Poplar ruse: the melampsora larici-populina genome sequencing project
Bibliographic record
Abstract
The basidiomycete Melampsora larici-populina is responsible for the leaf rust disease in Populus species. Urediniospore germlings of this obligate biotrophic fungus usually penetrate the host plant through stomatal openings, differentiates a series of infection structures in the intercellular space, and exhibits highly localized penetration of the host cell wall to establish a haustorium. Hyphae then proliferate in the leaf parenchyma and produce golden pustules filled with masses of urediniospores on the lower leaf surfaces. M. larici-populina causes severe economic losses in European poplar plantations and has recently been detected in Canada. Selection for resistance to this biotrophic pathogen is thus an important challenge for poplar breeders. Severe damages occur through decreased photosynthesis efficiency, early defoliation and increased susceptibility to other pests and diseases. The PGF is sequencing this organism by the whole genome shotgun (WGS) method. Generally we make genomic libraries containing 3 different insert sizes. For all libraries, the DNA is randomly sheared, fragments end repaired and size selected prior to cloning. After cleanup the 3kb insert is ligated into pUC18 vector and the 8kb and 40kb fragments are ligated into pMCL200 and pcc1Fos vectors. The libraries are sequenced to a depth of approximately 4X, 4X, and 0.5-1X coverage respectively. The JGI has recently sequenced the genome to approximately 4x coverage of this plant pathogen, and is currently sequencing to the 8-9X depth prior to final assembly. The initial size was estimated to be approximately 61 Million bases (Mb), and analysis at the 4X assembly allowed us to revise this estimate to approximately 95 Mb. Library construction, genome assembly and size analysis will be presented.
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 | 0.002 | 0.001 |
| Meta-epidemiology (narrow) | 0.002 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.003 | 0.005 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.005 | 0.005 |
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".