Abstract
Background
Melaleuca alternifolia is a commercially important medicinal tea tree native to Australia. Tea tree oil, the essential oil distilled from its branches and leaves, has broad-spectrum germicidal activity and is highly valued in the pharmaceutical and cosmetic industries. Thus, the study of genome, which can provide reference for the investigation of genes involved in terpinen-4-ol biosynthesis, is quite crucial for improving the productivity of Tea tree oil.
Methods and results
In our study, the next-generation sequencing was used to investigate the whole genome of Melaleuca alternifolia. About 114 Gb high quality sequence data were obtained and assembled into 1,838,159 scafolds with an N50 length of 1021 bp. The assembled genome size is about 595 Mb, twice of that predicted by flow cytometer (300 Mb) and k-mer analysis (345 Mb). Benchmarking Universal Single-Copy Orthologs analyses indicated that only 11.3% of the conserved single-copy genes were miss. Repetitive regions cover over 40.43% of the genome. A total of 44,369 protein-coding genes were predicted and annotated against Nr, Swissprot, Refseq, COG, KOG, and KEGG database. Among these genes, 32,909 and 16,241 genes were functionally annotated in Nr and KEGG, respectively. Moreover, 29,411 and 14,435 genes were functionally annotated in COG and KOG. Additionally, 457,661 simple sequence repeats and 1109 transcription factors (TFs) form 67 TF families were identified in the assembled genome.
Conclusion
Our findings provide a draft genome sequencing of M. alternifolia which can act as a reference for the deep sequencing strategies, and are useful for future functional and comparative genomics analyses.
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Data availability
The raw sequence data reported in this paper have been deposited in the Genome Sequence Archive (Genomics, Proteomics & Bioinformatics 2021) in National Genomics Data Center (Nucleic Acids Res 2021), China National Center for Bioinformation/Beijing Institute of Genomics, Chinese Academy of Sciences, under accession number CRA004893 that are publicly accessible at (https://ngdc.cncb.ac.cn/gsa) or at (https://ngdc.cncb.ac.cn/gsa/browse/CRA004893).
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Acknowledgements
We are grateful to Dr. Bowen Chen for the kind guidance to the project.
Funding
This study was funded by Guangxi Key Laboratory of Traditional Chinese Medicine Quality Standards Open Project (No. 202002); General Program of Guangxi Natural Science Foundation (2021GXNSFAA196069).
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Conceptualization: HY and HL; Data curation: XZ and SC; Formal analysis: YZ, YX and YQ; Funding acquisition: HL; Investigation: HY; Methodology: YZ, YX and YQ; Resources: QL, BL and LC; Supervision: HL; Visualization: QL, BL and LC; Writing-original draft: XZ and SC; Writing-review and editing: LL. All authors read and approved the final manuscript.
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Zhang, X., Chen, S., Zhang, Y. et al. Draft genome of the medicinal tea tree Melaleuca alternifolia. Mol Biol Rep 50, 1545–1552 (2023). https://doi.org/10.1007/s11033-022-08157-8
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DOI: https://doi.org/10.1007/s11033-022-08157-8