2024年3月1日 星期五
多齿红山茶叶绿体基因组序列特征分析
Analysis on sequence characteristics of chloroplast genome of Camellia polyodonta
2022年 第31卷 第5期 页码[27-36]    下载全文[8.7MB]  
摘要

本研究利用高通量测序技术对多齿红山茶(Camellia polyodonta How ex Hu)叶片进行核基因组重测序,并对组装得到叶绿体基因组进行注释、序列特征和系统发育分析。结果显示:多齿红山茶叶绿体基因组长度为156 778 bp,由4部分组成,其中,大单拷贝区长度为86 493 bp,小单拷贝区长度为18 219 bp,2个反向重复区长度均为26 033 bp。注释到87个CDS基因、37个tRNA基因和8个rRNA基因,分为光合作用基因、自我复制基因、其他基因和未知功能基因4类。多齿红山茶叶绿体基因组中共检测到52个SSR位点,且均为单碱基(A/T)的重复类型。多齿红山茶叶绿体基因组相对同义密码子使用度大于1.00的密码子共有30个(终止密码子除外),其中,有27个以A或U结尾,有3个以C或G结尾。山茶属(Camellia Linn.)植物rps19、rpl2和trnH基因相对保守,长度分别为279、1 495和75 bp,与反向重复区边界间的相对位置也保持一致,而ndhF、ycf1和trnN基因在种间具有特异性;与木荷(Schima superba Gardn. et Champ.)相比,rps19、rpl2和trnH基因位置和长度在属间差异明显,ndhF、ycf1和trnN基因位置和长度在属间差异更明显。基因不同程度的扩张和收缩是造成反向重复区和小单拷贝区长度差异的原因。聚类分析结果显示:多齿红山茶、滇山茶(C. reticulata Lindl.)和南山茶(C. semiserrata Chi)聚为一支,短柱茶〔C. brevistyla (Hayata) Coh. St〕、小果油茶(C. meiocarpa Hu)和茶梅(C. sasanqua Thunb.)聚为一支,聚在一支的种类亲缘关系较近;红山茶组〔Sect. Camellia (Linn.) Dyer〕、油茶组(Sect. Oleifera H. T. Chang)和短柱茶组(Sect. Paracamellia Sealy)的种类均聚在了不同的分支。综合研究结果表明:多齿红山茶叶绿体基因组呈典型的四分体结构,密码子偏好以A或U结尾,且高频率使用AGA密码子编码Arg;山茶属不同物种间ndhF、ycf1和trnN基因的扩张和收缩情况差异明显;系统发育分析结果支持将短柱茶组合并入油茶组。

Abstract

The nuclear genome of Camellia polyodonta How ex Hu leaf was re-sequenced by using high-throughput sequencing technology, and annotation, sequence characteristics and phylogenetic analysis were conducted for the assembled chloroplast genome. The results show that the length of chloroplast genome of C. polyodonta is 156 778 bp, which is composed of four regions, in which, the length of large single copy region is 86 493 bp, that of small single copy region is 18 219 bp, and the lengths of two inverted repeat regions are both 26 033 bp. 87 CDS genes, 37 tRNA genes, and 8 rRNA genes are annotated, which can be divided into 4 categories of photosynthesis genes, selfreplication genes, other genes and unknown function genes. 52 SSR loci are detected in chloroplast genome of C. polyodonta, and all of them are of single base (A/T) repeat type. There are 30 codons (except for stop codons) with the relative synonymous codon usage greater than 1.00 in chloroplast genome of C. polyodonta, in which, 27 codons are ended with A or U, 3 codons are ended with C or G. rps19, rpl2, and trnH genes of Camellia Linn. species are relatively conserved, their lengths are 279, 1 495, and 75 bp respectively, their relative locations with respect to boundarys of inverted repeat regions are also consistent, while ndhF, ycf1, and trnN genes are specific among species; compared with Schima superba Gardn. et Champ., the positions and lengths of rps19, rpl2 and trnH genes are significantly different among genera, while those of ndhF, ycf1 and trnN genes are more significantly different among genera. Different degrees of gene expansion and contraction are responsible for the differences in lengths of inverted repeat and small single copy regions. The clustering analysis result shows that C. polyodonta, C. reticulata Lindl. and C. semiserrata Chi are grouped into one branch, the species clustered in one clade are closely related; Sect. Camellia (Linn.) Dyer, Sect. Oleifera H. T. Chang and Sect. Paracamellia Sealy are all clustered in different branches, and C. brevistyla (Hayata) Coh. St, C. meiocarpa Hu and C. sasanqua Thunb. are grouped into one branch. The comprehensive analysis result shows that the chloroplast genome of C. polyodonta shows a typical tetrad structure, the codons prefer to end with A or U, and AGA codon is frequently used to code Arg; the differences in expansion and contraction of ndhF, ycf1 and trnN genes among different species in Camellia are evident; the phylogenetic analysis result supports that incorporation of Sect. Paracamellia Sealy into Sect. Oleifera H. T. Chang.

关键词多齿红山茶; 叶绿体基因组; 序列特征; 系统发育分析
Key wordsCamellia polyodonta How ex Hu; chloroplast genome; sequence characteristics; phylogenetic analysis
作者童一涵, 郑倩, 杜新明, 冯士令, 周莉君, 丁春邦, 陈涛
所在单位四川农业大学生命科学学院, 四川 雅安 625014
点击量824
下载次数1269
基金项目家自然科学基金资助项目(31801826); 四川省科技计划项目(2020YJ0143); 雅安市科技项目(21SXHZ0017)