广西植物2026，Vol.46Issue(3)：549-562,14.DOI:10.11931/guihaia.gxzw202503003
花椒主要栽培种叶绿体基因组比较及密码子使用偏好分析
Chloroplast genome comparison and codon usage bias analysis of major cultivated Zanthoxylum species
摘要
Abstract
Zanthoxylum bungeanum and Z.armatum are significant woody oil and spice tree species,which have a wide cultivation range and large planting area in China.To elucidate the characteristics of their chloroplast genomes,we employed bioinformatics methods on publicly available sequences to analyze chloroplast genome structure,gene function,sequence features,and codon usage bias.Comparative genomics was used to identify sequence variations and screen hypervariable regions for phylogenetic tree construction.The results were as follows:(1)The chloroplast genome structures of the two species of Zanthoxylum had high consistency,the numbers of coding genes were basically the same,and the gene function category was similar.(2)Multiple scattered repeats and tandem repeats were detected in chloroplast genome sequences of Z.bungeanum and Z.armatum,and 95 and 98 SSRs sites were selected,respectively,about 79％of SSRs were single nucleotide repeats with A/T motif.(3)The chloroplast genome codon GCall contents of Z.bungeanum and Z.armatum were less than 40％,and the average ENC(effective number of codon)was 48.5％,indicating that the codon preferred to use A/T base,the bias was weak,and both were more affected by natural selection.All the 11 selected optimal codons ended in A/U,among which UAU was the common optimal codon.(4)Using chloroplast genome of Z.bungeanum as the reference,a total of 130 SNP were detected in the coding region of chloroplast genome of Z.armatum.Among them,24 SNP of ycf1 gene accounted for 18.5％of the total variation sites.At the same time,a total of 14 indel sites were detected in the intron region of 8 coding genes.Three highly variable regions were selected with Pi＞0.010 as the standard,namely rpoB-trnC-GCA-petN,trnH-GUG-psbA and ycfl.Among them,the gene spacer region rpoB-trnC-GCA-petN had the highest degree of variation.(5)The phylogenetic tree constructed based on hypervariable regions accurately classified six species and cultivars within the genus Zanthoxylum with a strong bootstrap support(＞95％).The chloroplast genomes of major cultivated Zanthoxylum species exhibit high similarity in structure,number and function,while containing abundant repetitive sequences and SSR loci,and their codons have a relatively obvious A/T bias.Notably,sequence hypervariable regions are predominantly distributed within a few coding genes and intergenic spacers,and have high specificity within the genus.This study provides a theoretical foundation for molecular marker development,germplasm identification,and investigations into the genetic evolutionary mechanisms of cultivated Zanthoxylum species.关键词
花椒/竹叶花椒/叶绿体基因组/序列变异/密码子偏好性Key words
Zanthoxylum bungeanum/Zanthoxylum armatum/chloroplast genome/sequence variation/codon bias分类
农业科技引用本文复制引用
王飞,王必海,段见阳,周源洁,阮长明,刘镒娴,陈建雄,杜春花,陆斌..花椒主要栽培种叶绿体基因组比较及密码子使用偏好分析[J].广西植物,2026,46(3):549-562,14.基金项目
中央财政林业科技推广示范项目(云[2024]TG14) （云[2024]TG14）
凉山州农业科技项目(LSNY2024015). （LSNY2024015）
