The complete chloroplast genome of two Syzygium (Myrtaceae) species and comparative analysis with other related species

• Published in: Plant biotechnology reports Vol. 17; no. 5; pp. 753 - 765
• Main Authors: Zhang, Mengjie, Yang, Xiuyao, Zhu, Ling, Xi, Dengxian, Cai, Hanbing, Yin, Tuo, Zhang, Hanyao
• Format: Journal Article
• Language: English
• Published: Singapore Springer Nature Singapore 01.10.2023; Springer Nature B.V; 한국식물생명공학회
• Subjects: Agriculture; Biomedical and Life Sciences; Biotechnology; Cell Biology; chloroplast genome; Chloroplasts; Codons; Comparative analysis; Evolutionary genetics; Genes; genetic variation; Genomes; genus; Life Sciences; Medicinal plants; Myrtaceae; Nucleotides; Original Article; Phylogenetics; Phylogeny; Plant Biochemistry; Plant Sciences; Plinia; Preference analysis; RNA; rRNA; Species; species identification; Syzygium; Syzygium jambos; tRNA; vegetation; 농학; Cp genome; Phylogeny; Genomic characterisation; Comparative analysis
• ISSN: 1863-5466; 1863-5474
• DOI: 10.1007/s11816-023-00865-2

Syzygium , a vital genus under Myrtaceae, is aesthetically pleasing and resistant and is used for urban greenery. However, with intensive research in recent years, an increasing number of Syzygium plants have been explored for their medicinal value. Analysing the Syzygium chloroplast (cp) genome can help assess its phylogenetic relationships and provide a theoretical basis for the development and application of Syzygium plants. In this study, we first sequenced the complete cp genomes of Syzygium grijsii and Syzygium rehderianum to investigate their phylogenetic relationships in Myrtaceae. In the copy region and reverse repeat region, 129 genes were detected, including 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Preference analysis showed that the eight Syzygium species preferred codons ending in A/U and contained abundant repetitive sequences and SSR sites. The ycf1 , rpoC2 , matK and ndhB genes had the most RNA editable sites and more genes with Ka/Ks < 1, indicating that species evolution was mainly subject to purifying selection. Comparative analysis of the cp genome showed that the eight species boundaries of Syzygium were similar, but the variability of the LSC and SSC regions was higher than that of the IR region, with 280 sites with Pi > 0.015, showing a high level of nucleotide diversity. Phylogenetic analysis showed that Syzygium grijsii was closely related to Syzygium jambos , and S. rehderianum was close to Plinia aureana . The cp genome and phylogeny of S. grijsii and S. rehderianum provide a theoretical basis for Syzygium species identification and exploitation.