Chromosome-level genome assembly of the deep-sea solemyid bivalve Acharax haimaensis – Scientific Data
A new chromosome-scale reference genome for the deep-sea bivalve Acharax haimaensis offers a rare window into how an ancient lineage thrives in sulfide-rich sediments with the help of symbiotic bacteria. Published in Scientific Data, the study delivers the first genome from a deep-sea protobranch, setting the stage for discoveries in bivalve evolution, host–microbe partnerships, and adaptation to extreme environments.
Why Acharax haimaensis matters
Solemyidae—an ancient group of protobranch bivalves—stand out for their unusual body plan and obligate symbiosis with sulfur-oxidizing bacteria. These microbes power their hosts’ survival in toxic, low-oxygen, sulfide-laden sediments by converting chemical energy into nutrients. Despite their evolutionary importance, genomic insights into Solemyidae have been scarce, limiting progress on questions surrounding their origins, biology, and the genes that underpin a life built on symbiosis.
A chromosome-level assembly with modern sequencing
The research team combined PacBio long reads, Illumina short reads, and Hi-C chromatin conformation data to produce a high-quality assembly:
- Genome size: 4.27 Gb
- Scaffold N50: 195.52 Mb (indicating long, highly contiguous sequences)
- Chromosomal anchoring: 22 chromosomes
- Completeness: 98.2% based on BUSCO (a standard benchmarking tool for conserved single-copy genes)
In practical terms, the assembly’s contiguity and completeness make it suitable for detailed gene discovery, structural genome analyses, and comparative genomics across bivalves and other mollusks.
What’s inside the genome
The A. haimaensis genome is rich in repetitive DNA, a hallmark of many large animal genomes. Transposable elements account for 50.17% of the assembly, with long interspersed nuclear elements (LINEs) representing 14.20%. These mobile sequences can shape genome architecture and regulation, potentially influencing how species adapt to challenging environments.
The team predicted 38,343 protein-coding genes, and 87.25% of them could be functionally annotated using existing databases. This broad annotation coverage will accelerate efforts to pinpoint gene families linked to symbiosis, sulfur metabolism, detoxification, immunity, and other stress-response pathways vital to deep-sea living.
Rewriting bivalve chromosome history
Macrosynteny analyses—comparing large-scale chromosome structures across species—revealed that each A. haimaensis chromosome typically comprises two to four segments derived from ancestral linkage groups. This mosaic structure points to extensive chromosomal breakage and fusion early in bivalve evolution. Such rearrangements can have far-reaching biological consequences, from altering gene regulation to changing how traits are inherited over time.
An ancient divergence
Phylogenetic inference places A. haimaensis as diverging from the common ancestor of Autobranchia approximately 550 million years ago. That timeframe underscores Solemyidae’s deep evolutionary roots and suggests that their unique symbiosis and morphological traits arose against the backdrop of profound genomic restructuring.
Why this resource changes the game
This reference genome fills a critical gap for deep-sea and protobranch bivalves, unlocking several avenues for discovery:
- Symbiosis genetics: Dissect host–microbe interactions, from nutrient exchange to immune tolerance of sulfur-oxidizing partners.
- Extreme-environment adaptation: Identify gene networks for coping with sulfide toxicity, hypoxia, and fluctuating chemical gradients.
- Comparative evolution: Map conserved and novel pathways across bivalves to reconstruct how lineages diversified and adapted.
- Genome architecture: Explore how transposable elements and chromosome rearrangements shaped trait evolution over hundreds of millions of years.
Key technical takeaways at a glance
- First chromosome-level genome from a deep-sea protobranch bivalve.
- 4.27 Gb assembly with a 195.52 Mb scaffold N50 and 22 anchored chromosomes.
- High completeness (98.2% BUSCO), enabling robust downstream analyses.
- Half the genome is repetitive, dominated by LINEs (14.20%).
- 38,343 predicted protein-coding genes; 87.25% functionally annotated.
- Macrosynteny indicates widespread ancient chromosomal breakage and fusion.
- Divergence from the Autobranchia ancestor estimated at ~550 Mya.
The road ahead
With this genome as a foundation, researchers can now pursue targeted functional studies—such as transcriptomics of host tissues, population genomics across deep-sea habitats, and cross-species comparisons that track the evolution of symbiosis. The data also provide a baseline for investigating how environmental pressures sculpt genome content and organization in the deep sea.
Ultimately, the A. haimaensis genome is more than a reference: it’s a framework for decoding the molecular strategies that let life flourish where chemistry and geology rule—shedding light on the origins of bivalves and the genetic playbook for survival in Earth’s most extreme marine sediments.
