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

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

摘要:

花椒(Zanthoxylum bungeanum)和竹叶花椒(Z. armatum)均是重要的木本油料和香料树种,在我国栽培范围广、种植面积大。为明确这2种花椒属植物叶绿体基因组特征,基于现已公布的序列信息,利用生物信息学方法分析叶绿体基因组结构、基因功能、序列特点及其密码子使用偏好性,并通过比较基因组学解析序列变异情况,筛选高变区构建系统发育树。结果表明:(1)2种花椒属植物叶绿体基因组结构具有较高的一致性,各类编码基因数目基本相同,基因功能类别相似。(2)在花椒和竹叶花椒叶绿体基因组序列中检测出多个分散重复和串联重复,并分别筛选出95个和98个 SSRs 位点,并且约79%都是以A/T为基序的单核苷酸重复。(3)花椒和竹叶花椒叶绿体基因组密码子GC_all含量均小于40%、有效密码子数(ENC)均值为48.5%,表明其密码子整体偏好使用A/T碱基,偏好性较弱且受自然选择的影响较大; 筛选出的11个最优密码子均是以A/U结尾,其中UAU是两者共有最优密码子。(4)以花椒叶绿体基因组作为参照,在竹叶花椒叶绿体基因组编码区共检测到130个SNP,其中ycf1基因有24个SNP变异位点,占总变异位点的18.5%; 同时,在8个编码基因内含子区共检测到14个indel位点; 以P_i>0.010为标准筛选出3个高变区,分别为rpoB-trnC-GCA-petN、trnH-GUG-psbA和ycf1,其中基因间隔区rpoB-trnC-GCA-petN的变异程度最高。(5)基于高变区序列构建的系统发育树以95%以上的支持率将花椒属下的6个种及品种进行了准确归类划分。花椒主要栽培种叶绿体基因组的结构、数目和功能相似性较高,重复序列与SSR位点丰富,其密码子具有较明显的A/T偏好性; 序列高变区集中分布在少数编码基因上和几个特定基因间隔区内,并且在花椒属内具有较高特异性。该研究为花椒栽培种的分子标记开发、资源分类鉴定及其遗传演化机制研究提供了理论依据。

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 GC_all 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 P_i>0.010 as the standard, namely rpoB-trnC-GCA-petN, trnH-GUG-psbA and ycf1. 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.