ArticleBMC genomics2018
Analysis of codon usage patterns in Hirudinaria manillensis reveals a preference for GC-ending codons caused by dominant selection constraints.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
34 citing papers in PubMed, 81 citations in OpenAlex.
- Characterization ofEcology and evolution · 2026Article
- Codon usage bias and selective constraints in Gentianales mitogenomes.BMC genomics · 2026Article
- Comparative chloroplast genomics reveals codon usage bias, simple sequence repeat dynamics, and phylogenomic relationships in Urticaceae.Frontiers in plant science · 2026Article
- Codon usage bias and molecular evolution ofFrontiers in genetics · 2026Article
- Codon Usage Bias of the Polyphenol Oxidase Genes inPlants (Basel, Switzerland) · 2025Article
- Integrating multi-omic data to identify key genes and pathways involved in rice bacterial leaf streak disease.Scientific reports · 2025Article
- Mitochondrial PCGs Provide Novel Insights into Subspecies Classification, Codon Usage and Selection ofAnimals : an open access journal from MDPI · 2025Article
- The first complete mitochondrial genome of Curcuma amarissima (Zingiberaceae): insights into multi-branch structure, codon usage, and phylogenetic evolution.BMC genomics · 2025Article
- Analysis of Codon Usage Patterns in a Rare Palmitoleic Acid Production Oleaginous Yeast, Scheffersomyces segobiensis.Current microbiology · 2025Article
- Codon usage bias analysis of theFrontiers in genetics · 2025Article
- Complete chloroplast genome sequence and phylogenetic analysis of Symphytum officinale.Genetics and molecular biology · 2025Article
- Analysis of Codon Usage Bias in the Plastid Genome ofCurrent issues in molecular biology · 2024Article
- Comparative Analysis of Codon Usage Bias in SixInternational journal of molecular sciences · 2024Article
- Comparative analysis of codon usage bias in chloroplast genomes of ten medicinal species of Rutaceae.BMC plant biology · 2024Article
- Assembly, annotation and analysis of the chloroplast genome of the Algarrobo tree Neltuma pallida (subfamily: Caesalpinioideae).BMC plant biology · 2023Article
- Article
- De Novo Assembly and Characterization of the Transcriptome of an Omnivorous Camel Cricket (International journal of molecular sciences · 2023Article
- Comparative analysis of codon usage patterns in chloroplast genomes of ten Epimedium species.BMC genomic data · 2023Article
- Codon Pattern and Compositional Constraints Determination of Genes Associated with Chronic Periodontitis.Genes · 2022Article
- A Study on microRNAs Targeting the Genes Overexpressed in Lung Cancer and their Codon Usage Patterns.Molecular biotechnology · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
backgroundHirudinaria manillensis is an ephemeral, blood-sucking ectoparasite, possessing anticoagulant capacities with potential medical applications. Analysis of codon usage patterns would contribute to our understanding of the evolutionary mechanisms and genetic architecture of H. manillensis, which in turn would provide insight into the characteristics of other leeches. We analysed codon usage and related indices using 18,000 coding sequences (CDSs) retrieved from H. manillensis RNA-Seq data.
resultsWe identified four highly preferred codons in H. manillensis that have G/C-endings. Points generated in an effective number of codons (ENC) plot distributed below the standard curve and the slope of a neutrality plot was less than 1. Highly expressed CDSs had lower ENC content and higher GC content than weakly expressed CDSs. Principal component analysis conducted on relative synonymous codon usage (RSCU) values divided CDSs according to GC content and divided codons according to ending bases. Moreover, by determining codon usage, we found that the majority of blood-diet related genes have undergone less adaptive evolution in H. manillensis, except for those with homologous sequences in the host species.
conclusionsCodon usage in H. manillensis had an overall preference toward C-endings and indicated that codon usage patterns are mediated by differential expression, GC content, and biological function. Although mutation pressure effects were also notable, the majority of genetic evolution in H. manillensis was driven by natural selection.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.