濒危植物坡垒的叶绿体基因组特征及系统发育分析  

Genomic Characteristics and Phylogenic Analysis of Chloroplast of the Endangered Plant Hopea hainanensis

作　　者：陈玉凯[2] 杨勇[2] 金映虹[2] 姚俊 王芸 张颖 Chen Yukai;Yang Yong;Jin Yinghong;Yao Jun;Wang Yun;Zhang Ying(College of Life Sciences and Technology,Zhanjiang,524048;Ministry of Education Key Laboratory for Ecology of Tropical Islands,Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province,College of Life Sciences,Hainan Normal University,Haikou,571158)

机构地区：[1]岭南师范学院生命科学与技术学院,湛江524048 [2]海南师范大学生命科学学院,热带岛屿生态学教育部重点实验室,海南省热带动植物生态学重点实验室,海口571158

出　　处：《基因组学与应用生物学》2021年第1期365-374,共10页Genomics and Applied Biology

基　　金：国家自然科学基金(31760119);岭南师范学院校级重点项目和人才专项(LZ1906,ZL2003);湛江市科技计划项目(2018A03024)共同资助。

摘　　要：了解濒危植物坡垒(Hopea hainanensis)的叶绿体基因组结构,对揭示龙脑香科植物的系统进化关系具有重要意义。本研究通过高通量测序技术对坡垒叶绿体基因组的结构特征及与其近缘种的系统进化关系进行了分析。结果表明:坡垒叶绿体基因组具有典型被子植物叶绿体基因组的四分体结构,基因组全长151 795 bp,共注释得到124个基因,其中包括77个蛋白质编码蛋白基因(5个基因在反向重复区重复)、39个转运RNA (tRNA)基因和8个核糖体RNA (rRNA)基因。生物信息学分析表明,坡垒叶绿体基因组的密码子有19 662个,其中编码亮氨酸Leu的密码子数量最多,同义密码子使用度最高的是UUA/GCU/UCU。坡垒叶绿体基因组中鉴定得到94个SSR位点,其中3个以上核苷酸、三核苷酸、二核苷酸和单核苷酸的数目分别为7、4、24、59个。坡垒与龙脑香科其他植物叶绿体基因组全序列比较分析表明,其基因组大小、基因组成及排列特征相近,但也存在ycf1基因缺失现象。通过MEGA软件最大似然法分析比较锦葵目17种植物的叶绿体基因组,构建系统进化树发现,坡垒与龙脑香科新棒果香木(Neobalanocarpus heimii)亲缘关系相对较近,整个龙脑香科植物聚为一支。该研究丰富了坡垒的遗传信息,为构建龙脑香科植物的系统进化提供了新的材料,也为解决龙脑香科植物的分类问题提供参考。Understanding the chloroplast genome structure of the endangered plant Hopea hainanensis is of great significance in revealing the phylogenetic relationship of the family Dipterocarpaceae. The whole chloroplast genome,the structural characteristics and phylogenetic relationship with relative species of H. hainanensis were analyzed based on using high-throughput sequencing technology. The results showed that the chloroplast genome of H.hainanensis was discovered with the typical angiosperms and a tetrad structure including a total length of 151 795 bp.A total of 124 genes were annotated, including 77 protein coding protein genes(5 genes repeat in the reverse repeat region), 39 tRNA genes and 8 ribosomal RNA(rRNA) genes. Bioinformatics analysis showed that there were19 662 codons in the chloroplast genome. Leucine had the most codons and UUA/GCU/UCU were the most synonymous codon used in this chloroplast genome. A total of 94 SSR loci were predicted in the chloroplast genome,with 7 nucleotides SSRs, 4 trinucleotide SSRs, 24 dinucleotide and 59 single SSRs, respectively. Compared with other Dipterocarpaceae plants, there had a similar genome size, gene composition and arrangement characteristics in chloroplast genome, but there was also a lack of ycf1 gene only in the chloroplast genome of H. hainanensis.The phylogenetic tree constructed by comparing the chloroplast genomes of 17 species of Malvaceae with the maximum likelihood method of MEGA software showed that the phylogenetic relationship of species in Dipterocarpaceae was relatively close, and the whole family of Dipterocarpaceae was clustered into one branch. This study enriched the genetic information of Dipterocarpaceae, and provided new materials for the systematic evolution of Dipterocarpaceae, and references for the classification of Dipterocarpaceae.

关 键 词：濒危植物 坡垒 叶绿体基因组 系统发育 

分 类 号：Q943[生物学—植物学]