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Qin X, Hao Q, Wang X, Liu Y, Yang C, Sui M, Zhang Y, Hu Y, Chen X, Mao Z, Mao Y, Shen X. Complete chloroplast genome of the Malus baccata var. gracilis provides insights into the evolution and phylogeny of Malus species. Funct Integr Genomics 2024; 24:13. [PMID: 38236432 DOI: 10.1007/s10142-024-01291-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024]
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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Affiliation(s)
- Xin Qin
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Qiang Hao
- China National Botanical Garden (North Garden), Beijing, China
| | - Xun Wang
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Yangbo Liu
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Chen Yang
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Mengyi Sui
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Yawen Zhang
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Yanli Hu
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Xuesen Chen
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Zhiquan Mao
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Yunfei Mao
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China.
| | - Xiang Shen
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China.
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