Codon Use Bias Analysis Of Chloroplast Genome Of Cistanche
Mar 08, 2023
Abstract:
Objective To clarify the codon usage bias and influencing factors of chloroplast genome in four medicinal plants of Cistanche spp. Methods The codon usage bias parameters of Cistanche deserticola, Cistanche salsa and Cistanche tubulosa were analyzed by CUSP, CodonW 1.4.2, SPSS and Microsoft Excel.
Results The chloroplast genomes of four Cistanche species had similar codon usage patterns, with the third base of the codons all ending in A/T and tending to use the A/T bases more favorably.
The ENC (effective number of codon) values of the four species were all above 35, indicating that the codon preference of the chloroplast genes in Cistanche spp. is weak. The results of neutrality plot, ENC-plot, PR2-bias plot and correspondence analysis indicated that natural selection was the main factor influencing chloroplast genome codon usage bias in Cistanche spp. The RSCU (relative synonymous codon usage) values were used to identify four optimal codons shared by four species of Cistanche spp.
Conclusion In this study, we analyzed the codon usage bias of chloroplast genomes of four species of Cistanche tubulosa. and revealed the influencing factors affecting codon bias, which provided the corresponding theoretical basis for studying the systematic evolution, environmental adaptation and breed improvement of Cistanche at the molecular level.
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Cistanche Hoffmanns. & Link is a perennial parasitic herb of the family Orobanchaceae, mainly distributed in Europe and Asia, with four species of Cistanche in Inner Mongolia, Ningxia, Gansu, Qinghai and Xinjiang [1].
Among them, Cistanche deserticola Ma has the highest medicinal value and is known as "desert ginseng" because it grows mainly in desert areas. However, medicinal plants of the genus Cistanche are facing confusion in plant classification [2] and confusion in the use of commercially available species [3]. Chloroplasts are the site of photosynthesis in most green plants, are involved in developmental and secondary metabolic activities [4], and coordinate gene expression between organelles and the nuclear genome [5]. Chloroplasts have an autonomously inherited genome and are widely used in studies such as plant phylogenetic analysis, species identification and expression of genetic diversity. In recent years, with the maturation of chloroplast genome high-throughput sequencing technology, several plants of the genus Cistanche, Cistanche salina C. salsa (C. A. Mey.) G. Beck, Cistanche salsa C. sinensis G. Beck, and Cistanche tubulosa Wight have been subjected to chloroplast sequencing studies, and their phylogeny and genetic However, no studies on the codon preference of the chloroplast genome of Cistanche spp. have been reported.
The codon, also known as the genetic code, is the bridge between nucleic acids and proteins. bridge between nucleic acids and proteins, and is an important recognition and transmission of biological genetic information codons, also known as genetic code, are important vectors for the recognition and transmission of biological genetic information and are a crucial part in biological inheritance and variation [8].
Due to the differences in the protein translation process among species, there is a tendency to use one or translation process of different species, they tend to use one or several specific synonymous codons This phenomenon is called codon usage bias (CUB) [9]. This phenomenon is called codon usage bias (CUB) [9], and codon preference has a significant impact on mRNA translation, DNA transcription, protein structure, expression, and expression. codon preference plays an important role in mRNA translation, DNA transcription, protein structure, expression, function and co-translational folding, and other cellular metabolic processes. The codon preference plays an important role in cellular metabolic processes such as mRNA translation, DNA transcription, protein structure, expression, function and co-translational folding [10]. Shi Yanshuo et al [11] analyzed the codon preference of four Panax ginseng species by by analyzing the chloroplast genome preference of four Panax Linn. by analyzing the codon preference of chloroplast genomes of four Panax Linn. plants and inferred that the plants in the same genus are more closely related to each other. Song Yun et al [12] demonstrated that the ICE1 gene could be optimized based on codon preference, making it more resistant to low-temperature stress.
Song Yun et al [12] demonstrated that the ICE1 gene could be optimized for expression under low temperature stress based on codon preference; Li Xianhuang et al [13] found that Li Xianhuang et al [13] found that codon preference could reflect the evolutionary relationships among species; Zhang Jun Yan Li et al [13] found that codon preference reflects the evolutionary relationship between species; Jun Yan Zhang et al [14] demonstrated that mutation and natural selection together affect the expression of Swertia bimaculate (L.). Zhang Junyan et al [14] demonstrated that mutation and natural selection combined to affect the evolutionary relationship of Swertia bimaculate (Sieb. et Zucc.) Hook. f. et Thoms. ex C. B. Clark chloroplast genome codon preference for swertia bimaculate (Sieb. et Zucc.) Hook. f. et Thoms. The study of chloroplast genomic codon preferences in the plant chloroplast genomes was conducted to provide a basis for the domestication of swede. Therefore, studying the codon usage patterns of plant chloroplast genomes can provide a basis for the domestication of swede. Therefore, studying the codon usage patterns of chloroplast genomes can help improve the efficiency of gene expression vector construction molecular mechanisms of adaptation to the environment and improvement of plant varieties. Therefore, studying the codon usage patterns of plant chloroplast genomes can provide data support for improving the efficiency of gene expression vector construction, exploring the evolutionary relationships of species, understanding the molecular mechanisms of adaptation to the environment, and improving plant species [15].
