Abstract
Theaceae species are dicotyledonous angiosperms with extremely high ornamental and economic value. The chloroplast genome is traditionally used to study species evolution, expression of chloroplast genes and chloroplast transformation. Codon usage bias (CUB) analysis is beneficial for investigations of evolutionary relationships and can be used to improve gene expression efficiency in genetic transformation research. However, there are relatively few systematic studies of the CUB in the chloroplast genomes of Theaceae species. In this study, CUB and nucleotide compositions parameters were determined by the scripts written in the Perl language, CodonW 1.4.2, CU.Win2000, RStudio and SPSS 23.0. The chloroplast genome data of 40 Theaceae species were obtained to analyse the codon usage (CU) characteristics of the coding regions and the influence of the source of variation on CUB. To explore the relationship between the CUB and gene expression levels in these 40 Theaceae plastomes, the synonymous codon usage order (SCUO) and measure independent of length and composition (MILC) values were determined. Finally, phylogenetic analysis revealed the genetic evolutionary relationships among these Theaceae species. Our results showed that based on the chloroplast genomes of these 40 Theaceae species, the CUB was for codons containing A/T bases and those that ended with A/T bases. Moreover, there was great commonality in the CUB of the Theaceae species according to comparative analysis of relative synonymous codon usage (RSCU) and relative frequency of synonymous codon (RFSC): these species had 29 identical codons with bias (RSCU > 1), and there were 19 identical high-frequency codons. The CUB of Theaceae species is mainly affected by natural selection. The SCUO value of the 40 Theaceae species was 0.23 or 0.24, and the chloroplast gene expression level was moderate, according to MILC values. Additionally, we observed a positive correlation between the SCUO and MILC values, which indicated that CUB might affect gene expression. Furthermore, the phylogenetic analysis showed that the evolutionary relationships in these 40 Theaceae species were relatively conserved. A systematic study on the CUB and expression of Theaceae species provides further evidence for their evolution and phylogeny.
Highlights
IntroductionTheaceae, a characteristic family of subtropical evergreen broadleaved forests, is widely distributed in subtropical regions (Zhang et al, 2021)
This study revealed the relationships between the Codon usage bias (CUB) and gene expression frequency, and provided a reference direction for further genetic evolution research and transgenic research in these 40 Theaceae species
To ensure the accuracy of the experimental results, the scripts written in the Perl language (Wang et al, 2020) were used to process the original CDSs of the 40 chloroplast genomes, and the selected sequences were required to meet the following conditions: 1) the CDS is composed of only A, T, G, and C bases; 2) the sequence length is a multiple of three; 3) the sequence starts with the start codon ATG and ends with the stop codon TAA, TAG or TGA; 4) there is no stop codon in the middle of the sequence; 5) the length of the CDS is ≥ 300 bp (He et al, 2016; Li et al, 2016; Wang et al, 2020)
Summary
Theaceae, a characteristic family of subtropical evergreen broadleaved forests, is widely distributed in subtropical regions (Zhang et al, 2021). Kuntze.) varieties are popular in many countries around the world, including India, Vietnam and Japan (Teixeira and Sousa, 2021; Wang et al, 2021). Camellia originated in Southeast Asia, and 80% of the species of this genus come from China. Theaceae species have high ornamental value and high economic value, such as medicine, food and drink (Yuan et al, 2021). Tea is water soaked with Camellia leaves, known as “oriental magic water”, which is one of three most famous drinks in the world (Balentine et al, 1997). The seeds of Camellia are rich in oil that can be extracted and used for various purposes, such as edible and industrial oils
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