ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2009
Codon usages of genes on chromosome, and surprisingly, genes in plasmid are primarily affected by strand-specific mutational biases in Lawsonia intracellularis.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2009. 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, 37 citations in OpenAlex.
- Mitogenomic Codon Usage Patterns of Superfamily Certhioidea (Aves, Passeriformes): Insights into Asymmetrical Bias and Phylogenetic Implications.Animals : an open access journal from MDPI · 2022Article
- Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins.Genomics, proteomics & bioinformatics · 2022Article
- The Shift in Synonymous Codon Usage Reveals Similar Genomic Variation during Domestication of Asian and African Rice.International journal of molecular sciences · 2022Article
- Consistent Clustering Pattern of Prokaryotic Genes Based on Base Frequency at the Second Codon Position and its Association with Functional Category Preference.Interdisciplinary sciences, computational life sciences · 2022Article
- Alteration of synonymous codon usage bias accompanies polyploidization in wheat.Frontiers in genetics · 2022Article
- Asymmetric Somatic Hybridization Affects Synonymous Codon Usage Bias in Wheat.Frontiers in genetics · 2021Article
- Polyploidization is accompanied by synonymous codon usage bias in the chloroplast genomes of both cotton and wheat.PloS one · 2020Article
- Reconsidering plasmid maintenance factors for computational plasmid design.Computational and structural biotechnology journal · 2019Review
- Mutational Pressure in Zika Virus: Local ADAR-Editing Areas Associated with Pauses in Translation and Replication.Frontiers in cellular and infection microbiology · 2017Article
- Multiple Evolutionary Selections Involved in Synonymous Codon Usages in the Streptococcus agalactiae Genome.International journal of molecular sciences · 2016Article
- Multiple Factors Drive Replicating Strand Composition Bias in Bacterial Genomes.International journal of molecular sciences · 2015Article
- Comparative investigation of the various determinants that influence the codon and amino acid usage patterns in the genus Bifidobacterium.World journal of microbiology & biotechnology · 2015Article
- Synonymous codon usage bias in plant mitochondrial genes is associated with intron number and mirrors species evolution.PloS one · 2015Article
- Synonymous Codon Usage Bias in the Plastid Genome is Unrelated to Gene Structure and Shows Evolutionary Heterogeneity.Evolutionary bioinformatics online · 2015Article
- Microbial lifestyle and genome signatures.Current genomics · 2012Article
- DNA replication and strand asymmetry in prokaryotic and mitochondrial genomes.Current genomics · 2012Article
- A blueprint for a mutationist theory of replicative strand asymmetries formation.Current genomics · 2012Article
- Coding constraints modulate chemically spontaneous mutational replication gradients in mitochondrial genomes.Current genomics · 2012Article
- Measures of compositional strand bias related to replication machinery and its applications.Current genomics · 2012Article
- Comparative study on factors influencing the codon and amino acid usage in Lactobacillus sakei 23K and 13 other lactobacilli.Molecular biology reports · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this study, the factors driving genome-wide patterns of codon usages in Lawsonia intracellularis genome are determined. For genes on the chromosome of the bacterium, it is found that the most important source of variation results from strand-specific mutational biases. A lesser trend of variation is attributable to genes that are presumed as horizontally transferred. These putative alien genes are unusually GC richer than the other genes, whereas horizontally transferred genes have been observed to be AT rich in bacteria with medium and relatively low G + C contents. Hydropathy of encoded protein and expression level are also found to influence codon usage. Therefore, codon usage in L. intracellularis chromosome is the result of a complex balance among the different mutational and selectional factors. When analyzing genes in the largest plasmid, for the first time it is found that the strand-specific mutational biases are responsible for the primary variation of codon usages in plasmid. Genes, particularly highly expressed genes of this plasmid, are mainly located on the leading strands and this supposed to be the effects exerted by replicational-transcriptional selection. These facts suggest that this plasmid adopts the similar mechanism of replication as the chromosome in L. intracellularis. Common characters among the 10 bacteria in whose genomes the strand-specific mutational biases are the primary source of variation of codon usage are also investigated. For example, it is found that genes dnaT and fis that are involved in DNA replication initiation and re-initiation pathways are absent in all of the 10 bacteria.
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.