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Sequence Characteristics, Codon Bias, and Phylogenetic Analysis of Chloroplast Genome of Ilex asprella (Hook.et Arn.) Champ. ex Benth
HONGSenrong, ZHANGZhiyao, MINLingrui, DUJingyi, ADILEWumar, HELingting, HARIMILLANAhemaiti, WULijuan, HULiexin
Chin Agric Sci Bull ›› 2026, Vol. 42 ›› Issue (8) : 67-76.
PDF(3363 KB)
Abbreviation (ISO4): Chin Agric Sci Bull
Editor in chief: Yulong YIN
PDF(3363 KB)
Sequence Characteristics, Codon Bias, and Phylogenetic Analysis of Chloroplast Genome of Ilex asprella (Hook.et Arn.) Champ. ex Benth
In order to understand the sequence characteristics, codon usage preferences, and phylogenetic relationships of the chloroplast genome of Ilex asprella (Hook.et Arn.) Champ.ex Benth, the leaves of wild Ilex asprella (Hook.et Arn.) Champ.ex Benth from Guangxin District, Shangrao were used as materials. The DNBSEQ-T7 BGI gene sequencer was used to sequence, assemble, annotate, and analyze the chloroplast genome of Ilex asprella (Hook.et Arn.) Champ.ex Benth, and bioinformatics analysis software was used to analyze its codon usage preferences and species relationships. The results showed that the chloroplast genome size of Ilex asprella was 157871 bp, with an average GC content of 37.62%. It had a four zone circular structure consisting of one LSC, one SSC, and two IRs. The chloroplast genome of Ilex asprella was annotated with a total of 136 genes, including 91 CDS genes, 37 tRNA genes, and 8 rRNA genes. A total of 56 SSRs (including only 53 A/T single nucleotide repeats, 2 AT/AT dinucleotide repeats, and 1 AAT/ATT trinucleotide repeat) and 43 Longrepeats (including only 22 forward repeats and 21 palindromic repeats) were detected in the chloroplast genome of Ilex asprella. The chloroplast genome boundaries of Ilex asprella were highly conserved, with small differences in gene location and boundaries, and 10 highly variable regions (rps16_trnQ-UUG, trnS-UGA, trnS-UGA_lhbA, lhbA, ycf4_cemA, petD, rpl32_trnL-UAG, ndhD, ndhD_psaC, psaC); The codon usage bias of the chloroplast genome in Ilex asprella was relatively weak, mainly influenced by natural selection, followed by internal mutation pressure. The chloroplast genes of Ilex asprella had five optimal codons (UAA, GUA, CGU, CUU, and UCA), all ending in U or A. The genetic relationship between Ilex asprella and Ilex asprella OP104164 was relatively close. A high-quality chloroplast genome of Ilex asprella (Hook.et Arn.) Champ. ex BenthWe had been successfully assembled, obtaining the sequence structure, sequence characteristics, and codon usage preference information of its chloroplast genome, which laying the foundation for the identification, evolution, and phylogenetic research of medicinal plants in the genus Ilex.
Ilex asprella (Hook.et Arn.) Champ.ex Benth / chloroplast genome / sequence structure characteristics / codon bias / phylogenetic evolution
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Rutaceae family comprises economically important plants due to their extensive applications in spices, food, oil, medicine, etc. The Rutaceae plants is able to better utilization through biotechnology. Modern biotechnological approaches primarily rely on the heterologous expression of functional proteins in different vectors. However, several proteins are difficult to express outside their native environment. The expression potential of functional genes in heterologous systems can be maximized by replacing the rare synonymous codons in the vector with preferred optimal codons of functional genes. Codon usage bias plays a critical role in biogenetic engineering-based research and development. In the current study, 727 coding sequences (CDSs) obtained from the chloroplast genomes of ten Rutaceae plant family members were analyzed for codon usage bias. The nucleotide composition analysis of codons showed that these codons were rich in A/T(U) bases and preferred A/T(U) endings. Analyses of neutrality plots, effective number of codons (ENC) plots, and correlations between ENC and codon adaptation index (CAI) were conducted, which revealed that natural selection is a major driving force for the Rutaceae plant family's codon usage bias, followed by base mutation. In the ENC vs. CAI plot, codon usage bias in the Rutaceae family had a negligible relationship with gene expression level. For each sample, we screened 12 codons as preferred and high-frequency codons simultaneously, of which GCU encoding Ala, UUA encoding Leu, and AGA encoding Arg were the most preferred codons. Taken together, our study unraveled the synonymous codon usage pattern in the Rutaceae family, providing valuable information for the genetic engineering of Rutaceae plant species in the future.© 2024. The Author(s).
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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.
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