Draft genome of the medicinal tea tree Melaleuca alternifolia.

Szczegóły
Abstrakt

Tytuł:: Draft genome of the medicinal tea tree Melaleuca alternifolia.
Autorzy:: Zhang X; Guangxi Forestry Research Institute, YongWu Road 23, Xixiangtang District, Nanning, 530002, Guangxi, China.
Chen S; State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China.
Zhang Y; Guangxi Forestry Research Institute, YongWu Road 23, Xixiangtang District, Nanning, 530002, Guangxi, China.
Xiao Y; Guangxi Forestry Research Institute, YongWu Road 23, Xixiangtang District, Nanning, 530002, Guangxi, China.
Qin Y; Guangxi Forestry Research Institute, YongWu Road 23, Xixiangtang District, Nanning, 530002, Guangxi, China.
Li Q; State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China.
Liu L; State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China.
Liu B; Guangxi Key Laboratory of Traditional Chinese Medicine Quality Standards, Nanning, China.
Chai L; Guangxi Key Laboratory of Traditional Chinese Medicine Quality Standards, Nanning, China.
Yang H; State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China. .
Liu H; Guangxi Forestry Research Institute, YongWu Road 23, Xixiangtang District, Nanning, 530002, Guangxi, China. hailon_.
Źródło:: Molecular biology reports [Mol Biol Rep] 2023 Feb; Vol. 50 (2), pp. 1545-1552. Date of Electronic Publication: 2022 Dec 13.
Typ publikacji:: Journal Article
Język:: English
Imprint Name(s):: Original Publication: Dordrecht, Boston, Reidel.
MeSH Terms:: Tea Tree Oil*
Melaleuca*/genetics
Oils, Volatile*
Humans ; Trees ; Teas, Medicinal
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Grant Information:: GuiCaiSheHan [2018]112 Department of Human Resources and Social Security of 325 Guangxi Zhuang Autonomous Region, China; 202002 Guangxi Key Laboratory of Traditional Chinese Medicine Quality Standards Open Project; Gui Ke AD18281083 Guangxi Science and Technology Project; Gui Ke AB18221058 Guangxi Science and Technology Project
Contributed Indexing:: Keywords: De novo assembly; Genome annotation; Genome sequencing; Melaleuca alternifolia; Tea tree oil; Whole-genome shotgun sequencing
Substance Nomenclature:: 68647-73-4 (Tea Tree Oil)
0 (Oils, Volatile)
Entry Date(s):: Date Created: 20221213 Date Completed: 20230202 Latest Revision: 20230202
Update Code:: 20240105
DOI:: 10.1007/s11033-022-08157-8
PMID:: 36513867
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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.
(© 2022. The Author(s), under exclusive licence to Springer Nature B.V.)

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