Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in picea gene families.
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.
Department of Ecology and Environmental Science, Umeå University, Sweden amanda.delatorre@emg.umu.se.
Amanda R
AR
De La Torre
Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
Yao-Cheng
YC
Lin
Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium Genomics Research Institute, University of Pretoria, South Africa.
Yves
Y
Van de Peer
Department of Ecology and Environmental Science, Umeå University, Sweden Umeå Plant Science Centre, Umeå, Sweden.
Pär K
PK
Ingvarsson
D003062:Codon; D019143:Evolution, Molecular; D020440:Gene Duplication; D015870:Gene Expression; D018745:Genome, Plant; D023281:Genomics; D005810:Multigene Family; D028222:Picea / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics
D003062:Codon; D010940:Plant Proteins
codon usage; gene duplication; gene expression; sequence divergence; single-copy genes