Skip to main content
SpringerLink
Log in

Draft genome of the medicinal tea tree Melaleuca alternifolia

  • Original Article
  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

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).

References

  1. Wu ZY, Raven PH (2013) Flora of China. Science Press: Beijing, China & Missouri Botanical Garden Press, St. Louis, MO, USA, p 321

    Google Scholar 

  2. Zhang X, Liang G, Yan Y, Yu Y, Yang G, Yang T (2000) Rapid propagation and polyploid induction in Melaleuca alternifolia. J Southwest Agric Univ 22(6):507–509

    CAS  Google Scholar 

  3. Chidi F, Bouhoudan A, Khaddor M (2020) Antifungal effect of the tea tree essential oil (Melaleuca alternifolia) against Penicillium griseofulvum and Penicillium verrucosum. J King Saud Univ Sci 32(3):2041–2045

    Article  Google Scholar 

  4. Yadav E, Kumar S, Mahant S, Khatkar S, Rao R (2016) Tea tree oil: a promising essential oil. J Essent Oil Res 29(3):201–213

    Article  Google Scholar 

  5. Redondo-Blanco S, Fernandez J, Lopez-Ibanez S, Miguelez EM, Villar CJ, Lombo F (2020) Plant phytochemicals in food preservation: antifungal bioactivity: a review. J Food Prot 83(1):163–171

    Article  CAS  Google Scholar 

  6. Lee JY, Lee J, Ko SW, Son BC, Lee JH, Kim CS et al (2020) Fabrication of antibacterial nanofibrous membrane infused with essential oil extracted from tea tree for packaging applications. Polymers (Basel) 12(1):125

    Article  CAS  Google Scholar 

  7. Bustos-Segura C, Padovan A, Kainer D, Foley WJ, Külheim C (2017) Transcriptome analysis of terpene chemotypes of Melaleuca alternifolia across different tissues. Plant Cell Environ 40(10):2406–2425

    Article  CAS  Google Scholar 

  8. Felipe LO, Junior W, Araujo KC, Fabrino DL (2018) Lactoferrin, chitosan and Melaleuca alternifolia-natural products that show promise in candidiasis treatment. Braz J Microbiol 49(2):212–219

    Article  Google Scholar 

  9. Sharifi-Rad J, Salehi B, Varoni EM, Sharopov F, Yousaf Z, Ayatollahi SA et al (2017) Plants of the Melaleuca genus as antimicrobial agents: from farm to pharmacy. Phytother Res 31(10):1475–1494

    Article  CAS  Google Scholar 

  10. Hong Y, Huang X, Li C, Ruan X, Wang Z, Su Y et al (2020) Genome survey sequencing of in vivo mother plant and in vitro plantlets of Mikania cordata. Plants 9(12):1665

    Article  CAS  Google Scholar 

  11. Calvert J, Baten A, Butler J, Barkla B, Shepherd M (2017) Terpene synthase genes in Melaleuca alternifolia: comparative analysis of lineage-specific subfamily variation within Myrtaceae. Plant Syst Evol 304(1):111–121

    Article  Google Scholar 

  12. Wang W, Das A, Kainer D, Schalamun M, Morales-Suarez A, Schwessinger B et al (2020) The draft nuclear genome assembly of Eucalyptus pauciflora: a pipeline for comparing de novo assemblies. Gigascience 9(1):1–12

    Article  Google Scholar 

  13. Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, Hayes RD, Grimwood J et al (2014) The genome of Eucalyptus grandis. Nature 510(7505):356–362

    Article  CAS  Google Scholar 

  14. Izuno A, Hatakeyama M, Nishiyama T, Tamaki I, Shimizu-Inatsugi R, Sasaki R et al (2016) Genome sequencing of Metrosideros polymorpha (Myrtaceae), a dominant species in various habitats in the Hawaiian Islands with remarkable phenotypic variations. J Plant Res 129(4):727–736

    Article  Google Scholar 

  15. Thrimawithana AH, Jones D, Hilario E, Grierson E, Ngo HM, Liachko I et al (2019) A whole genome assembly of Leptospermum scoparium (Myrtaceae) for mānuka research. N Z J Crop Hortic Sci 47(4):233–260

    Article  CAS  Google Scholar 

  16. Chen Y, Chen Y, Shi C, Huang Z, Zhang Y, Li S et al (2018) SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and prepro-cessing of high-throughput sequencing data. Gigascience 7:1–6

    Article  Google Scholar 

  17. Marçais G, Kingsford C (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27(6):764–770

    Article  Google Scholar 

  18. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J et al (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1(1):18

    Article  Google Scholar 

  19. Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210–3212

    Article  Google Scholar 

  20. Buchfink B, Xie C, Huson DH (2015) Fast and sensitive protein alignment using DIAMOND. Nat Meth 12(1):59–60

    Article  CAS  Google Scholar 

  21. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35(Web Server issue):182–5

    Article  Google Scholar 

  22. Flynna JM, Hubleyb R, Gouberta C, Rosenb J, Clarka AG, Feschottea C et al (2020) RepeatModeler2 for automated genomic discovery of transposable element families. Proc Natl Acad Sci U S A 1:9451–9457

    Article  Google Scholar 

  23. Tempel S (2012) Using and understanding RepeatMasker. Methods Mol Biol 859:29–51

    Article  CAS  Google Scholar 

  24. Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B (2006) AUGUSTUS: Ab initio prediction of alternative transcripts. Nucleic Acids Res 34:W435–W439

    Article  CAS  Google Scholar 

  25. Beier S, Thiel T, Münch T, Scholz U, Mascher M (2017) MISA-web: a web server for microsatellite prediction. Bioinformatics (Oxford) 33(16):2583–2585

    Article  CAS  Google Scholar 

  26. Zheng Y, Jiao C, Sun H, Rosli HG, Pombo MA, Zhang PM et al (2016) iTAK: a program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators, and protein kinases. Mol Plant 9(12):1667–1670

    Article  CAS  Google Scholar 

  27. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326(5956):1112–1115

    Article  CAS  Google Scholar 

  28. Camillo J, Leao AP, Alves AA, Formighieri EF, Azevedo AL, Nunes JD et al (2014) Reassessment of the genome size in Elaeis guineensis and Elaeis oleifera, and its interspecific hybrid. Genom Insights 7:13–22

    Google Scholar 

  29. Wu Y, Xiao F, Xu H, Zhang T, Jiang X (2014) Genome survey in Cinnamomum camphora L. Presl J Plant Genet Resour 15(1):149–152

    Google Scholar 

  30. Baskorowati L, Moncur MW, Doran JC, Kanowski PJ (2010) Reproductive biology of Melaleuca alternifolia (Myrtaceae) 1. Floral biology. Aust J Bot 58:373–383

    Article  Google Scholar 

  31. Baskorowati L, Moncur MW, Cunningham SA, Doran JC, KanowskiA PJ (2010) Reproductive biology of Melaleuca alternifolia (Myrtaceae) 2. Incompatibility and pollen transfer in relation to the breeding system. Aust J Bot 58:384–391

    Article  Google Scholar 

  32. ButcherBell PJC, Moran GF (1992) Patterns of genetic diversity and nature of the breeding system in Melaleuca alternifolia (Myrtaceae). Aust J Bot 40:365–375

    Article  Google Scholar 

  33. Wei C, Yang H, Wang S, Zhao J, Liu C, Gao L et al (2018) Draft genome sequence of Camellia sinensis var. sinensis provides insights into the evolution of the tea genome and tea quality. Proc Natl Acad Sci U S A. 115(18):4151–8

    Article  Google Scholar 

  34. Wei Y, Jing W, Hua D, Youxiang Z, Mingming Z, Dingjin H (2013) Characteristic analysis and application of microsatellites from EST sequence of Camellia sinensis (in Chinese). Hubei Agric Sci 52(24):6178–6181

    Google Scholar 

Download references

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).

Author information

Author notes

  1. Xiaoning Zhang and Silin Chen have contributed equally to this work.

Authors and Affiliations

  1. Guangxi Forestry Research Institute, YongWu Road 23, Xixiangtang District, Nanning, 530002, Guangxi, China

    Xiaoning Zhang, Ye Zhang, Yufei Xiao, Yufeng Qin & Hailong Liu

  2. State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China

    Silin Chen, Qing Li, Li Liu & Hong Yang

  3. Guangxi Key Laboratory of Traditional Chinese Medicine Quality Standards, Nanning, China

    Buming Liu & Ling Chai

Authors
  1. Xiaoning Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Silin Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ye Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yufei Xiao
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yufeng Qin
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Qing Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Li Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Buming Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Ling Chai
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Hong Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Hailong Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

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.

Corresponding authors

Correspondence to Hong Yang or Hailong Liu.

Ethics declarations

Conflict of interest

The authors declare there are no competing interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (RAR 33822 kb)

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-022-08157-8

Keywords

Search

Navigation