轮叶蒲桃叶绿体基因组特征及系统发育分析

轮叶蒲桃(Syzygium grijsii)系桃金娘科(Myrtaceae)蒲桃属(Syzygium)常绿灌木，其开发前景较好，但其叶绿体基因组特征及系统发育关系尚未有相关报道。为弥补轮叶蒲桃基因组学方面的空缺，该文对轮叶蒲桃的叶绿体基因组进行了系统的研究。运用Illumina高通量测序，并在GetOrganelle平台进行完整组装，同时利用组装好的数据分析轮叶蒲桃叶绿体基因组的结构特征和系统发育关系，其中包括轮叶蒲桃叶绿体基因组结构、功能及特征、密码子偏好性分析、叶绿体基因组的比较分析和系统发育的分析。结果表明：(1)轮叶蒲桃叶绿体基因组大小为158 591 bp,包含129个基因。其中，rRNA基因8个，tRNA基因37个，蛋白编码基因84个。分析检测到39个重复序列和84个SSR位点。(2)密码子偏好性分析发现轮叶蒲桃叶绿体基因组中末端存在对A/U的偏性，使用最多的是编码亮氨酸的密码子。(3)与近缘种比较，轮叶蒲桃的边界长度保守，边界处的基因种类与多个蒲桃属物种相似；轮叶蒲桃叶绿体基因组在LSC和SSC区变异度较大，有45处0.010i<0....

Analysis of chloroplast genomic characteristics and phylogeny in Syzygium grijsii

Syzygium grijsii, an evergreen shrub of Myrtaceae and Syzygium, has good prospects for exploitation, but its chloroplast genome characteristics and phylogenetic relationships have not been reported. To fill the gap in the genomics of S. grijsii, a systematic study of the chloroplast genome of S. grijsii was conducted in this paper. Illumina high-throughput sequencing was used to perform complete assembly in the GetOrganelle platform, and the assembled data were also used to analyze the structural features and phylogenetic relationships of the S. grijsii chloroplast genome, including the structure, function and characteristics of the S. grijsii chloroplast genome, codon preference analysis, comparative analysis of the chloroplast genome and phylogenetic analyses. The results were as follows:(1)The chloroplast genome of S. grijsii was 158 591 bp in size, which contained 129 genes. Among them, 8 were rRNA genes, 37 were tRNA genes and 84 were protein-coding genes. The analysis detected 39 repetitive sequences and 84 SSR loci.(2)Codon preference analysis revealed that there was a bias towards A/U at the ends of the S. grijsii chloroplast genome, and the most used codon was the one encoding leucine.(3)In comparison with closely related species, the boundary length of S. grijsii was conserved, and the gene species at the boundary were similar to several Syzygium species; the S. grijsii chloroplast genome had a high degree of variability in the LSC and SSC regions, with 45 sites of 0.010 < P_i < 0.015 and a high level of nucleotide diversity.(4)Phylogenetic analysis showed that S. grijsii was most closely related to S. jambos, S. forrestii and S. cumini, followed by S. malaccense. The study concluded that S. grijsii had a conserved chloroplast genome structure with distinct features, sequence similarity and nucleotide diversity compared to Syzygium species, and affinity between it and various Myrtaceae species. In this paper, the genomic characterization and phylogenetic analysis of the chloroplast genome of S. grijsii are conducted to lay the theoretical foundation for the identification and exploitation of the germplasm resources of S. grijsii.