Chloroplast genome in <i>Malus floribunda</i> Siebold.

Xun Wang; Ziquan Feng; Daru Wang; Yuepeng Han; Xiaofei Wang; Xiang Shen; Chunxiang You

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Chloroplast genome in Malus floribunda Siebold.

Author: Xun WANG ¹ ; Ziquan FENG ¹ ; Daru WANG ¹ ; Yuepeng HAN ² ; Xiaofei WANG ¹ ; Xiang SHEN ¹ ; Chunxiang YOU ¹
Author Information

1. State Key Laboratory of Crop Biology, College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China.
2. Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, China.
Publication Type:Journal Article
Keywords: Malus floribunda; bioinformatics; chloroplast genome; comparative genomics analysis; phylogenetic
MeSH: Genome, Chloroplast; Malus; Phylogeny; Plant Breeding; Codon
From: Chinese Journal of Biotechnology 2022;38(10):3713-3727
CountryChina
Language:Chinese
Abstract: Malus floribunda Siebold. (Malus) is widely cultivated all over the world, which is of high ornamental value and breeding significance. Comparative analysis of the chloroplast genome can help enrich the phylogenetic relationship and facilitate germplasm utilization of Malus. Based on the whole genome sequencing data, a complete chloroplast genome (M. floribunda) with tetrad structure was assembled. The chloroplast genome (160 037 bp) was composed of a large single-copy (LSC) region (88 142 bp), inverted repeat (IR) B (26 353 bp), a small single-copy (SSC) region (19 189 bp), and IRA (26 353 bp). A total of 111 genes were annotated: 78 protein-coding genes, 29 tRNA genes and 4 rRNA genes. In addition, a large number of repeat sequences were identified in the genome, which was slightly different from that of M. sieboldii and M. toringoides. As for the relative synonymous codon usage, 30 high-frequency codons were found, and the codons tended to end with A/T. The results of interspecific sequence alignment and boundary analysis suggested the sequence variation of the LSC region was large, and the expansion and contraction of the SC region and IR region of the eight Malus species were generally similar. According to the phylogenetic analysis of chloroplast genome sequences, M. floribunda, M. hupehensis, and M. toringoides were grouped into one clade. The findings in this study can provide data support for the development of genetic markers and utilization of germplasm resources in the future.