Abstract
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.
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Data availability
The complete chloroplast genome sequences of S. grijsii and S. rehderianum were deposited in the GenBank database (https://www.ncbi.nlm.nih.gov/genbank, ON 243764 and ON 2573450). Raw sequencing reads used in this study have been deposited in the SRA database (https://www.ncbi.nlm.nih.gov/sra). The BioProject, SRA and Bio-Sample numbers are PRJNA826323 and PRJNA864556, SRR18740564 and SRR18554143, and SAMN27554785 and SAMN27067607.
Abbreviations
- CTAB:
-
Cetyltrimethylammonium bromide
- cp:
-
Chloroplast
- LSC:
-
Large single copy
- SSC:
-
Small single copy
- IR:
-
Inverted repeat
- CDS:
-
Coding sequences
- rRNA :
-
Ribosomal RNA
- tRNA :
-
Transfer RNA
- RSCU:
-
Relative synonymous codon usage
- Pi:
-
Nucleotide diversity
- Ka:
-
Nonsynonymous locus
- Ks:
-
Synonymous locus
- ML:
-
Maximum likelihood
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Funding
The study was supported by the Yunnan Academician (expert) Workstation Project (202305AF150020), Agricultural Joint key projects in Yunnan Province (202301BD070001-003), and the National Natural Science Foundation of China (Grant No. 31760450). The funders had no role in the design of the study and collection, analysis and interpretation of data and in writing the manuscript.
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No permission was necessary for this study for sample collection. S. grijsii and S. rehderianum are widely distributed in China and are not listed as national key-protected plants.
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Zhang, M., Yang, X., Zhu, L. et al. The complete chloroplast genome of two Syzygium (Myrtaceae) species and comparative analysis with other related species. Plant Biotechnol Rep 17, 753–765 (2023). https://doi.org/10.1007/s11816-023-00865-2
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DOI: https://doi.org/10.1007/s11816-023-00865-2