Comparison of AFLP fingerprints and ITS sequences as phylogenetic markers in Ustilaginomycetes
Why is this work in the frame?
A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.
Full frame distilled prediction
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.
- Candidate categories
- none
- Consensus categories
- none
- Domain
- Candidate signal: noneConsensus signal: none
- Study design
- Candidate signal: ObservationalConsensus signal: none
- Genre
- Candidate signal: EmpiricalConsensus signal: Empirical
- Teacher disagreement score
- 0.566
- Threshold uncertainty score
- 0.369
- Validation status
machine_predicted_unvalidated·codex-gemma-dda1882f352a
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)
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
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.
- Teacher spread
- 0.261 · how far apart the two teachers sit on this one work
- Validation status
score_only:v0-immature-baseline· verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it
Abstract
We have compared the use of DNA sequences from the genomic internal transcribed spacer (ITS) ribosomal RNA region, with a newer method, the amplified fragment length polymorphism (AFLP) technique. ITS sequences encompass only a small part of the genome but normally reveal sufficient variability to distinguish isolates at the genus and often the species level. Although the AFLP technology reveals genome-wide restriction fragment length polymorphisms, it has not been employed extensively in establishing phylogenetic relationships. We have adapted the AFLP technology for fungal genomes and compared AFLP fingerprints generated from several fungal species and isolates from the order Ustilaginales: Ustilago hordei, U. nigra, U. aegilopsidis, U. avenae, U. kolleri, U. bullata, U. nuda, U. tritici, U. maydis, U. scitaminea, Sporisorium reilianum, and Tilletiales: Tilletia indica and T. walkeri. Geographical isolates of U. hordei and related species, particularly those infecting small-grain cereals, were difficult to distinguish when comparing ITS sequences, but were clearly separated when comparing AFLP fingerprints. The abundance of polymorphisms makes the AFLP technique more suitable to distinguish organisms in clusters of closely related species and at the isolate level. Phylogenetic analyses of the data sets generated with the two methods revealed that the AFLP-derived phylogenetic relationships were not in disagreement with the ITS-derived tree. The fungal phylogenetic tree correlated additionally with one from the graminaceous hosts generated from literature data, suggesting coevolution of some specialized host-pathogen systems. The clustering of small grain-infecting smuts due to limited genetic variability, in combination with other molecular, mating and literature data, suggests reclassification of this group possibly to include varietas designations to define host range.
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.
The record
- Venue
- Mycologia
- Topic
- Plant Pathogens and Fungal Diseases
- Field
- Biochemistry, Genetics and Molecular Biology
- Canadian institutions
- University of British ColumbiaAgriculture and Agri-Food Canada
- Funders
- not available
- Keywords
- BiologyAmplified fragment length polymorphismPhylogenetic treeEvolutionary biologyPhylogeneticsDNA profilingGeneticsComputational biologyGenetic diversityGeneDNA
- Has abstract in OpenAlex
- yes