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; Chloroplasts; Codons; Comparative analysis; Evolutionary genetics; Genes; Genomes; Life Sciences; Medicinal plants; Myrtaceae; Nucleotides; Original Article; Phylogenetics; Phylogeny; Plant Biochemistry; Plant Sciences; Preference analysis; rRNA; Species; Syzygium; tRNA; 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.