Abstract
The relationship between evolutionary rates and gene expression in model plant orthologs is well documented. However, little is known about the relationships between gene expression and evolutionary trends in Arachis orthologs. We identified 7,435 one-to-one orthologs, including 925 single-copy and 6,510 multiple-copy sequences in Arachis duranensis and Arachis ipaënsis. Codon usage was stronger for shorter polypeptides, which were encoded by codons with higher GC contents. Highly expressed coding sequences had higher codon usage bias, GC content, and expression breadth. Additionally, expression breadth was positively correlated with polypeptide length, but there was no correlation between gene expression and polypeptide length. Inferred selective pressure was also negatively correlated with both gene expression and expression breadth in all one-to-one orthologs, while positively but non-significantly correlated with gene expression in sequences with signatures of positive selection. Gene expression levels and expression breadth were significantly higher for single-copy genes than for multiple-copy genes. Similarly, the gene expression and expression breadth in sequences with signatures of purifying selection were higher than those of sequences with positive selective signatures. These results indicated that gene expression differed between single-copy and multiple-copy genes as well as sequences with signatures of positive and purifying selection.
Highlights
The relationship between evolutionary rates and gene expression in model plant orthologs is well documented
We identified orthologs from A. duranensis and A. ipaënsis, and used codon usage bias, polypeptide length, GC content, substitution rate, expression breadth, and gene expression level as explanatory variables to evaluate patterns among orthologs in A. duranensis and A. ipaënsis
A total of 7,435 one-to-one ortholog pairs were used in this study after the filtering criteria were applied to the A. duranensis and A. ipaënsis genomes (Table S1)
Summary
The relationship between evolutionary rates and gene expression in model plant orthologs is well documented. Expressed coding sequences had higher codon usage bias, GC content, and expression breadth. The gene expression and expression breadth in sequences with signatures of purifying selection were higher than those of sequences with positive selective signatures These results indicated that gene expression differed between single-copy and multiple-copy genes as well as sequences with signatures of positive and purifying selection. Orthologs typically perform equivalent functions across different species These genes can be used to construct phylogenetic relationships and provide insight into the processes of molecular evolution[2]. A growing body of studies has revealed that several gene sequence architecture features, including synonymous codon usage, amino acid composition, coding sequences (CDSs) length, GC content, and intron size, are correlated with expression levels in prokaryotes and eukaryotes[15,16,17]. Tissue-specific expression was more often observed among genes in multiple-copy gene families than genes in single-copy gene families[17]
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