| 引用本文: | 张梦洁, 杨秀瑶, 尹 拓, 韩沛辰, 杜朝金, 张汉尧.轮叶蒲桃叶绿体基因组特征及系统发育分析[J].广西植物,2023,43(10):1849-1860.[点击复制] |
| ZHANG Mengjie, YANG Xiuyao, YIN Tuo, HAN Peichen,
DU Chaojin, ZHANG Hanyao.Analysis of chloroplast genomic characteristics and phylogeny in Syzygium grijsii[J].Guihaia,2023,43(10):1849-1860.[点击复制] |
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| 轮叶蒲桃叶绿体基因组特征及系统发育分析 |
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张梦洁1, 杨秀瑶1, 尹 拓2, 韩沛辰2, 杜朝金2, 张汉尧1*
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1. 西南林业大学 林学院, 西南地区生物多样性保育国家林业与草原局重点实验室, 昆明 650224;2. 西南林业大学 林学院, 云南省高校林木遗传改良与繁育重点实验室, 昆明 650224
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| 摘要: |
| 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0.010<Pi<0.015,核苷酸多样性水平高。(4)系统发育分析表明,轮叶蒲桃与蒲桃(S. jambos)、滇边蒲桃(S. forrestii)和乌墨(S. cumini)亲缘关系最近,其次是马六甲蒲桃(S. malaccense)。因此,该文结果表明轮叶蒲桃的叶绿体基因组结构保守,特征明显,与同属物种相比,其序列具有相似性,核苷酸具有多样性,并且其与多种桃金娘科物种之间存在亲缘关系。该文对轮叶蒲桃叶绿体基因组进行基因组特征和系统发育分析,为轮叶蒲桃的种质资源鉴定和开发利用奠定理论基础。 |
| 关键词: 轮叶蒲桃, 叶绿体基因组, 系统发育关系, 基因组特征, 比较分析 |
| DOI：10.11931/guihaia.gxzw202207030 |
| 分类号:Q943 |
| 文章编号:1000-3142(2023)10-1849-12 |
| 基金项目:国家自然科学基金项目(32160556)。 |
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| Analysis of chloroplast genomic characteristics and phylogeny in Syzygium grijsii |
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ZHANG Mengjie1, YANG Xiuyao1, YIN Tuo2, HAN Peichen2,
DU Chaojin2, ZHANG Hanyao1*
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1. Key Laboratory of Biodiversity Conservation of Southwest China, National Forestry and Grassland Administration, Forestry College of
Southwest Forestry University, Kunming 650224, China;2. Key Laboratory of Forest Genetic Improvement and Breeding,
Forestry College of Southwest Forestry University, Kunming 650224, China
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| Abstract: |
| 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 < Pi < 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. |
| Key words: Syzygium grijsii, chloroplast genome, phylogenetic relationship, genomic characteristics, comparative analysis |
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