Complete chloroplast genome of the Malus baccata var. gracilis provides insights into the evolution and phylogeny of Malus species.

Abstract

Malus baccata (L.) var. gracilis (Rehd.) has high ornamental value and breeding significance, andcomparative chloroplast genome analysis was applied to facilitate genetic breeding for desired traits andresistance and provide insight into the phylogeny of this genus. Using data from whole-genomesequencing, a tetrameric chloroplast genome with a length of 159,992 bp and a total GC content of36.56% was constructed. The M. baccata var. gracilis chloroplast genome consists of a large single-copy sequence (88,100 bp), a short single-copy region (19,186 bp), and two inverted repeat regions, IRa(26,353 bp) and IRb (26,353 bp). This chloroplast genome contains 112 annotated genes, including 79protein-coding genes (nine multicopy), 29 tRNA genes (eight multicopy), and four rRNA genes (allmulticopy). Calculating the relative synonymous codon usage revealed a total of 32 high-frequencycodons, and the codons exhibited a biased usage pattern towards A/U as the ending nucleotide.Interspecific sequence comparison and boundary analysis revealed significant sequence variation in thevast single-copy region, as well as generally similar expansion and contraction of the SSC and IRregions for 10 analyzed Malus species. M. baccata var. gracilis and Malus hupehensis were groupedtogether into one branch based on phylogenetic analysis of chloroplast genome sequences. Thechloroplast genome of Malus species provides an important foundation for species identification, geneticdiversity analysis, and Malus chloroplast genetic engineering. Additionally, the results can facilitate theuse of pendant traits to improve apple tree shape.