Analysis of chloroplast genomic characteristics and phylogeny in Syzygium grijsii

Mengjie ZHANG; Xiuyao YANG; Tuo YIN; Peichen HAN; Chaojin DU; Hanyao ZHANG

doi:10.11931/guihaia.gxzw202207030

Guangxi Zhiwu (Oct 2023)

Analysis of chloroplast genomic characteristics and phylogeny in Syzygium grijsii

Mengjie ZHANG,
Xiuyao YANG,
Tuo YIN,
Peichen HAN,
Chaojin DU,
Hanyao ZHANG

Affiliations

Mengjie ZHANG: Key Laboratory of Biodiversity Conservation of Southwest China, National Forestry and Grassland Administration, Forestry College of Southwest Forestry University, Kunming 650224, China
Xiuyao YANG: Key Laboratory of Biodiversity Conservation of Southwest China, National Forestry and Grassland Administration, Forestry College of Southwest Forestry University, Kunming 650224, China
Tuo YIN: Key Laboratory of Forest Genetic Improvement and Breeding, Forestry College of Southwest Forestry University, Kunming 650224, China
Peichen HAN: Key Laboratory of Forest Genetic Improvement and Breeding, Forestry College of Southwest Forestry University, Kunming 650224, China
Chaojin DU: Key Laboratory of Forest Genetic Improvement and Breeding, Forestry College of Southwest Forestry University, Kunming 650224, China
Hanyao ZHANG: Key Laboratory of Biodiversity Conservation of Southwest China, National Forestry and Grassland Administration, Forestry College of Southwest Forestry University, Kunming 650224, China

DOI: https://doi.org/10.11931/guihaia.gxzw202207030
Journal volume & issue: Vol. 43, no. 10
pp. 1849 – 1860

Abstract

Read online

Syzygium grijsii, an evergreen shrub of Myrtaceae and Syzygium, has good prospects for exploitation, but its chloroplast genome characteristics and phylogenetic relationships have not been reported. To fill the gap in the genomics of S. grijsii, a systematic study of the chloroplast genome of S. grijsii was conducted in this paper. Illumina high-throughput sequencing was used to perform complete assembly in the GetOrganelle platform, and the assembled data were also used to analyze the structural features and phylogenetic relationships of the S. grijsii chloroplast genome, including the structure, function and characteristics of the S. grijsii chloroplast genome, codon preference analysis, comparative analysis of the chloroplast genome and phylogenetic analyses. The results were as follows: (1) The chloroplast genome of S. grijsii was 158 591 bp in size, which contained 129 genes. Among them, 8 were rRNA genes, 37 were tRNA genes and 84 were protein-coding genes. The analysis detected 39 repetitive sequences and 84 SSR loci. (2) Codon preference analysis revealed that there was a bias towards A/U at the ends of the S. grijsii chloroplast genome, and the most used codon was the one encoding leucine. (3) In comparison with closely related species, the boundary length of S. grijsii was conserved, and the gene species at the boundary were similar to several Syzygium species; the S. grijsii chloroplast genome had a high degree of variability in the LSC and SSC regions, with 45 sites of 0.010 < Pi < 0.015 and a high level of nucleotide diversity. (4) Phylogenetic analysis showed that S. grijsii was most closely related to S. jambos, S. forrestii and S. cumini, followed by S. malaccense. The study concluded that S. grijsii had a conserved chloroplast genome structure with distinct features, sequence similarity and nucleotide diversity compared to Syzygium species, and affinity between it and various Myrtaceae species. In this paper, the genomic characterization and phylogenetic analysis of the chloroplast genome of S. grijsii are conducted to lay the theoretical foundation for the identification and exploitation of the germplasm resources of S. grijsii.

Published in Guangxi Zhiwu

ISSN: 1000-3142 (Print)
Publisher: China Science Publishing & Media Ltd. (CSPM)
Country of publisher: China
LCC subjects: Science: Botany
Website: http://www.guihaia-journal.com/gxzwen/ch/index.aspx

About the journal

Abstract

Keywords