Biodiversity of <i>Tricholoma matsutake</i> (syn. <i>T. nauseosum</i>) and its related species based on repetitive DNA and genomics
Bibliographic record
Abstract
Tricholoma matsutake and its related species are ectomycorrhizal Agaricomycetes that produce prized mushrooms collectively called “ matsutake”. These mushrooms are mainly distributed in the Northern Hemisphere. In this review, we describe both the pioneering work and recent advances in our understanding of the distribution and evolution of matsutake, with a special focus on genomic studies. Deoxyribonucleic acid (DNA) sequence analyses revealed that Tricholoma caligatum was the earliest species within this group, followed by Tricholoma fulvocastaneum, the cluster with Tricholoma ilkkae, Tricholoma dulciolens, and Tricholoma bakamatsutake, and finally the cluster with Tricholoma murrillianum, Tricholoma mesoamericanum, Tricholoma anatolicum, and Tricholoma matsutake. Although analyses based on mobile DNAs and whole-genome sequences revealed a similar clustering pattern, there are distinct differences in the distribution of mobile DNAs and genomic structure of Tricholoma bakamatsutake and Tricholoma matsutake. Furthermore, repetitive DNA can be used as markers to distinguish among strains and populations of Tricholoma matsutake from different geographical regions, including identifying dispersals of basidiospores. “Telomere-to-telomere genome sequencing” analyses unearthed that both Tricholoma matsutake and Tricholoma bakamatsutake underwent explosive multiplications of retrotransposons within their genomes but with different mobile DNA elements expanded between them. Contrastingly, the structure of the mating loci between Tricholoma matsutake and Tricholoma bakamatsutake is highly conserved.
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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 | 0.000 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.001 |
| 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".