Abstract
Malus baccata (L.) var. gracilis (Rehd.) has high ornamental value and breeding significance, and comparative chloroplast genome analysis was applied to facilitate genetic breeding for desired traits and resistance and provide insight into the phylogeny of this genus. Using data from whole-genome sequencing, a tetrameric chloroplast genome with a length of 159,992 bp and a total GC content of 36.56% 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 79 protein-coding genes (nine multicopy), 29 tRNA genes (eight multicopy), and four rRNA genes (all multicopy). Calculating the relative synonymous codon usage revealed a total of 32 high-frequency codons, 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 the vast single-copy region, as well as generally similar expansion and contraction of the SSC and IR regions for 10 analyzed Malus species. M. baccata var. gracilis and Malus hupehensis were grouped together into one branch based on phylogenetic analysis of chloroplast genome sequences. The chloroplast genome of Malus species provides an important foundation for species identification, genetic diversity analysis, and Malus chloroplast genetic engineering. Additionally, the results can facilitate the use of pendant traits to improve apple tree shape.
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Funding
This research was funded by the National Natural Science Foundation of China, award number 32072520; China National Botanical Garden (North Garden) Project: BZ202206; Fruit innovation team project of Shandong Province (CN), award number SDAIT-06-07; and the Natural Science Foundation of Shandong Province (CN), award number ZR2020MC132.
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Data will be made available on request. The data supporting the findings of this study are openly available in the GenBank database at https://www.ncbi.nlm.nih.gov/ under accession number OQ737737.
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Q Hao, YF Mao and X Shen collected samples. X Qin performed the experiments, analysed the results and wrote the manuscript. X Wang assisted in the experiment operation. YB Liu, C Yang were involved in the design of these experiments and data interpretation. MY Sui, YW Zhang, YL Hu, XS Chen, ZQ Mao and X Shen conceived and directed the experiments and writing. All authors have read and agreed to the published version of the manuscript.
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Qin, X., Hao, Q., Wang, X. et al. Complete chloroplast genome of the Malus baccata var. gracilis provides insights into the evolution and phylogeny of Malus species. Funct Integr Genomics 24, 13 (2024). https://doi.org/10.1007/s10142-024-01291-5
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DOI: https://doi.org/10.1007/s10142-024-01291-5