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. 2020 Jan 6:8:e8251.
doi: 10.7717/peerj.8251. eCollection 2020.

Comparative analysis of codon usage patterns in chloroplast genomes of six Euphorbiaceae species

Zhanjun Wang #  1 , Beibei Xu #  1   2 , Bao Li  1 , Qingqing Zhou  1 , Guiyi Wang  1 , Xingzhou Jiang  1 , Chenchen Wang  1 , Zhongdong Xu  1
Affiliations

Comparative analysis of codon usage patterns in chloroplast genomes of six Euphorbiaceae species

Zhanjun Wang et al. PeerJ. .

Abstract

Euphorbiaceae plants are important as suppliers of biodiesel. In the current study, the codon usage patterns and sources of variance in chloroplast genome sequences of six different Euphorbiaceae plant species have been systematically analyzed. Our results revealed that the chloroplast genomes of six Euphorbiaceae plant species were biased towards A/T bases and A/T-ending codons, followed by detection of 17 identical high-frequency codons including GCT, TGT, GAT, GAA, TTT, GGA, CAT, AAA, TTA, AAT, CCT, CAA, AGA, TCT, ACT, TAT and TAA. It was found that mutation pressure was a minor factor affecting the variation of codon usage, however, natural selection played a significant role. Comparative analysis of codon usage frequencies of six Euphorbiaceae plant species with four model organisms reflected that Arabidopsis thaliana, Populus trichocarpa, and Saccharomyces cerevisiae should be considered as suitable exogenous expression receptor systems for chloroplast genes of six Euphorbiaceae plant species. Furthermore, it is optimal to choose Saccharomyces cerevisiae as the exogenous expression receptor. The outcome of the present study might provide important reference information for further understanding the codon usage patterns of chloroplast genomes in other plant species.

Keywords: Chloroplast genome; Codon usage bias; Euphorbiaceae plants.

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Conflict of interest statement

The authors declare there are no competing interests.

Figures

Figure 1
Figure 1. ENc-plot of chloroplast genomes of six Euphorbiaceae plant species.
(A) Euphorbia esula; (B) Hevea brasiliensis; (C) Jatropha curcas; (D) Manihot esculenta; (E) Ricinus communis; (F) Vernicia fordii.
Figure 2
Figure 2. PR2-plot of chloroplast genomes six Euphorbiaceae plant species.
(A) Euphorbia esula; (B) Hevea brasiliensis; (C) Jatropha curcas; (D) Manihot esculenta; (E) Ricinus communis; (F) Vernicia fordii.
Figure 3
Figure 3. Neutrality plot of chloroplast genomes six Euphorbiaceae plant species.
(A) Euphorbia esula; (B) Hevea brasiliensis; (C) Jatropha curcas; (D) Manihot esculenta; (E) Ricinus communis; (F) Vernicia fordii.
Figure 4
Figure 4. Correspondence analysis of chloroplast genomes of six Euphorbiaceae plant species.
(A) Euphorbia esula; (B) Hevea brasiliensis; (C) Jatropha curcas; (D) Manihot esculenta; (E) Ricinus communis; (F) Vernicia fordii.
See this image and copyright information in PMC

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References

    1. Aranda-Rickert A, Morzán L, Fracchia S. Seed oil content and fatty acid profiles of five Euphorbiaceae species from arid regions in Argentina with potential as biodiesel source. Seed Science Research. 2011;21:63–68. doi: 10.1017/S0960258510000383. - DOI
    1. Asif MH, Mantri SS, Sharma A, Srivastava A, Trivedi I, Gupta P, Mohanty CS, Sawant SV, Tuli R. Complete sequence and organisation of the Jatropha curcas (Euphorbiaceae) chloroplast genome. Tree Genetics & Genomes. 2010;6:941–952. doi: 10.1007/s11295-010-0303-0. - DOI
    1. Boynton JE, Gillham NW, Harris EH, Hosler JP, Johnson AM, Jones AR, Randolph-Anderson BL, Robertson D, Klein TM, Shark KB, Sanford JC. Chloroplast transformation in Chlamydomonas with high velocity microprojectiles. Science. 1988;240:1534–1538. doi: 10.1126/science.2897716. - DOI - PubMed
    1. Chang SH, Lee S, Um TY, Kim JK, Do Choi Y, Jang G. pTAC10, a key subunit of plastid-encoded RNA polymerase, promotes chloroplast development. Plant Physiology. 2017;174:435–449. doi: 10.1104/pp.17.00248. - DOI - PMC - PubMed
    1. Chen C, Zheng Y, Liu S, Zhong Y, Wu Y, Li J, Xu LA, Xu M. The complete chloroplast genome of Cinnamomum camphora and its comparison with related Lauraceae species. PeerJ. 2017;5:e3820. doi: 10.7717/peerj.3820. - DOI - PMC - PubMed