ABSTRACT
Here, we report a draft genome sequence of endophytic fungus Phoma sp. strain YAFEF320, isolated from the roots of Gerbera jamesonii. The genome size of Phoma sp. YAFEF320 was 32,542,820 bp with 52.08% GC content. The genome resource will support future research into potential secondary metabolite diversity of this fungus.
KEYWORDS: Phoma sp., genome, Gerbera jamesonii
ANNOUNCEMENT
Endophytic species of the fungus Phoma can produce abundant bioactive metabolites, including polyketides, terpenes and terpenoids, thio-diketopiperazines, macrosporin, isocoumarin and cytochalasin derivatives, phenolic compounds, and alkaloids (1 – 3). These bioactive metabolites have anti-proliferative (4), antiviral (5), antimicrobial (6) anti-inflammatory (7, 8) anticancer (9, 10), and phytotoxic activities (11, 12). Several reviews have discussed the potential values for applying these species, including their bioherbicidal (13), antimicrobial (14), and anticancer properties (10). Three genomes of Phoma spp. were sequenced, including those of Phoma herbarum JCM15942 and Phoma sp. strains XZ068 and RAV-16-625 (15). BII-Rafflesfungin and a humulene biosynthetic gene cluster were identified by genome mining (16). In this study, we report a new genome of Phoma sp. YAFEF320 from the roots of Barberton daisy (Gerbera jamesonii).
Phoma sp. strain YAFEF320 was isolated from the roots of G. jamesonii. The isolation process was as follows. The roots were collected from the Gerbera planting base, Yunnan Academy of Agricultural Sciences, Yunnan Province, China (25°18′11″ N, 102°85′14″ E) in 2020 and soaked in tap water for 24 h to clean them. They were then rinsed with sterile water for 5 min. The roots were ground in a ball mill (GT100; Grinder, Beijing, China) at 180 rpm and 25°C, and sterile water was added to obtain a slurry. Finally, the root slurry was diluted and spread onto solid potato dextrose agar (PDA) with 100 µg/mL ampicillin, kanamycin, and streptomycin. Single colonies were transferred to fresh media after 5 days of incubation at 28°C. A single colony (strain YAFEF048) was identified by sequencing its amplified ITS region with ITS1 and ITS2 primers and comparing it with the known ITS region of Phoma to identify the new Phoma sp. The ITS sequence was deposited in GenBank (accession number: OR487462), and Phoma sp. strain YAFEF320 was deposited in the China Center for Type Culture Collection (deposit number: CCTCC M 20211093).
The mycelia of this strain were harvested from filter paper after 5 days of cultivation at 28°C in liquid PDA on a rotary shaker at 150 rpm. Its genomic DNA was extracted using a DNeasy Mini Kit (Qiagen, Valencia, CA, USA) following the manufacturer’s instructions. Illumina (San Diego, CA, USA) sequencing libraries were prepared using a TruSeq DNA Sample Prep Kit (Illumina) with insert sizes of 400 bp. The library was sequenced on an Illumina NovaSeq 6000 platform with a 2 × 150 bp paired-end configuration. A total of 48,949,704 raw reads were obtained (Table 1). High-quality cleaned sequences (7.22 Gb; coverage, 225×) were obtained by trimming the adapter sequences with AdapterRemoval version 2 (17). The de novo genome assembly was conducted using SPAdes version 3.10.1 (18). The default parameters were used for all the software unless otherwise specified. The genome assembly size of the YAFEF320 isolate was 32,542,820 bp with 76 scaffolds. The longest scaffold was 2,364,249 bp, with an N50 value of 1,076,372 bp and an N90 value of 326,747 bp. The GC content was 52.08%. The completeness of the genome assembly was assessed using BUSCO version 5.4.2 (19), and its completeness value was 97.2%.
TABLE 1.
Genome sequencing statistics
| Parameter | Value |
|---|---|
| Raw reads | |
| Read number | 48,949,704 |
| Coverage | 225× |
| Genome assembly | |
| Total base | 32.5 Mb |
| Total scaffolds | 76 |
| Max sequence length | 2,364,249 bp |
| N50 | 1,076,372 bp |
| N90 | 326,747 bp |
| Genome assembly assessment | |
| Complete BUSCOs | 97.20% |
| Complete and single-copy BUSCOs | 96.90% |
| Complete and duplicated BUSCOs | 0.30% |
ACKNOWLEDGMENTS
This project was funded by Yunnan Academy of Agricultural Sciences pre-research project (2023KYZX-07), Yunnan Province rural revitalization science and technology project (202304Bl090016), the National Natural Science Foundation of China (31860177), and the Reserve Talents for Young and Middle-aged Academic and Technical Leaders of the Yunnan Province (202205AC160044).
Contributor Information
Yi Wang, Email: wangyi@yafg.ac.cn.
Jason E. Stajich, University of California, Riverside, Riverside, California, USA
DATA AVAILABILITY
This study project is available under NCBI BioProject accession number PRJNA1011515 and BioSample accession number SAMN37222078. The complete genome assembly of Phoma sp. is available under GenBank accession number JAVLWG000000000. The Illumina NovaSeq sequencing raw data were deposited in GenBank under the accession number SRX21629953.
REFERENCES
- 1. Kong F, Wang Y, Liu P, Dong T, Zhu W. 2014. Thiodiketopiperazines from the marine-derived fungus Phoma sp. OUCMDZ-1847. J Nat Prod 77:132–137. doi: 10.1021/np400802d [DOI] [PubMed] [Google Scholar]
- 2. Chen Y, Yang W, Zou G, Chen S, Pang J, She Z. 2019. Bioactive polyketides from the mangrove endophytic fungi Phoma sp. SYSU-SK-7. Fitoterapia 139:104369. doi: 10.1016/j.fitote.2019.104369 [DOI] [PubMed] [Google Scholar]
- 3. Rai M, Gade A, Zimowska B, Ingle AP, Ingle P. 2018. Marine-derived Phoma-the gold mine of bioactive compounds. Appl Microbiol Biotechnol 102:9053–9066. doi: 10.1007/s00253-018-9329-2 [DOI] [PubMed] [Google Scholar]
- 4. Ku H, Baek J-Y, Kang KS, Shim SH. 2022. A new anti-proliferative compound from an endophytic fungus, Phoma sp. Nat Prod Res 36:5584–5590. doi: 10.1080/14786419.2021.2022663 [DOI] [PubMed] [Google Scholar]
- 5. Liu S-S, Jiang J-X, Huang R, Wang Y-T, Jiang B-G, Zheng K-X, Wu S-H. 2019. A new antiviral 14-nordrimane sesquiterpenoid from an endophytic fungus Phoma sp.. Phytochemistry Letters 29:75–78. doi: 10.1016/j.phytol.2018.11.005 [DOI] [Google Scholar]
- 6. Zhang H, Xiong Y, Zhao H, Yi Y, Zhang C, Yu C, Xu C. 2013. An antimicrobial compound from the endophytic fungus Phoma sp. isolated from the medicinal plant Taraxacum mongolicum. J Taiwan Inst Chem Eng 44:177–181. doi: 10.1016/j.jtice.2012.11.013 [DOI] [Google Scholar]
- 7. Lee M-S, Wang S-W, Wang G-J, Pang K-L, Lee C-K, Kuo Y-H, Cha H-J, Lin R-K, Lee T-H. 2016. Angiogenesis inhibitors and anti-inflammatory agents from Phoma sp. NTOU4195. J Nat Prod 79:2983–2990. doi: 10.1021/acs.jnatprod.6b00407 [DOI] [PubMed] [Google Scholar]
- 8. Kim JW, Ko W, Kim E, Kim GS, Hwang GJ, Son S, Jeong M-H, Hur J-S, Oh H, Ko S-K, Jang J-H, Ahn JS. 2018. Anti-inflammatory phomalichenones from an endolichenic fungus Phoma sp.. J Antibiot 71:753–756. doi: 10.1038/s41429-018-0058-7 [DOI] [PubMed] [Google Scholar]
- 9. Yu C, Nian Y, Chen H, Liang S, Sun M, Pei Y, Wang H. 2022. Pyranone derivatives with antitumor activities, from the endophytic fungus Phoma sp. YN02-P-3. Front Chem 10:950726. doi: 10.3389/fchem.2022.950726 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10. Rai M, Zimowska B, Gade A, Ingle P. 2023. Phoma spp. an untapped treasure of cytotoxic compounds: current status and perspectives. Appl Microbiol Biotechnol 107:4991–5001. doi: 10.1007/s00253-023-12635-9 [DOI] [PubMed] [Google Scholar]
- 11. Rivero-Cruz JF, Macías M, Cerda-García-Rojas CM, Mata R. 2003. A new phytotoxic nonenolide from Phoma herbarum. J Nat Prod 66:511–514. doi: 10.1021/np020501t [DOI] [PubMed] [Google Scholar]
- 12. Kalam S, Khan NA, Singh J. 2014. A novel phytotoxic phenolic compound from Phoma herbarum FGCC#54 with Herbicidal potential. Chem Nat Compd 50:644–647. doi: 10.1007/s10600-014-1043-4 [DOI] [Google Scholar]
- 13. Rai M, Zimowska B, Shinde S, Tres MV. 2021. Bioherbicidal potential of different species of Phoma: opportunities and challenges. Appl Microbiol Biotechnol 105:3009–3018. doi: 10.1007/s00253-021-11234-w [DOI] [PubMed] [Google Scholar]
- 14. Rai M, Zimowska B, Gade A, Ingle P. 2022. Promising antimicrobials from Phoma spp.: progress and prospects. AMB Express 12:60. doi: 10.1186/s13568-022-01404-y [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15. Zhai Y, Li Y, Zhang J, Zhang Y, Ren F, Zhang X, Liu G, Liu X, Che Y. 2019. Identification of the gene cluster for bistropolone-humulene meroterpenoid biosynthesis in Phoma sp.. Fungal Genet Biol 129:7–15. doi: 10.1016/j.fgb.2019.04.004 [DOI] [PubMed] [Google Scholar]
- 16. Sinha S, Nge C-E, Leong CY, Ng V, Crasta S, Alfatah M, Goh F, Low K-N, Zhang H, Arumugam P, Lezhava A, Chen SL, Kanagasundaram Y, Ng SB, Eisenhaber F, Eisenhaber B. 2019. Genomics-driven discovery of a biosynthetic gene cluster required for the synthesis of BII-Rafflesfungin from the fungus Phoma sp. F3723. BMC Genomics 20:374. doi: 10.1186/s12864-019-5762-6 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 17. Schubert M, Lindgreen S, Orlando L. 2016. Adapterremoval V2: rapid adapter trimming, identification, and read merging. BMC Res Notes 9:88. doi: 10.1186/s13104-016-1900-2 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 18. Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. 2020. Using spades de novo assembler. Curr Protoc Bioinformatics 70:e102. doi: 10.1038/s41598-020-75855-3 [DOI] [PubMed] [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. doi: 10.1093/bioinformatics/btv351 [DOI] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
This study project is available under NCBI BioProject accession number PRJNA1011515 and BioSample accession number SAMN37222078. The complete genome assembly of Phoma sp. is available under GenBank accession number JAVLWG000000000. The Illumina NovaSeq sequencing raw data were deposited in GenBank under the accession number SRX21629953.