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Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in Picea gene families

(2015) GENOME BIOLOGY AND EVOLUTION. 7(4). p.1002-1015
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Bioinformatics: from nucleotids to networks (N2N)
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.
Keywords
codon usage, DOSAGE SENSITIVITY, WHOLE-GENOME, TRANSLATIONAL ACCURACY, NATURAL-SELECTION, ESCHERICHIA-COLI, CONIFER GENOME, DUPLICATED GENES, COPY NUCLEAR GENES, MOLECULAR EVOLUTION, sequence divergence, PROTEIN EVOLUTION, single-copy genes, gene duplication, gene expression

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Citation

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Chicago
De La Torre, Amanda R, Yao-Cheng Lin, Yves Van de Peer, and Pär K Ingvarsson. 2015. “Genome-wide Analysis Reveals Diverged Patterns of Codon Bias, Gene Expression, and Rates of Sequence Evolution in Picea Gene Families.” Genome Biology and Evolution 7 (4): 1002–1015.
APA
De La Torre, A. R., Lin, Y.-C., Van de Peer, Y., & Ingvarsson, P. K. (2015). Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in Picea gene families. GENOME BIOLOGY AND EVOLUTION, 7(4), 1002–1015.
Vancouver
1.
De La Torre AR, Lin Y-C, Van de Peer Y, Ingvarsson PK. Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in Picea gene families. GENOME BIOLOGY AND EVOLUTION. 2015;7(4):1002–15.
MLA
De La Torre, Amanda R, Yao-Cheng Lin, Yves Van de Peer, et al. “Genome-wide Analysis Reveals Diverged Patterns of Codon Bias, Gene Expression, and Rates of Sequence Evolution in Picea Gene Families.” GENOME BIOLOGY AND EVOLUTION 7.4 (2015): 1002–1015. Print.
@article{6864066,
  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 ({\textrangle} 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.},
  author       = {De La Torre, Amanda R and Lin, Yao-Cheng and Van de Peer, Yves and Ingvarsson, P{\"a}r K},
  issn         = {1759-6653},
  journal      = {GENOME BIOLOGY AND EVOLUTION},
  keyword      = {codon usage,DOSAGE SENSITIVITY,WHOLE-GENOME,TRANSLATIONAL ACCURACY,NATURAL-SELECTION,ESCHERICHIA-COLI,CONIFER GENOME,DUPLICATED GENES,COPY NUCLEAR GENES,MOLECULAR EVOLUTION,sequence divergence,PROTEIN EVOLUTION,single-copy genes,gene duplication,gene expression},
  language     = {eng},
  number       = {4},
  pages        = {1002--1015},
  title        = {Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in Picea gene families},
  url          = {http://dx.doi.org/10.1093/gbe/evv044},
  volume       = {7},
  year         = {2015},
}

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