De novo assembly, functional annotation and comparative alignment of whole genome of a halo-tolerant Exiguobacterium profundum PHM11 with related genomes
Bibliographic record
Abstract
Advances in the next-generation sequencing (NGS) technologies have invigorated the exploration of microbial genomes in retrieving the hidden traits. In this study, high-throughput next generation whole genome sequencing of a halotolerant E. profundum PHM11 was performed on Illumina HiSeq paired end sequencing plateform and assembled through de novo Linux based approaches using Velvet (V 1.2.10.) algorithm package. Quality filtering in de novo sequencing produced 72,947,390 reads with total size of 7335195362 bp (7335.1 Mb). High quality reads having minimum and maximum contig lengths of 202 and 958471 (~0.95 Mb) bp were further considered for assembly. Final PHM11 genome has a size of ~2.92 Mb comprising 70 contigs, 47.93% G+C content with 761858 (26.08%), 757313 (25.92%), 699924 (23.96%), and 700172 (23.97%) percentages of adenine, thymine, cytosine and guanine nucleotides. Throughout micro-satellite mining of genome showed a total of 3005 SSRs, covering 0.1 of whole PHM11 genome, with relative abundance; 1029, relative density; 10951, and percentages of penta repeats; 65.75, hexa repeats; 28.75, mono repeats; 3.89, and tetra-repeats; 1.59, respectively. Gene networks related to the arrangement of key genes and presence of lysogenic phage DNA were reflected through generating the chromosome map of PHM11 genome. Functional annotations of genome reflected the different protein families, and hidden inherent metabolic pathways providing unusual features. A total of 3033 protein coding genes and 33 non-protein coding genes were identified; out of these only 2316 could be characterized and 737 were reported as hypothetical. Random genes of different metabolic pathways were amplified from its genome and authenticated through their sequencing. Genome-rearrangements in PHM11 could be deciphered through aligning its genome with thirteen other genomes of different Exiguobacterium species.
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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 | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 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".