收稿日期: 2022-02-10
录用日期: 2022-05-10
网络出版日期: 2022-05-10
基金资助
国家自然科学基金(31601782)
Analysis of Chloroplast Genomes of Aleurites moluccana
Received date: 2022-02-10
Accepted date: 2022-05-10
Online published: 2022-05-10
石栗(Aleurites moluccana)是大戟科石栗属的常绿阔叶乔木, 具有能源、药用和观赏价值。为填补石栗叶绿体基因组研究的空白, 通过二代高通量全基因组测序, 组装和注释了石栗叶绿体基因组, 并进行基因组特征和系统发育分析。结果显示, 石栗叶绿体基因组为典型的四段式结构, 总长度为163 298 bp, LSC、SSC及IR的长度分别为91 301、18 501和26 748 bp。石栗叶绿体基因组共有131个基因, 包括8个rRNA基因, 37个tRNA基因, 86个蛋白质编码基因。研究发现145个SSR位点, 检测到重复单元有单核苷酸、二核苷酸、三核苷酸和四核苷酸, 数目分别为80、53、10和2个。共线性分析结果表明, 石栗叶绿体基因组存在基因倒位和重排现象。利用最大似然法和贝叶斯法构建了系统发育树, 显示石栗与油桐(Vernicia fordii)和东京桐(Deutzianthus tonkinensis)亲缘关系较近, 并形成姐妹群。利用化石时间进行定年分析, 表明石栗属、油桐属和东京桐属的分化时间为25.94 Ma (95% HPD: 24.71-63.32 Ma)。该研究丰富了石栗基因组信息, 可为石栗种质资源的开发利用提供基础遗传数据, 同时为石栗属物种鉴定及系统发育研究提供参考。
包金波, 丁志杰, 苗浩宇, 李雪丽, 任书贤, 焦若岩, 李浩, 邓茜茜, 李英姿, 田新民 . 石栗叶绿体基因组研究[J]. 植物学报, 2023 , 58(2) : 248 -260 . DOI: 10.11983/CBB22026
Aleurites moluccana is an evergreen broad-leaved tree of the genus Aleurites in the family Euphorbiaceae, with energy, medicinal and ornamental values. To fill the gap in study of the chloroplast genome of A. moluccana, we assembled and annotated the chloroplast genome of A. moluccana by next-generation high-throughput whole genome sequencing, and performed genomic characterization and phylogenetic analysis. The results showed that the chloroplast genome of A. moluccana exhibited typical quadripartite and circular structures with a total length of 163 298 bp, the length of LSC, SSC, and IR was 91 301, 18 501, and 26 748 bp, respectively. It contains 131 genes, including 8 rRNA genes, 37 tRNA genes and 86 protein coding genes. A total of 145 SSR loci were found, with mononucleotide, dinucleotide, trinucleotide and tetranucleotide repeat units, and the numbers detected were 80, 53, 10, and 2, respectively. The results of collinearity analysis showed that the chloroplast genome of A. moluccana has the phenomenon of gene inversion and rearrangement. Phylogenetic trees were constructed using the maximum likelihood and Bayesian methods. It was found that A. moluccana was closely related to Vernicia fordii and Deutzianthus tonkinensis, and formed a sister group. The results of the dating analysis using fossil time showed that the differentiation time of the Aleurites, Vernicia and Deutzianthus was 25.94 Ma (95% HPD: 24.71-63.32 Ma). This study enriched the genomic information of A. moluccana and provided basic genetic data for the development and utilization of A. moluccana germplasm resources, as well as a reference for species identification and phylogenetic study of the Aleurites.
Key words： Aleurites moluccana; chloroplast genome; phylogeny
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