Abstract
Key message
Our results reveal that Ks is a determining factor affecting selective pressure and different evolution and expression patterns are detected between PSGs and NSGs in wild Arachis duplicates.
Abstract
Selective pressure, including purifying (negative) and positive selection, can be detected in organisms. However, studies on comparative evolutionary rates, gene expression patterns and gene features between negatively selected genes (NSGs) and positively selected genes (PSGs) are lagging in paralogs of plants. Arachis duranensis and Arachis ipaënsis are ancestors of the cultivated peanut, an important oil and protein crop. Here, we carried out a series of systematic analyses, comparing NSG and PSG in paralogs, using genome sequences and transcriptome datasets in A. duranensis and A. ipaënsis. We found that synonymous substitution rate (Ks) is a determining factor affecting selective pressure in A. duranensis and A. ipaënsis duplicated genes. Lower expression level, lower gene expression breadth, higher codon bias and shorter polypeptide length were found in PSGs and not in NSGs. The correlation analyses showed that gene expression breadth was positively correlated with polypeptide length and GC content at the first codon site (GC1) in PSGs and NSGs, respectively. There was a negative correlation between expression level and polypeptide length in PSGs. In NSGs, the Ks was positively correlated with expression level, gene expression breadth, GC1, and GC content at the third codon site (GC3), but selective pressure was negatively correlated with expression level, gene expression breadth, polypeptide length, GC1, and GC3 content. The function of most duplicated gene pairs was divergent under drought and nematode stress. Taken together, our results show that different evolution and expression patterns occur between PSGs and NSGs in paralogs of two wild Arachis species.
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Acknowledgements
We thank Steven B. Cannon for valuable comments on an earlier version of this paper. This study was supported by the Forage Industrial Innovation Team, Shandong Modern Agricultural Industrial and Technical System (SDAIT-23-01) and China Agriculture Research System (CARS-34).
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HS and GY conceived and designed this research. HS analyzed data and wrote the manuscript. JS participated in the discussion of the results. GY contributed to the evaluation and discussion of the results and manuscript revision.
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11103_2018_784_MOESM1_ESM.tif
Supplementary material 1—Supplementary Fig. S1 Comparisons of evolutionary rate of asymmetric and symmetric duplicated genes after drought stress and nematode infection in A. duranensis. (A) Comparisons of Ks values between asymmetric and symmetric duplicated genes after drought stress in A. duranensis; (B) Comparisons of Ka values between asymmetric and symmetric duplicated genes after drought stress in A. duranensis; (C) Comparisons of Ka/Ks values between asymmetric and symmetric duplicated genes after drought stress in A. duranensis; (D) Comparisons of Ks values between asymmetric and symmetric duplicated genes after nematode infection in A. duranensis; (E) Comparisons of Ka values between asymmetric and symmetric duplicated genes after nematode infection in A. duranensis; (F) Comparisons of Ka/Ks values between asymmetric and symmetric duplicated genes after nematode infection in A. duranensis. (TIF 761 KB)
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Song, H., Sun, J. & Yang, G. Comparative analysis of selection mode reveals different evolutionary rate and expression pattern in Arachis duranensis and Arachis ipaënsis duplicated genes. Plant Mol Biol 98, 349–361 (2018). https://doi.org/10.1007/s11103-018-0784-z
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DOI: https://doi.org/10.1007/s11103-018-0784-z