Full genome corresponding to the full annotation file in fasta format
Code/software
Genome files in fasta format and annotation files in .gtf or .gff format can be viewed with any text editor
Access information
Other publicly accessible locations of the data:
- BioProject: SAMN43593757; genome submission number SUB14896682 pending final approval at NCBI
Data was derived from the following sources:
- Newly generated by DNA sequencing and genome annotation