目的 以牛茄子Solanum capsicoides新鲜叶片为材料，对叶绿体基因组序列进行组装、注释和分析，探究牛茄子的序列特征和同属其他物种的系统发育关系。方法 基于Illumina HiSeq高通量测序，获得牛茄子完整叶绿体基因组序列，利用生物信息学方法进一步对其功能及特征、密码子偏好性、IR区域边界、核苷酸多样性、系统发育关系进行分析。结果 牛茄子叶绿体基因组全长为155 465 bp，为典型的四分体结构，总GC含量为37.85%，其中大单拷贝区、小单拷贝区和反向重复序列的长度分别为88 265、18 462、24 369 bp；共编码131个基因，包括86个蛋白编码基因、37个tRNA基因、8个rRNA基因。简单重复序列检测表明，叶绿体基因组包括51个SSR位点，其中以A和T组成的单核苷酸重复次数最多，占45.1%。密码子偏好性分析表明，亮氨酸是使用频率最高的氨基酸，AUU是使用次数最多的密码子，密码子偏向使用A/U结尾。属内叶绿体基因组比较分析显示，IR边界区域相对保守，但仍存在部分基因扩张和收缩等现象；核苷酸多样性分析获得了4个高突变热点：trnQ-psbK、psbF-psbE、clpP、ycf1，可作为物种鉴定和遗传多样性研究的潜在特征。系统发育分析显示牛茄子和喀西茄的亲缘关系更近，存在姐妹关系。结论 牛茄子叶绿体基因组的组装和系统发育分析，为茄属植物的分类和群体间遗传多样性的研究提供理论依据。

Objective The chloroplast genome sequence was assembled, annotated and analyzed using fresh leaves of Solanum capsicoides to explore the sequence characteristics of the S. capsicoides and the phylogenetic relationships with other species in the genus. Methods Based on Illumina HiSeq high-throughput sequencing, the complete chloroplast (cp) genome sequence of S. capsicoides was obtained, and its function and characteristics, codon preference, IR region boundary, nucleotide diversity and phylogenetic relationship were further analyzed by bioinformatics method. Results The cp genome of S. capsicoides exhibited a typical quadripartite structure with a length of 155 465 bp, and the total GC content was 37.85%. The lengths of large single copy region, small single copy region, and reverse repeat sequence were 88 265 bp, 18 462 bp and 24 369 bp, respectively. A total of 131 genes were encoded, including 86 protein-coding genes, 37 tRNA genes, eight rRNA genes. Simple repeat sequence analysis showed that the chloroplast genome contained 51 SSR loci, with the single nucleotide repeats consisting of A and T being the most numerous at 45.1%. Codon preference analysis showed that leucine was the most frequently used amino acid and AUU was the most frequently used codon. Besides, codon preference was ending by using A/U. Comparative analysis of chloroplast genomes within the genus showed that the IR boundary region was relatively conserved, while expansion and contraction still existed in some genes. Nucleotide diversity analysis obtained four mutation hotspots: trnQ-psbK, psbF-psbE, clpP, and ycf1, which could be used as a potential characterization for species identification and genetic diversity study. Phylogenetic analysis showed that S. capsicoides and S. aculeatissimum were more closely related and exhibited a sister relationship. Conclusion The assembly and phylogenetic analysis of the chloroplast genome of S. capsicoides provide theoretical basis for the classification of Solanum plants and genetic diversity among populations.

R286.12

国家自然科学基金面上项目（82074071）；浙江中医药大学校级科研项目（2021JKGJYY004）