Genome Survey and Mitochondrial Genome Analysis of Wild Silkworm, <i>Bombyx mandarina</i>
Bibliographic record
Abstract
In this study, the genome of Bombyx mandarina is investigated and the mitochondrial genome is analyzed, which lays a reference for the whole genome sequencing and to provide basic data for the genetic relationships between Bombyx mandarina and Bombyx mori . Using the Illumina HiSeq2000 pair-end sequencing platform, a female Bombyx mandarina was sequenced. K-mer analysis was adopted to estimate genome size, heterozygosity and GC contend. SOAPdenove tools was applied to genome pre-assembled. The mitochondrial genome was assembled by NOVOPlasty, annotated and visualized by GeSeq online tool, MEGA-X used to build phylogenetic tree. Obtained 25.8 GB clean data, the estimated genome size of Bombyx mandarina is 456.5 Mb, the heterozygosity rate is 1.94%. After preliminary assembly, the scaffold N50 is 1792 bp, scaffold number is 737055, contig N50 is 587 bp, contig number is 1477268. As assembly and annotation, the mitochondrial genome of Qin-Ba wild silkworm is 15662 bp, a total of 37 genes were arranged in the mitochondrial genome, which did not have a gene rearrangement. According the phylogenetic tree of mitochondrial genome, wild silkworm could be divided into north or south group according to the geographical source. Wild silkworm came from the North China as Shaanxi, Shandong and Liaoning province has the closest genetical relationship with the domestic silkworm. Since the genome of Qin-ba wild silkworm belong to the complex genome, integrating the second-, the third- generation sequencing and Hi-C technology could be helpful to obtain high quality genomic of Bombyx mandarina . This study also supports the contention that domestic of silkworm descended from the northern of China, and implied that the Qin-ba mountain area could be one of the original regions of domestic silkworm.
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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 | 0.002 |
| Science and technology studies | 0.001 | 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) | 0.002 | 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".