Oligo-FISH Validates Genome Assemblies and Delivers the Most Precise Karyotype for <i>Lens</i> Mill. Species
Bibliographic record
Abstract
Abstract Chromosome structural rearrangements play a significant role in karyotype evolution and speciation. These rearrangements pose challenges for precise karyotyping, leading to asymmetric chromosomes and complicating the assembly of a genus pan-genome for crops and their wild relatives. Lens culinaris , an important cool-season legume primarily cultivated in India and Canada, is the cultivated species among six wild relatives. All seven species of Lens face significant challenges due to chromosomal rearrangements, ranging from introgression issues to difficulties in developing a precise karyotype and advancing genomic studies. Using the gene synteny analysis between the cultivated Lens species and six wild relatives, we developed cross-species oligo-FISH (Fluorescent in situ hybridization) probes aiming to further attest to the genome assembly and synteny analysis of Lens species. Roots of seven Lens spp. accessions were harvested and used for chromosome spread preparations. Those slides were then used for Oligo-FISH experiments, where the DNA present in the slides was denatured, and a set of red and green oligo probes was hybridized to the chromosomes. Pictures were taken using a fluorescence microscope. The combination of both oligo sets/probes resulted in a distinct pattern for each Lens spp. chromosome, allowing the inference of the most precise karyotype to date for six Lens species. The number of oligo probe signals reflects the species’ phylogenetic proximity, while the distribution of those signals changed drastically within the same gene pool. The karyotyping of Lens confirmed the proper assignment of chromosomes in the genome assemblies and validated the rearrangements detected in the synteny analysis. Differences in the assembly probe prediction and the oligo-FISH results were used to improve the assemblies. The results attest to a higher sequence-level similarity among the closest related species despite the occurrence of several structural changes among them. The oligo-FISH probes can be used in conjunction with plant genome assembly projects, supporting the delivery of a precise representation of their physical chromosomes.
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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 | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.004 | 0.002 |
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".