Comparative Analysis of the Chloroplast Genomes of the Chinese Endemic Genus Urophysa and Their Contribution to Chloroplast Phylogeny and Adaptive Evolution
Bibliographic record
Abstract
Urophysa is a Chinese endemic genus comprising two species, Urophysa rockii and Urophysa henryi. In this study, we sequenced the complete chloroplast (cp) genomes of these two species and of their relative Semiquilegia adoxoides. Illumina sequencing technology was used to compare sequences, elucidate the intra- and interspecies variations, and infer the phylogeny relationship with other Ranunculaceae family species. A typical quadripartite structure was detected, with a genome size from 158,473 to 158,512 bp, consisting of a pair of inverted repeats separated by a small single-copy region and a large single-copy region. We analyzed the nucleotide diversity and repeated sequences components and conducted a positive selection analysis by the codon-based substitution on single-copy coding sequence (CDS). Seven regions were found to possess relatively high nucleotide diversity, and numerous variable repeats and simple sequence repeats (SSR) markers were detected. Six single-copy genes (atpA, rpl20, psaA, atpB, ndhI, and rbcL) resulted to have high posterior probabilities of codon sites in the positive selection analysis, which means that the six genes may be under a great selection pressure. The visualization results of the six genes showed that the amino acid properties across each column of all species are variable in different genera. All these regions with high nucleotide diversity, abundant repeats, and under positive selection will provide potential plastid markers for further taxonomic, phylogenetic, and population genetics studies in Urophysa and its relatives. Phylogenetic analyses based on the 79 single-copy genes, the whole complete genome sequences, and all CDS sequences showed same topologies with high support, and U. rockii was closely clustered with U. henryi within the Urophysa genus, with S. adoxoides as their closest relative. Therefore, the complete cp genomes in Urophysa species provide interesting insights and valuable information that can be used to identify related species and reconstruct their phylogeny.
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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 | 0.000 | 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) | 0.001 | 0.000 |
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".