Updated Sequence and Annotation of the Broad Host Range Rhizobial Symbiont Sinorhizobium fredii HH103 Genome
Bibliographic record
Abstract
Background: Sinorhizobium fredii HH103 is a fast-growing rhizobial strain capable of infecting a broad range of legumes, including plants forming determinate and indeterminate nodules, such as Glycine max (its natural host) and Glycyrrhiza uralensis, respectively. Previous studies reported the sequence and annotation of the genome of this strain (7.25 Mb), showing the most complex S. fredii genome sequenced to date. It comprises seven replicons: one chromosome and six plasmids. Among these plasmids, pSfHH103d, also known as the symbiotic plasmid pSymA, harbors most of the genes involved in symbiosis. Due to limitations of the sequencing technology used at the time and the presence of high number of clusters of transposable elements, this plasmid could only be partially assembled as four separated contigs. Methods: In this work, we have used a combination of PacBio and Illumina sequencing technologies to resolve these complex regions, obtaining an updated genome sequence (7.27 Mb). Results: This updated version includes an increase in size of the largest replicons (chromosome, pSfHH103d, and pSfHH103e) and a complete and closed symbiotic plasmid (pSfHH103d or pSymA). Additionally, we carried out a re-annotation of the updated genome, merging the previous annotation and the new one found in the remaining gaps. Notably, we found a high number of transposable elements in the HH103 genome, especially in three plasmids (pSfHH103b, pSfHH103c, and pSymA), a feature that is common among S. fredii strains. Conclusions: The combination of PacBio and Illumina sequencing technologies has allowed us to obtain a complete version of the HH103 pSymA. The presence of a high number of mobile elements seems to be a general characteristic among S. fredii strains, a fact that might be related to a high genome plasticity.
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 distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| 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 | 0.000 |
| 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) | 0.000 | 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 teacher head, 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".