ArticleGenome biology and evolution2011
Evolution of synonymous codon usage in Neurospora tetrasperma and Neurospora discreta.
Article in Genome biology and evolution, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 34 citations in OpenAlex.
- The identification of conserved sequence features of co-translationally decayed mRNAs and upstream open reading frames in angiosperm transcriptomes.Plant direct · 2023Article
- Adaptation of codon and amino acid use for translational functions in highly expressed cricket genes.BMC genomics · 2021Article
- Evidence of multifaceted functions of codon usage in translation within the model beetle Tribolium castaneum.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Comprehensive profiling of codon usage signatures and codon context variations in the genus Ustilago.World journal of microbiology & biotechnology · 2019Article
- Article
- Expression-Linked Patterns of Codon Usage, Amino Acid Frequency, and Protein Length in the Basally Branching Arthropod Parasteatoda tepidariorum.Genome biology and evolution · 2016Article
- Introgression maintains the genetic integrity of the mating-type determining chromosome of the fungus Neurospora tetrasperma.Genome research · 2016Article
- Codon and Amino Acid Usage Are Shaped by Selection Across Divergent Model Organisms of the Pancrustacea.G3 (Bethesda, Md.) · 2015Article
- Nonoptimal codon usage influences protein structure in intrinsically disordered regions.Molecular microbiology · 2015Article
- Intron evolution in Neurospora: the role of mutational bias and selection.Genome research · 2015Article
- Evaluation of codon biology in citrus and Poncirus trifoliata based on genomic features and frame corrected expressed sequence tags.DNA research : an international journal for rapid publication of reports on genes and genomes · 2013Article
- Statistical analysis of pentose phosphate pathway genes from eubacteria and eukarya reveals translational selection as a major force in shaping codon usage pattern.Bioinformation · 2013Article
- Evolution of codon usage in the smallest photosynthetic eukaryotes and their giant viruses.Genome biology and evolution · 2013Article
- Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma.Genetics · 2011Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Neurospora comprises a primary model system for the study of fungal genetics and biology. In spite of this, little is known about genome evolution in Neurospora. For example, the evolution of synonymous codon usage is largely unknown in this genus. In the present investigation, we conducted a comprehensive analysis of synonymous codon usage and its relationship to gene expression and gene length (GL) in Neurospora tetrasperma and Neurospora discreta. For our analysis, we examined codon usage among 2,079 genes per organism and assessed gene expression using large-scale expressed sequenced tag (EST) data sets (279,323 and 453,559 ESTs for N. tetrasperma and N. discreta, respectively). Data on relative synonymous codon usage revealed 24 codons (and two putative codons) that are more frequently used in genes with high than with low expression and thus were defined as optimal codons. Although codon-usage bias was highly correlated with gene expression, it was independent of selectively neutral base composition (introns); thus demonstrating that translational selection drives synonymous codon usage in these genomes. We also report that GL (coding sequences [CDS]) was inversely associated with optimal codon usage at each gene expression level, with highly expressed short genes having the greatest frequency of optimal codons. Optimal codon frequency was moderately higher in N. tetrasperma than in N. discreta, which might be due to variation in selective pressures and/or mating systems.
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