肖蒲桃叶绿体基因组结构特征及系统发育关系  

Structural Characteristics and Phylogenetic Relationship of Chloroplast Genome of Syzygium acuminatissimum

作　　者：邓演文 刘晓洲 卓定龙 曾凤 DENG Yanwen;LIU Xiaozhou;ZHUO Dinglong;ZENG Feng(Pubang Landscape Architecture Co.,Ltd,Guangzhou 510627,China)

机构地区：[1]广州普邦园林股份有限公司,广东广州510627

出　　处：《广东农业科学》2021年第6期38-46,共9页Guangdong Agricultural Sciences

摘　　要：【目的】肖蒲桃(Syzygium acuminatissimum)是我国南方高价值的硬木树种之一,适宜作为行道树或园景树。研究揭示肖蒲桃叶绿体基因组的结构特征及系统发育关系,对蒲桃属甚至桃金娘科的分类学研究具有重要意义。【方法】使用CTAB法提取肖蒲桃叶片基因组DNA。利用Illumina HiSeq X TEN平台进行高通量测序,在SPAdes v3.13.0上组装叶绿体基因组,并通过GeSeq注释肖蒲桃的完整叶绿体基因组。分析了肖蒲桃叶绿体基因组的结构特征、序列特征及系统发育关系。【结果】肖蒲桃完整的叶绿体基因组长度为159352 bp,共有109个基因,包括78个蛋白质编码基因、27个tRNA基因和4个rRNA基因,其中17个基因具有内含子;检测到21379个密码子,其中丝氨酸密码子最丰富、蛋氨酸密码子最匮乏;检测到47个RNA可编辑位点,其中ndhB基因最多(10个);检测到48个长片段重复序列,其中18个正向重复、6个反向重复、22个回文重复和2个互补重复;检测到230个简单重复序列,其中绝大多数为单核苷酸(205个)。基因组比较分析结果表明,4个蒲桃属植物的IR边界有较小差异,核苷酸多样性高于0.015的区间有7个。系统发育分析结果表明,肖蒲桃与丁香蒲桃(S.aromaticum)关系密切。【结论】研究结果有助于开展后续的蒲桃属系统发育研究和物种鉴定工作。【Objective】Syzygium acuminatissimum is a high-value hardwood tree species in southern China.It is suitable to be planted as a street tree or landscape tree.The study revealed the structural characteristics and phylogenetic relationship of the chloroplast genome of S.acuminatissimum,which will be of great importance for the taxonomic researches of Syzygium and even Myrtaceae.【Method】The CTAB method was used to extract genomic DNA from the leaves of S.acuminatissimum.High-throughput sequencing was conducted through the Illumina HiSeq X TEN platform,the chloroplast genome was assembled on SPAdes v3.13.0,and the complete chloroplast genome of S.acuminatissimum was annotated on GeSeq.Then,the structural characteristics,sequence characteristics and phylogenetic relationship of the chloroplast genome of S.Acuminatissimum were analyzed.【Result】The complete chloroplast genome of S.acuminatissimum was 159352 bp in length,with 109 annotated genes,including 78 protein-coding genes,27 tRNA genes and 4 rRNA genes,of which 17 genes had introns.A total of 21379 codons were detected,of which serine codons were the most abundant and methionine codons were the least.47 RNA editable sites were detected,of which the ndhB genes were the most(10).48 long repeat sequences were detected,of which 18 were forward repeats,6 inverted repeats,22 palindrome repeats and 2 complementary repeats.230 simple repeats were detected,most of which were single nucleotides(205).Results of genome comparison analysis showed that the IR boundaries of the 4 Syzygium plants were slightly different,and there were 7 regions with nucleotide diversity higher than 0.015.Results of the phylogenetic analysis showed that S.acuminatissimum and S.aromaticum were closely related.【Conclusion】The research results will help to carry out the follow-up researches on the phylogeny and species identification of Syzygium.

关 键 词：肖蒲桃 叶绿体 系统进化 桃金娘科 蒲桃属 

分 类 号：S792.99[农业科学—林木遗传育种]