目的 明确野生和栽培酸枣Ziziphus jujuba var. spinosa叶绿体基因组特征与系统发育关系，为酸枣的分子鉴定提供依据。方法 以2种不同品种的酸枣为研究对象，采用高通量测序技术，获得酸枣叶绿体基因组序列，并对其结构区及功能区进行注释，对密码子偏好性、重复序列、IR区收缩与扩张、核酸多态性以及分子进化等方面进行研究。结果 野生和栽培酸枣叶绿体基因组均具有典型的四分体结构，全长序列分别为161 343、161 601 bp，总GC含量均为37.0%，均编码129个基因；野生和栽培酸枣分别检测到73、71个散在重复序列，均为F型和P型，简单重复序列SSR位点分别为89、91个；野生和栽培酸枣叶绿体基因组密码子偏好性较弱，偏向于以A/T碱基结尾，野生酸枣较栽培酸枣最优密码子多1个，核苷酸多态性指数（nucleotide polymorphism index，P_i）显示野生酸枣位于大单拷贝区（large single-copy region，LSC）的rpoC2基因和rpoB基因具有高变异性，栽培酸枣位于LSC区的atPA基因有高变异性；IR区域收缩与扩张显示JLB（LSC/IRb）区域、JSB（IRb/SSC）区域和JSA（SSC/Ira）区域存在不同程度的基因变异及序列收缩与扩张现象；系统发育树结果表明野生酸枣与参考序列KU351660.1聚为一支、栽培酸枣则与参考序列KX266829.1（骏枣Ziziphus jujube ‘Junzao’）、KU351660.1（枣Ziziphus jujuba）、KX266830.1、MF781071.1（冬枣Ziziphus jujuba ‘Dongzao’）亲缘关系比较密切。结论 野生和栽培酸枣叶绿体基因组在简单重复序列、IR区收缩与扩张、最优密码子数目、核酸多态性片段及系统发育树几个方面存在差异，后续可以利用存在差异的SSR位点、高变异片段及IR区域基因类型对野生和栽培酸枣有效鉴别，为野生和栽培酸枣的分子标记提供理论依据。

Objective To clarify the relationship between chloroplast genome characteristics and phylogeny of wild and cultivated Ziziphus jujuba var. spinosa (ZS) and provide the basis for molecular identification of ZS. Methods In this study, the whole-genome sequence of two different varieties of ZS was obtained using high-throughput sequencing technology. Its structural and functional regions were annotated, and the coding preference, repeat sequence, contraction and expansion of the IR region, nucleic acid polymorphism and molecular evolution were studied. Results The chloroplast genomes of both wild and cultivated ZS had typical tetrad structure, with full-length sequences of 161 343 and 161 601 bp, total GC content of 37.0%, encoding 129 genes. There were 73 and 71 scattered repeats in wild and cultivated ZS, which were F type and P type, respectively, and 89 and 91 simple repeat SSR loci were detected, respectively. The codon preference of the chloroplast genome of wild and cultivated ZS was weak and tended to end in A/T base. Wild ZS had one more optimal codon than cultivated ZS. The nucleotide polymorphism index (P_i) value showed that there were two fragments with high variability in the wild ZS, rpoC2 gene and rpoB gene in the large single-copy region (LSC) region, and one fragment with high variability in cultivated ZS, atPA gene in the LSC region. The contraction and expansion of IR region showed that JLB (LSC/IRb) region, JSB (IRb/SSC) region and JSA (SSC/Ira) region had different degrees of gene variation and sequence contraction and expansion; Phylogenetic trees showed that wild ZS was closely related to the reference sequence KU351660.1, and cultivated ZS was closely related to the reference sequences KX266829.1 (Ziziphus jujuba ‘Junzao’), KU351660.1 (Ziziphus jujuba), KX266830.1, MF781071.1 (Ziziphus jujuba ‘Dongzao’). Conclusion The chloroplast genomes of wild and cultivated ZS are different in simple repeats, IR contraction and expansion, the number of optimal codons, nucleic acid polymorphic fragments and phylogenetic trees, which can be used to distinguish wild and cultivated ZS effectively by using different SSR loci, highly variable fragments and IR genotype and provide a theoretical basis for molecular markers of wild and cultivated ZS.

R286.12

陕西省重点研发计划(2024CY-JJQ-41); 咸阳市重点研发计划(L2024-ZDYF-ZDYF-SF-0035); 现代农业产业技术体系建设专项(CARS-21)