A complete genome of Bathymodiolus thermophilus thioautotrophic symbiont reveals a unique hydrogenase operon among hydrothermal vent mussel symbionts
Bibliographic record
Abstract
The mytilid mussel Bathymodiolus thermophilus lives in the deep-sea hydrothermal vent regions due to its symbiotic relationship with chemosynthetic Gammaproteobacteria species which reside inside specialized gill cells. The symbionts in the gill bacteriocytes oxidize the reduced sulfur amply available in the vent environment. Here we sequenced and assembled the complete genome of a gill symbiont sampled from an individual mussel from the East Pacific Rise (EPR9N), using PacBio sequencing technology. The final symbiont assembly consists of a single contig size of 2.83 Mb, with a GC content of 38.6% and encodes for 2,133 protein-coding genes. CRISPR diversity analysis confirmed this genome originated from a single symbiont strain. Comparative analysis revealed 2,554 core gene clusters were shared with other B. thermophilus thiotrophic gill symbiont genomes, whereas 125 were unique to this EPR9N strain. In addition, we found that EPR9N strain has a unique hydrogenase operon among Bathymodiolus mussels consisting of additional H2-sensing hydrogenase subunits and a histidine kinase gene. Also, we found methylated regions sparsely distributed throughout the EPR9N genome, mainly in the transposases regions and densely present in the rRNA gene regions. Variation in genome size, gene content and genome re-arrangements across individual hosts suggest multiple symbiont strains can associate with B. thermophilus. This complete mussel symbiont genome will be invaluable for further comparative genomic analyses studying structural genome evolution, symbiont population diversity, and symbiont ecology in deep-sea chemosynthetic environments.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".