Comparative analysis of codon usage patterns in chloroplast genomes of the Asteraceae family

Nie, Xiaojun; Deng, Pingchuan; Feng, Kewei; Liu, Peixun; Du, Xianghong; You, Frank M.

doi:10.1007/s11105-013-0691-z

Cited by 73 publications

(60 citation statements)

References 53 publications

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“…In addition, the average GC content of three locations in Ricinus communis and Vernicia fordii is the same (0.375), but the contents of the other four Euphorbiaceae plant species are slightly different (0.371-0.374; Table 1). Zhang et al (2012) revealed the average third base of codons were biased towards A/T in the 23 Poaceae chloroplast genome codons as 0.613, which coincides with the findings of Nie et al (2013) who reported that the average AT content (0.625) of the Asteraceae chloroplast genome was significantly higher than the GC content (0.375). Moreover, Zhang and colleagues (2018) also described the higher AT content of the whole genome (0.620) for the chloroplast genome codons in different Solanum species.…”

Section: Indices Of Codon Usagesupporting

confidence: 84%

“…Previous researches on codon usage bias of the chloroplast genomes can improve the expression efficiency of exogenous genes by selecting appropriate codons for transgenic research (Zhou, Tong & Shi, 2007). At present, many studies validated the applicability of synonymous codon bias for the chloroplast genome level of within-species and between-species in higher plants, such as Poaceae (Zhang et al, 2012), Asteraceae (Nie et al, 2013), Cinnamomum camphora (Chen et al, 2017), Morus (Kong & Yang, 2017), Strawberry (Cheng et al, 2017) and Solanum (Zhang et al, 2018). However, the codon usage bias of chloroplast genomes in six Euphorbiaceae plant species has not been reported.…”

Section: Introductionmentioning

confidence: 99%

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

Wang

et al. 2020

PeerJ

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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.

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Section: Indices Of Codon Usagesupporting

confidence: 84%

Section: Introductionmentioning

confidence: 99%

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

Wang

et al. 2020

PeerJ

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“…Identification of the RNA editing sites in chloroplasts will not only provide the vital information on the proper function of the proteins encoded by plastids but also reveal the evolutionary features of RNA editing (Tillich et al 2006;Nie et al 2014). To investigate the RNA editing in Asteraceae plastids, we systematically analyzed and compared the RNA editing sites in the eight Asteraceae cp genomes using the computational analysis approach (Table 3).…”

Section: Sequence Divergence In Asteraceae Cp Genomes and Marker Idenmentioning

confidence: 99%

Comparative Analysis of Asteraceae Chloroplast Genomes: Structural Organization, RNA Editing and Evolution

et al. 2015

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Comparative chloroplast genome analysis presents new opportunities for performing molecular phylogeny studies and revealing the significant evolutionary features in higher plants, which has been widely documented from conifers to grass family. However, a systematic analysis of chloroplast genomes in Asteraceae family has not been conducted up to now. In this study, we compared and analyzed the gene content, genomic organization, and RNA editing sites of eight representative Asteraceae chloroplast genomes. Results showed that Asteraceae chloroplast had relatively conservative gene content. No gain or loss events occurred in the proteincoding genes, while some differences were found to be present in the gene structure and transfer RNA (tRNA) abundance. Genome structure analysis found some Asteraceae-specific or species-specific structure variations, and sequence rearrangement events were present in these genomes, suggesting specific evolutionary processes have occurred in this family. Some DNA regions containing parsimony-informative characters higher than 5 % were also identified, which could be used as the new molecular markers for phylogenetic analysis and plant identification of Asteraceae species. Furthermore, RNA editing in these genomes was investigated through computational analysis, and some species-specific sites were identified. Finally, phylogenetic analysis of 81 genes from 70 species supported the monophyly of the Asteraceae. Our study for the first time compared the organization, structure, and sequence divergence of eight Asteraceae chloroplast genomes, which will provide the valuable resource for molecular phylogeny of Asteraceae species and also facilitate the genetic and evolutionary studies in this family.

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“…If the relationship was statistically significant and the slope of the best-fitting line was close to 1.0, mutational bias was taken as the main force that affects CUB. Conversely, selection predominating against mutational bias caused no correlation between GC 12 and GC 3 and/or the smaller slope of their regression line [29,30]. The GC 12 and GC 3 were significantly correlated in platyhelminth tyrosinase genes, although the slope was much closer to 0.0 than 1.0 (a=0.2168, R=0.8272, P <0.0001; Fig.…”

Section: Discussionmentioning

confidence: 99%

Codon Usage Patterns of Tyrosinase Genes in Clonorchis sinensis

Bae

2017

Korean J Parasitol

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Codon usage bias (CUB) is a unique property of genomes and has contributed to the better understanding of the molecular features and the evolution processes of particular gene. In this study, genetic indices associated with CUB, including relative synonymous codon usage and effective numbers of codons, as well as the nucleotide composition, were investigated in the Clonorchis sinensis tyrosinase genes and their platyhelminth orthologs, which play an important role in the eggshell formation. The relative synonymous codon usage patterns substantially differed among tyrosinase genes examined. In a neutrality analysis, the correlation between GC12 and GC3 was statistically significant, and the regression line had a relatively gradual slope (0.218). NC-plot, i.e., GC3 vs effective number of codons (ENC), showed that most of the tyrosinase genes were below the expected curve. The codon adaptation index (CAI) values of the platyhelminth tyrosinases had a narrow distribution between 0.685/0.714 and 0.797/0.837, and were negatively correlated with their ENC. Taken together, these results suggested that CUB in the tyrosinase genes seemed to be basically governed by selection pressures rather than mutational bias, although the latter factor provided an additional force in shaping CUB of the C. sinensis and Opisthorchis viverrini genes. It was also apparent that the equilibrium point between selection pressure and mutational bias is much more inclined to selection pressure in highly expressed C. sinensis genes, than in poorly expressed genes.

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Comparative analysis of codon usage patterns in chloroplast genomes of the Asteraceae family

Cited by 73 publications

References 53 publications

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

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

Comparative Analysis of Asteraceae Chloroplast Genomes: Structural Organization, RNA Editing and Evolution

Codon Usage Patterns of Tyrosinase Genes in Clonorchis sinensis

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