ArticleGenome biology and evolution2015
Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in picea gene families.
Article in Genome biology and evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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35 citing papers in PubMed, 71 citations in OpenAlex.
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- Comparative Analysis on the Codon Usage Pattern of the Chloroplast Genomes in Malus Species.Biochemical genetics · 2023Article
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- The evolutionary patterns, expression profiles, and genetic diversity of expanded genes in barley.Frontiers in plant science · 2023Article
- The good, the bad, and the ugly: Evolutionary and pathological aspects of gene dosage alterations.PLoS genetics · 2021Review
- Context-dependent and -independent selection on synonymous mutations revealed by 1,135 genomes of Arabidopsis thaliana.BMC ecology and evolution · 2021Article
- Comprehensive analysis of coding sequence architecture features and gene expression inPhysiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- Efficient Multi-Sites Genome Editing and Plant RegenerationFrontiers in plant science · 2021Article
- Comparative Analysis of Genomic and Transcriptome Sequences Reveals Divergent Patterns of Codon Bias in Wheat and Its Ancestor Species.Frontiers in genetics · 2021Article
- Codon-based indices for modeling gene expression and transcript evolution.Computational and structural biotechnology journal · 2021Review
- Correlation between gene expression levels under drought stress and synonymous codon usage in rice plant by in-silico study.PloS one · 2020Article
- Functional and morphological evolution in gymnosperms: A portrait of implicated gene families.Evolutionary applications · 2020Article
- Parsing the synonymous mutations in the maize genome: isoaccepting mutations are more advantageous in regions with codon co-occurrence bias.BMC plant biology · 2019Article
- Utilization of Tissue Ploidy Level Variation inG3 (Bethesda, Md.) · 2019Article
- Variation of gene expression in plants is influenced by gene architecture and structural properties of promoters.PloS one · 2019Article
- A catalog of annotated high-confidence SNPs from exome capture and sequencing reveals highly polymorphic genes in Norway spruce (Picea abies).BMC genomics · 2018Article
- Comparative analysis of selection mode reveals different evolutionary rate and expression pattern in Arachis duranensis and Arachis ipaënsis duplicated genes.Plant molecular biology · 2018Article
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Authors and funding
4 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The recent sequencing of several gymnosperm genomes has greatly facilitated studying the evolution of their genes and gene families. In this study, we examine the evidence for expression-mediated selection in the first two fully sequenced representatives of the gymnosperm plant clade (Picea abies and Picea glauca). We use genome-wide estimates of gene expression (>50,000 expressed genes) to study the relationship between gene expression, codon bias, rates of sequence divergence, protein length, and gene duplication. We found that gene expression is correlated with rates of sequence divergence and codon bias, suggesting that natural selection is acting on Picea protein-coding genes for translational efficiency. Gene expression, rates of sequence divergence, and codon bias are correlated with the size of gene families, with large multicopy gene families having, on average, a lower expression level and breadth, lower codon bias, and higher rates of sequence divergence than single-copy gene families. Tissue-specific patterns of gene expression were more common in large gene families with large gene expression divergence than in single-copy families. Recent family expansions combined with large gene expression variation in paralogs and increased rates of sequence evolution suggest that some Picea gene families are rapidly evolving to cope with biotic and abiotic stress. Our study highlights the importance of gene expression and natural selection in shaping the evolution of protein-coding genes in Picea species, and sets the ground for further studies investigating the evolution of individual gene families in gymnosperms.
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