ArticleBMC genomics2024
Intraspecific and interspecific variations in the synonymous codon usage in mitochondrial genomes of 8 pleurotus strains.
Article in BMC genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 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
24 citing papers in PubMed.
- Comparative analysis of multi-chromosomal mitochondrial genome of Bletilla striata: homologous recombination mediated by repetitive sequences.BMC plant biology · 2026Article
- Mitochondrial Graph-Based Pan-Genome Analysis ofInternational journal of molecular sciences · 2026Article
- Natural Selection Drives AT-Biased Codon Usage in Mitochondrial Genomes of Early-DivergingJournal of fungi (Basel, Switzerland) · 2026Article
- Article
- Analysis and comparison of chloroplast genome codon usage patterns in five accessions of Toxicodendron vernicifluum.BMC genomics · 2026Article
- Article
- Mitogenome characterization and phylogenetic analysis ofMitochondrial DNA. Part B, Resources · 2026Article
- The complete mitochondrial genome sequence of the angel-wing mushroomMitochondrial DNA. Part B, Resources · 2026Article
- Codon Usage Bias of the Polyphenol Oxidase Genes inPlants (Basel, Switzerland) · 2025Article
- Comparative mitogenomics reveals evolutionary drivers of Strongyloidea nematodes dwelling in gastrointestinal tract.BMC genomics · 2025Article
- Characterization of the Mitochondrial Genome ofPlants (Basel, Switzerland) · 2025Article
- Article
- Genetic Characteristics and Phylogenetic Relationships of 18 Anchovy Species Based on Mitochondrial Genomes in the Seas Around China.Ecology and evolution · 2025Article
- Multiple Horizontal Transfers of Immune Genes Between Distantly Related Teleost Fishes.Molecular biology and evolution · 2025Article
- Assembly and comparative analysis of the complete mitochondrial genome of Lactuca sativa var. ramosa Hort.Scientific reports · 2025Article
- Characterization and phylogenetic analysis of the complete mitochondrial genome ofMitochondrial DNA. Part B, Resources · 2025Article
- Comparative analysis of codon usage patterns in 16 chloroplast genomes of suborder Halimedineae.BMC genomics · 2024Article
- The impact of kaolin mining activities on bacterial diversity and community structure in the rhizosphere soil of three local plants.Frontiers in microbiology · 2024Article
- Characterization and phylogenetic analysis of theMitochondrial DNA. Part B, Resources · 2024Article
- Characterization of the complete mitochondrial genome ofMitochondrial DNA. Part B, Resources · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this study, we investigated the codon bias of twelve mitochondrial core protein coding genes (PCGs) in eight Pleurotus strains, two of which are from the same species. The results revealed that the codons of all Pleurotus strains had a preference for ending in A/T. Furthermore, the correlation between codon base compositions and codon adaptation index (CAI), codon bias index (CBI) and frequency of optimal codons (FOP) indices was also detected, implying the influence of base composition on codon bias. The two P. ostreatus species were found to have differences in various base bias indicators. The average effective number of codons (ENC) of mitochondrial core PCGs of Pleurotus was found to be less than 35, indicating strong codon preference of mitochondrial core PCGs of Pleurotus. The neutrality plot analysis and PR2-Bias plot analysis further suggested that natural selection plays an important role in Pleurotus codon bias. Additionally, six to ten optimal codons (ΔRSCU > 0.08 and RSCU > 1) were identified in eight Pleurotus strains, with UGU and ACU being the most widely used optimal codons in Pleurotus. Finally, based on the combined mitochondrial sequence and RSCU value, the genetic relationship between different Pleurotus strains was deduced, showing large variations between them. This research has improved our understanding of synonymous codon usage characteristics and evolution of this important fungal group.
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.