Variation and selection on codon usage bias across an entire subphylum.

08:00 EDT 31st July 2019 | BioPortfolio

Summary of "Variation and selection on codon usage bias across an entire subphylum."

Variation in synonymous codon usage is abundant across multiple levels of organization: between codons of an amino acid, between genes in a genome, and between genomes of different species. It is now well understood that variation in synonymous codon usage is influenced by mutational bias coupled with both natural selection for translational efficiency and genetic drift, but how these processes shape patterns of codon usage bias across entire lineages remains unexplored. To address this question, we used a rich genomic data set of 327 species that covers nearly one third of the known biodiversity of the budding yeast subphylum Saccharomycotina. We found that, while genome-wide relative synonymous codon usage (RSCU) for all codons was highly correlated with the GC content of the third codon position (GC3), the usage of codons for the amino acids proline, arginine, and glycine was inconsistent with the neutral expectation where mutational bias coupled with genetic drift drive codon usage. Examination between genes' effective numbers of codons and their GC3 contents in individual genomes revealed that nearly a quarter of genes (381,174/1,683,203; 23%), as well as most genomes (308/327; 94%), significantly deviate from the neutral expectation. Finally, by evaluating the imprint of translational selection on codon usage, measured as the degree to which genes' adaptiveness to the tRNA pool were correlated with selective pressure, we show that translational selection is widespread in budding yeast genomes (264/327; 81%). These results suggest that the contribution of translational selection and drift to patterns of synonymous codon usage across budding yeasts varies across codons, genes, and genomes; whereas drift is the primary driver of global codon usage across the subphylum, the codon bias of large numbers of genes in the majority of genomes is influenced by translational selection.


Journal Details

This article was published in the following journal.

Name: PLoS genetics
ISSN: 1553-7404
Pages: e1008304


DeepDyve research library

PubMed Articles [8923 Associated PubMed Articles listed on BioPortfolio]

Nucleotide composition affects codon usage toward the 3'-end.

The 3'-end of the coding sequence in several species is known to show specific codon usage bias. Several factors have been suggested to underlie this phenomenon, including selection against translatio...

Genome-wide codon usage pattern analysis reveals the correlation between codon usage bias and gene expression in Cuscuta australis.

The protein-coding genes and pseudogenes of Cuscuta australis had the diverse contribution to the formation and evolution of parasitism. The codon usage pattern analysis of these two type genes could ...

Comprehensive codon usage analysis of Porcine Deltacoronavirus.

Porcine deltacoronavirus (PDCoV) is a newly identified coronavirus of pigs that was first reported in Hong Kong in 2012. Since then, many PDCoV isolates have been identified worldwide. In this study, ...

The fit of codon usage of human-isolated avian influenza A viruses to human.

Avian influenza A viruses (AIVs) classify into 18 hemagglutinin (HA) and 11 neuraminidase (NA) subtypes. Even though H1N1 and H3N2 subtypes usually circulate among humans leading to infection, occasio...

Compositional features and codon usage pattern of TP63 gene.

The tumor protein p63encoded by the gene TP63 acts as a homologue of p53 protein. TP63 gene is the transformation factor with two initiation sites for transcriptional process and is related with stres...

Clinical Trials [3121 Associated Clinical Trials listed on BioPortfolio]

Efficacy of Cognitive Bias Modification in Residential Treatment for Addiction

The purpose of this study is to determine whether computer bias modification for interpretation bias (CBM-I) is effective in the reduction of suicidal ideation in substance use disorders.

I-Gel vs Ambu Laryngeal Mask Airways in Infants and Children Undergoing Surgical Procedures

This study will guide the anesthetists regarding the appropriate selection of the LMA in neonatal age group based on scientific basis. This study will add up to existing literature about ...

Epidemiology of Burkitt Lymphoma in East Africa Children or Minors (EMBLEM)

Burkitt lymphoma (BL) is an aggressive monoclonal B-cell malignancy that is rare (sporadic) worldwide, but is 100-fold more common (endemic) in equatorial Africa, particularly among childr...

Development of Attention Bias Modification for Depression

Although negatively biased attention has a central theoretical and empirical role in the maintenance of depression, there are few behavioral treatments that successfully target and improve...

Cognitive Bias Modification for OCD

This study will conduct the development and preliminary evaluation of Cognitive Bias Modification for Interpretation (CBM-I) as an augmentation to treatment as usual for OCD and related di...

Medical and Biotech [MESH] Definitions

Adverse of favorable selection bias exhibited by insurers or enrollees resulting in disproportionate enrollment of certain groups of people.

The introduction of error due to systematic differences in the characteristics between those selected and those not selected for a given study. In sampling bias, error is the result of failure to ensure that all members of the reference population have a known chance of selection in the sample.

A method of analyzing the variation in utilization of health care in small geographic or demographic areas. It often studies, for example, the usage rates for a given service or procedure in several small areas, documenting the variation among the areas. By comparing high- and low-use areas, the analysis attempts to determine whether there is a pattern to such use and to identify variables that are associated with and contribute to the variation.

An amino acid-specifying codon that has been converted to a stop codon (CODON, TERMINATOR) by mutation. Its occurance is abnormal causing premature termination of protein translation and results in production of truncated and non-functional proteins. A nonsense mutation is one that converts an amino acid-specific codon to a stop codon.

A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).

Quick Search

DeepDyve research library

Relevant Topic

Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...

Searches Linking to this Article