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Genomewide comparative analysis of codon usage bias in three sequenced Jatropha curcas

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Abstract

Jatropha curcas has recently emerged as an important bioenergy plant which is an ideal alternative for fossil fuels. It is particularly significant to analyse the codon usage bias (CUB) and further evaluate the intraspecific genetic divergence of three J. curcas in Asia, considering its potential economic benefits and various utilities. In the present study, the patterns of CUB were systematically compared, and the factors shaping CUB were identified in all three genomes of J. curcas. Our observations indicate that the preference for A/T nucleotides and A/T ending codons was present in all the three genomes. Moreover, 11 identical high-frequency codons as well as the optimal expression receptor Nicotiana tabacum were confirmed. Besides, it was observed that CUB resulted from the combined effects of natural selection and mutation pressure, while the natural selection was the determining factor. Eventually, similarity indices based on relative synonymous codon usage (RSCU) values implied low intraspecific genetic divergence in three Asian J. curcas. This study provides useful clues for improving the expression level of exogenous genes and optimizing breeding programmes by molecular-assisted breeding in J. curcas.

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Acknowledgements

The authors are grateful to the three versions of whole-genome sequences of Jatropha curcas from public databases released by three teams (Sato et al. 2012; Wu et al. 2015; Ha et al. 2019). The raw whole-genome data have enabled us to explore the codon usage bias of Jatropha curcas and further carry out relevant research. The authors are also grateful to Dr Hao Huang, College of Mathematics and Statistics, Hefei Normal University, for help with the calculation model of genetic divergence. This research was financially supported by the General Project of Natural Science Foundation of Anhui Province (1708085MC76), the Key Project Support Plan to Excellent Young Talents in Colleges and University of Anhui Province (gxyq2020040), the Open Fund of State Key Laboratory of Tea Plant Biology and Utilization (SKLTOF20200129), the Priority Academic Programme Development of Jiangsu Higher Education Institutions (PAPD), the Project of the Provincial Quality Engineering of Colleges and Universities in Anhui Province (2020szsfkc0744, 2020jyxm1566) and the College Students' Innovation and Entrepreneurship Project in Anhui Province (201914098165, S202014098018).

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  1. Zhanjun Wang and Guiyi Wang contributed equally to this work.

Authors and Affiliations

  1. College of Life Sciences, Hefei Normal University, Hefei, 230601, People’s Republic of China

    ZHANJUN WANG, GUIYI WANG, QIANWEN CAI, CHENCHEN WANG, ZIQI WU, JIE LI, ZULAN OU & ZHONGDONG XU

  2. Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, People’s Republic of China

    ZHANJUN WANG, JISEN SHI & JINHUI CHEN

  3. Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People’s Republic of China

    YAO JIANG

  4. School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK

    HAIMENG XIA

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  1. ZHANJUN WANG
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Correspondence to JINHUI CHEN.

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Corresponding editor: Qingpo Liu

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WANG, Z., WANG, G., CAI, Q. et al. Genomewide comparative analysis of codon usage bias in three sequenced Jatropha curcas. J Genet 100, 20 (2021). https://doi.org/10.1007/s12041-021-01271-9

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