红边龙血树叶绿体基因组特征及其系统发育分析

Characteristics of the chloroplast genome of Dracaena marginata and phylogenetic analysis

摘要:

红边龙血树（Dracaena marginata）是一种在全球广泛种植的龙血树属园艺植物，具有较高的观赏价值和药用价值。本研究首次利用高通量测序技术对红边龙血树叶片进行全基因组测序，组装得到完整的叶绿体基因组序列，并进行注释、序列特征比较和系统发育分析。结果表明，红边龙血树叶绿体基因组包含一个典型的四分体结构，长度为154 926 bp，是目前已报道的龙血树属中叶绿体基因组最小的物种；共拥有132个基因，包含86个编码蛋白基因、38个转运RNA基因和8个核糖体RNA基因；密码子偏好性分析发现存在偏好使用A/U碱基结尾的现象，整体上密码子偏好性较低；共鉴定出46个简单重复序列位点和54个长重复序列，分别在大单拷贝区与反向重复区有最大检出率；种间边界分析发现边界区域基因存在相对位置差异，扩张收缩情况总体较为相似；与近缘种进行系统发育分析，红边龙血树与细枝龙血树聚为一类，关系最近，符合形态学分类特征。对红边龙血树叶绿体基因组的解析为龙血树属植物的物种鉴定、遗传多样性和叶绿体转基因工程等提供了重要数据基础。

关键词:红边龙血树;叶绿体基因组;简单重复序列位点分析;系统发育;比较基因组学分析

Abstract:

Dracaena marginata is a widely cultivated horticultural plant in the world, which has high ornamental and medicinal value. In this study, the whole genome of leaves from D. marginata was sequenced by Illumina HiSeq 4000 platform. The chloroplast genome were assembled for functional annotation, sequence characteristics and phylogenetic analysis. The results showed that the chloroplast genome of D. marginata composed of four regions with a size of 154 926 bp, which was the smallest chloroplast genome reported for Dracaena species to date. A total of 132 genes were identified, including 86 coding genes, 38 tRNA genes and 8 rRNA genes. Codon bias analysis found that the codon usage bias was weak and there was a bias for using A/U base endings. 46 simple sequence repeat and 54 repeats loci were detected in the chloroplast genome, with the maximum detection rate in the large single copy region and inverted repeat region, respectively. The inverted repeats boundaries of D. marginata and Dracaena were highly conserved, whereas gene location differences occurred. Phylogenetic analysis revealed that D. serrulata and D. cinnabari form a monophyletic clade, which was the closest relationship and conformed to the morphological classification characteristics. The analysis of the chloroplast genome of D. marginata provides important data basis for species identification, genetic diversity and chloroplast genome engineering of Dracaena.

Key words:Dracaena marginata;chloroplast genome;simple sequence repeat site analysis;phylogeny;comparative genomics analysis