Complete chloroplast genome studies of different apple varieties indicated the origin of modern cultivated apples from Malus sieversii and Malus sylvestris

Background: Apple is one of the most important temperate deciduous fruit trees worldwide, with a wide range of cultivation. In this study, we assessed the variations and phylogenetic relationships between the complete chloroplast genomes of wild and cultivated apples (Malus spp.). Method: We obtained the complete chloroplast genomes of 24 apple varieties using next-generation sequencing technology and compared them with genomes of (downloaded from NCBI) the wild species. Result: The chloroplast genome of Malus is highly conserved, with a genome length of 160,067-160,290 bp, and all have a double-stranded circular tetrad structure. The gene content and sequences of genomes of wild species and cultivated apple were almost the same, but several mutation hotspot regions (psbI-atpA, psbM-psbD, and ndhC-atpE) were detected in these genomes. These regions can provide valuable information for solving specific molecular markers in taxonomic research. Phylogenetic analysis revealed that Malus formed a new Glade and four cultivated varieties clustered into a branch with M. sylvestris and M. sieversii, which indicated that M. sylvestris and M. sieversii were the ancestor species of the cultivated apple.

Automated summary

The chloroplast genomes of apples are highly conserved, but mutation hotspot regions were found in both wild and cultivated species. Phylogenetic analysis indicated that M. sylvestris and M. sieversii are the ancestor species of cultivated apple varieties.