ArticleMolecular biology and evolution2022
Kingdom-Wide Analysis of Fungal Protein-Coding and tRNA Genes Reveals Conserved Patterns of Adaptive Evolution.
Article in Molecular biology and evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 32 citations in OpenAlex.
- Discriminating models of trait evolution.Evolution; international journal of organic evolution · 2026Article
- Comparative analysis of tRNAs across mouse strains reveals gene-specific conservation, divergence, and copy number variation.BMC genomics · 2026Article
- A previously unrecognized class of fungal ice-nucleating proteins with bacterial ancestry.Science advances · 2026Article
- Extreme GC3 codon bias in a novel brown seaweed virus results in pseudoambigrammatic characteristics.Virus evolution · 2026Article
- Genus-wide comparative genomics ofIMA fungus · 2026Article
- mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset.Nature communications · 2025Article
- Macroevolutionary changes in natural selection on codon usage reflect evolution of the tRNA pool across a budding yeast subphylum.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Genomic factors shaping codon usage across the Saccharomycotina subphylum.G3 (Bethesda, Md.) · 2024Article
- Comparative genomic analysis of thermophilic fungi reveals convergent evolutionary adaptations and gene losses.Communications biology · 2024Article
- CodonBERT large language model for mRNA vaccines.Genome research · 2024Article
- Codon Optimization Improves the Prediction of Xylose Metabolism from Gene Content in Budding Yeasts.Molecular biology and evolution · 2023Article
- De Novo Assembly and Characterization of the Transcriptome of an Omnivorous Camel Cricket (International journal of molecular sciences · 2023Article
- Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi.G3 (Bethesda, Md.) · 2023Article
- Analysis of synonymous codon usage patterns in mitochondrial genomes of nineFrontiers in microbiology · 2023Article
- Article
- Composition and Codon Usage Pattern Results in Divergence of theJournal of fungi (Basel, Switzerland) · 2022Article
- Tempo of Degeneration Across Independently Evolved Nonrecombining Regions.Molecular biology and evolution · 2022Article
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Authors and funding
3 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Protein-coding genes evolved codon usage bias due to the combined but uneven effects of adaptive and nonadaptive influences. Studies in model fungi agree on codon usage bias as an adaptation for fine-tuning gene expression levels; however, such knowledge is lacking for most other fungi. Our comparative genomics analysis of over 450 species supports codon usage and transfer RNAs (tRNAs) as coadapted for translation speed and this is most likely a realization of convergent evolution. Rather than drift, phylogenetic reconstruction inferred adaptive radiation as the best explanation for the variation of interspecific codon usage bias. Although the phylogenetic signals for individual codon and tRNAs frequencies are lower than expected by genetic drift, we found remarkable conservation of highly expressed genes being codon optimized for translation by the most abundant tRNAs, especially by inosine-modified tRNAs. As an application, we present a sequence-to-expression neural network that uses codons to reliably predict highly expressed transcripts. The kingdom Fungi, with over a million species, includes many key players in various ecosystems and good targets for biotechnology. Collectively, our results have implications for better understanding the evolutionary success of fungi, as well as informing the biosynthetic manipulation of fungal genes.
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