Telomere-to-telomere genome assembly of matsutake ( <i>Tricholoma matsutake</i> )
Bibliographic record
Abstract
Abstract Here, we report the first telomere-to-telomere genome assembly of matsutake ( Tricholoma matsutake ), which consists of 13 chromosomes (spanning 160.7 Mb) and a 76 kb circular mitochondrial genome. The chromosome sequences were supported with telomeric repeats at the ends. GC-rich regions are located at the middle of the chromosomes and are enriched with long interspersed nuclear elements (LINEs). Repetitive sequences including long-terminal repeats (LTRs) and LINEs occupy 71.7% of the genome. A total of 28,322 potential protein-coding genes and 324 tRNA genes were predicted. Sequence and structure variant analysis revealed 2,322,349 single nucleotide polymorphisms and 102,831 insertions and deletions, 0.6% of which disrupted gene structure and function and were therefore classified as deleterious mutations. As many as 683 copies of the LTR retrotransposon MarY1 were detected in the matsutake genome, 91 of which were inserted in gene sequences. In addition, 187 sequence variations were found in the mitochondrial genome. The genomic data reported in this study would serve as a great reference for exploring the genetics and genomics of matsutake in the future, and the information gained would ultimately facilitate the conservation of this vulnerable genetic resource.
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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 | 0.001 |
| Bibliometrics | 0.001 | 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 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.001 |
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".