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Comprehensive analysis of coding sequence architecture features and gene expression in Arachis duranensis

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Abstract

Coding sequence (CDS) architecture affects gene expression levels in organisms. Codon optimization can increase the gene expression level. Therefore, understanding codon usage patterns has important implications for research on genetic engineering and exogenous gene expression. To date, the codon usage patterns of many model plants have been analyzed. However, the relationship between CDS architecture and gene expression in Arachis duranensis remains poorly understood. According to the results of genome sequencing, A. duranensis has many resistant genes that can be used to improve the cultivated peanut. In this study, bioinformatic approaches were used to estimate A. duranensis CDS architectures, including frequency of the optimal codon (Fop), polypeptide length and GC contents at the first (GC1), second (GC2) and third (GC3) codon positions. In addition, Arachis RNA-seq datasets were downloaded from PeanutBase. The relationships between gene expression and CDS architecture were assessed both under normal growth as well as nematode and drought stress conditions. A total of 26 codons with high frequency were identified, which preferentially ended with A or T in A. duranensis CDSs under the above-mentioned three conditions. A similar CDS architecture was found in differentially expressed genes (DEGs) under nematode and drought stresses. The GC1 content differed between DEGs and non-differentially expressed genes (NDEGs) under both drought and nematode stresses. The expression levels of DEGs were affected by different CDS architectures compared with NDEGs under drought stress. In addition, no correlation was found between differential gene expression and CDS architecture neither under nematode nor under drought stress. These results aid the understanding of gene expression in A. duranensis.

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Acknowledgements

The work was supported by the First Class Grassland Science Discipline Program of Shandong Province, China, the Natural Science Foundation of Shandong Province, China (ZR2019QC017, ZR2020MC172 and ZR2020QC185), Key Research and Development Program in Shandong Province (2019GNC106077), and Start-up Foundation for High Talents of Qingdao Agricultural University (No. 665/1120012, No. 663/1119038 and No. 663/1119040).

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  1. Shuwei Dong and Long Zhang contributed equally to this work.

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  1. Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China

    Shuwei Dong, Long Zhang, Wenhui Pang, Yongli Zhang, Chang Wang, Zhenyi Li, Lichao Ma, Wei Tang, Guofeng Yang & Hui Song

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Dong, S., Zhang, L., Pang, W. et al. Comprehensive analysis of coding sequence architecture features and gene expression in Arachis duranensis. Physiol Mol Biol Plants 27, 213–222 (2021). https://doi.org/10.1007/s12298-021-00938-y

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