Malusbaccata,苹果属的宝贵种质资源,是中国本土的,分布广泛。然而,对“ZA”的谱系组成和遗传基础知之甚少,一种突变型的M.baccata.在这项研究中,我们从形态学和超微结构的角度比较了\'ZA\'和野生型之间的差异,并基于生化方法分析了它们的叶绿体色素含量。Further,完整的有丝分裂基因组M.baccata\'ZA\'被组装并通过下一代测序获得。随后,使用Geneious分析了其分子特征,MISA-Web,和CodonW工具包。此外,通过对106份苹果属种质和42种玫瑰科植物的研究,我们推导并阐明了M.baccata\'ZA\'的进化位置,以及不同个体之间的种间差异。相比之下,ZA有丝分裂体的总长度(GC含量:45.4%)为374,023bp,约2.33倍的大小(160,202bp)的塑性体(GC:36.5%)。共线分析结果揭示了不同苹果属物种之间发生的大量重复和基因组重排。此外,我们确定了14个质体驱动的片段转移事件。在\'ZA\'有丝分裂基因组中总共注释了54个基因,包括35个蛋白质编码基因,16个tRNA,和三个rRNA。通过计算来自42种玫瑰科物种(包括“ZA”)的24个共享核心线粒体CDS的核苷酸多态性和选择压力,我们观察到nad3基因表现出最小的变异,而nad4L似乎正在迅速发展。群体遗传学分析共检测到1578个高质量变异(1424个SNP,60插入,和94个缺失;变异率:1/237)来自106个苹果个体的样本。此外,通过基于苹果属植物和玫瑰科类群数据集构建系统发育树,初步证明\'ZA\'与M.baccata密切相关,M.Sieversii,和其他近缘物种在进化方面。本研究获得的测序数据,连同我们的发现,有助于扩大玫瑰科研究的有丝分裂基因组学资源。它们对于分子鉴定研究以及专注于优良种质的保护和育种工作也具有参考意义。
Malus baccata, a valuable germplasm resource in the genus Malus, is indigenous to China and widely distributed. However, little is known about the lineage composition and genetic basis of \'ZA\', a mutant type of M. baccata. In this study, we compared the differences between \'ZA\' and wild type from the perspective of morphology and ultrastructure and analyzed their chloroplast pigment content based on biochemical methods. Further, the complete mitogenome of M. baccata \'ZA\' was assembled and obtained by next-generation sequencing. Subsequently, its molecular characteristics were analyzed using Geneious, MISA-web, and CodonW toolkits. Furthermore, by examining 106 Malus germplasms and 42 Rosaceae species, we deduced and elucidated the evolutionary position of M. baccata \'ZA\', as well as interspecific variations among different individuals. In comparison, the total length of the \'ZA\' mitogenome (GC content: 45.4%) is 374,023 bp, which is approximately 2.33 times larger than the size (160,202 bp) of the plastome (GC: 36.5%). The collinear analysis results revealed abundant repeats and genome rearrangements occurring between different Malus species. Additionally, we identified 14 plastid-driven fragment transfer events. A total of 54 genes have been annotated in the \'ZA\' mitogenome, including 35 protein-coding genes, 16 tRNAs, and three rRNAs. By calculating nucleotide polymorphisms and selection pressure for 24 shared core mitochondrial CDSs from 42 Rosaceae species (including \'ZA\'), we observed that the nad3 gene exhibited minimal variation, while nad4L appeared to be evolving rapidly. Population genetics analysis detected a total of 1578 high-quality variants (1424 SNPs, 60 insertions, and 94 deletions; variation rate: 1/237) among samples from 106 Malus individuals. Furthermore, by constructing phylogenetic trees based on both Malus and Rosaceae taxa datasets, it was preliminarily demonstrated that \'ZA\' is closely related to M. baccata, M. sieversii, and other proximate species in terms of evolution. The sequencing data obtained in this study, along with our findings, contribute to expanding the mitogenomic resources available for Rosaceae research. They also hold reference significance for molecular identification studies as well as conservation and breeding efforts focused on excellent germplasms.