A chromosome-level genome assembly of Korean mint (Agastache rugosa)

被引:5
作者
Park, Hyun-Seung [1 ]
Jo, Ick Hyun [2 ]
Raveendar, Sebastin [3 ]
Kim, Nam-Hoon [4 ]
Gil, Jinsu [3 ]
Shim, Donghwan [5 ]
Kim, Changsoo [6 ]
Yu, Ju-Kyung [7 ]
So, Yoon-Sup [7 ]
Chung, Jong-Wook [3 ]
机构
[1] Sejong Univ, Convergence Res Ctr Nat Prod, Dept Integrat Biol Sci & Ind, Seoul 05006, South Korea
[2] Dankook Univ, Dept Crop Sci & Biotechnol, Cheonan 31116, South Korea
[3] Chungbuk Natl Univ, Dept Ind Plant Sci & Technol, Cheongju, South Korea
[4] Phyzen Co Ltd, Seongnam, South Korea
[5] Chungnam Natl Univ, Dept Biol Sci, Daejeon, South Korea
[6] Chungnam Natl Univ, Dept Crop Sci, Daejeon, South Korea
[7] Chungbuk Natl Univ, Dept Crop Sci, Cheongju, South Korea
关键词
ROSMARINIC ACID; ALIGNMENT; IDENTIFICATION; ANNOTATION; ACCURATE; EXTRACT; LEAF;
D O I
10.1038/s41597-023-02714-x
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Agastache rugosa, also known as Korean mint, is a perennial plant from the Lamiaceae family that is traditionally used for various ailments and contains antioxidant and antibacterial phenolic compounds. Molecular breeding of A. rugosa can enhance secondary metabolite production and improve agricultural traits, but progress in this field has been delayed due to the lack of chromosome-scale genome information. Herein, we constructed a chromosome-level reference genome using Nanopore sequencing and Hi-C technology, resulting in a final genome assembly with a scaffold N50 of 52.15 Mbp and a total size of 410.67 Mbp. Nine pseudochromosomes accounted for 89.1% of the predicted genome. The BUSCO analysis indicated a high level of completeness in the assembly. Repeat annotation revealed 561,061 repeat elements, accounting for 61.65% of the genome, with Copia and Gypsy long terminal repeats being the most abundant. A total of 26,430 protein-coding genes were predicted, with an average length of 1,184 bp. The availability of this chromosome-scale genome will advance our understanding of A. rugosa's genetic makeup and its potential applications in various industries.
引用
收藏
页数:9
相关论文
共 50 条
  • [41] BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
    Simao, Felipe A.
    Waterhouse, Robert M.
    Ioannidis, Panagiotis
    Kriventseva, Evgenia V.
    Zdobnov, Evgeny M.
    [J]. BIOINFORMATICS, 2015, 31 (19) : 3210 - 3212
  • [42] RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
    Stamatakis, Alexandros
    [J]. BIOINFORMATICS, 2014, 30 (09) : 1312 - 1313
  • [43] AUGUSTUS:: ab initio prediction of alternative transcripts
    Stanke, Mario
    Keller, Oliver
    Gunduz, Irfan
    Hayes, Alec
    Waack, Stephan
    Morgenstern, Burkhard
    [J]. NUCLEIC ACIDS RESEARCH, 2006, 34 : W435 - W439
  • [44] The Effects of Root Temperature on Growth, Physiology, and Accumulation of Bioactive Compounds of Agastache rugosa
    Vu Phong Lam
    Kim, Sung Jin
    Bok, Gwon Jeong
    Lee, Jong Won
    Park, Jong Seok
    [J]. AGRICULTURE-BASEL, 2020, 10 (05):
  • [45] The complete chloroplast genomes of Lycopus lucidus and Agastache rugosa, two herbal species in tribe Mentheae of Lamiaceae family
    Wang, Yan
    Wang, Hanping
    Zhou, Baozhen
    Yue, Zhiyong
    [J]. MITOCHONDRIAL DNA PART B-RESOURCES, 2021, 6 (01): : 89 - 90
  • [46] Performance of neural network basecalling tools for Oxford Nanopore sequencing
    Wick, Ryan R.
    Judd, Louise M.
    Holt, Kathryn E.
    [J]. GENOME BIOLOGY, 2019, 20 (1)
  • [47] Effects of Carbohydrates on Rosmarinic Acid Production and In Vitro Antimicrobial Activities in Hairy Root Cultures of Agastache rugosa
    Yeo, Hyeon Ji
    Kwon, Min Jae
    Han, Sang Yeon
    Jeong, Jae Cheol
    Kim, Cha Young
    Park, Sang Un
    Park, Chang Ha
    [J]. PLANTS-BASEL, 2023, 12 (04):
  • [48] Zaharia M, 2011, Arxiv, DOI arXiv:1111.5572
  • [49] Incipient diploidization of the medicinal plant Perilla within 10,000 years
    Zhang, Yujun
    Shen, Qi
    Leng, Liang
    Zhang, Dong
    Chen, Sha
    Shi, Yuhua
    Ning, Zemin
    Chen, Shilin
    [J]. NATURE COMMUNICATIONS, 2021, 12 (01)
  • [50] Phytochemistry and bioactivity of aromatic and medicinal plants from the genus Agastache (Lamiaceae)
    Zielinska, Sylwia
    Matkowski, Adam
    [J]. PHYTOCHEMISTRY REVIEWS, 2014, 13 (02) : 391 - 416