Abstract
To detect the codon usage characteristics of chloroplast genomes in Platycarya genus, the CodonW 、 CUSP and SPSSAU software were employed to analyze the codon usage patterns of the chloroplast genomes protein-coding sequence in Platycarya longipes and Platycarya strobilacea in this research. Results show that the GC content of chloroplast genomes was 37.75% and 37.80%, the average GC content in the 3rd position was 27.16% and 27.25%. the range of effective codon number from 35.19 to 56.98, and there were more than 2/3 genes when ENC value greater than 45, which indicated a weak preference. According to the results of neutrality plot analysis, ENC-plot analysis and PR2-plot analysis, codon bias in most Platycarya chloroplast genes were affected by natural selection, while a few were affected by mutations or other factors. And based on the ENC value, five groups of high-expressed and low-expressed genes were identified, 16 codons were ended with A/U among the 18 optimal codons. The research has implications on codon optimization, enhancing the expression efficiency of exogenous gene and phylogenetic analysis.
Highlights
Chloroplast is an important photosynthetic organelle, which provides energy for plant growth and development, the genetic information independent of nucleus and the chloroplast genome has a simple structure and a large number of gene copies (Niu et al, 2018; Wang et al, 2019)
According to the results of neutrality plot analysis, effective number of codon (ENC)-plot analysis and PR2-plot analysis, codon bias in most Platycarya chloroplast genes were affected by natural selection, while a few were affected by mutations or other factors
It was found that the ENC values of rps14, ndhC, petD, rp12, ndhA and ndhB were quite different between the two species, and the GC content and ENC value of most of the genes had very little difference, indicating that the chloroplast coding genes of Platycarya are relatively conserved
Summary
Chloroplast is an important photosynthetic organelle, which provides energy for plant growth and development, the genetic information independent of nucleus and the chloroplast genome has a simple structure and a large number of gene copies (Niu et al, 2018; Wang et al, 2019). It has the characteristics of self-reproduction and maternal inheritance, and the genome size is between 120 and 160 KB (Suiura, 1992). The base composition and codon usage patterns of chloroplast genomes of two species of Platycarya were analyzed, and the optimal codons were obtained, which would provide scientific reference for the application and research of chloroplast genomes and genetic engineering of Platycarya plants
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