High-Quality Draft Nuclear and Mitochondrial Genome Sequence of Fusarium oxysporum f. sp. albedinis strain 9, the Causal Agent of Bayoud Disease on Date Palm

HomePlant DiseaseVol. 106, No. 7High-Quality Draft Nuclear and Mitochondrial Genome Sequence of Fusarium oxysporum f. sp. albedinis strain 9, the Causal Agent of Bayoud Disease on Date Palm PreviousNext RESOURCE ANNOUNCEMENT OPENOpen Access licenseHigh-Quality Draft Nuclear and Mitochondrial Genome Sequence of Fusarium oxysporum f. sp. albedinis strain 9, the Causal Agent of Bayoud Disease on Date PalmSiham Khoulassa, Benaissa Elmoualij, Mohamed Benlyas, Reda Meziani, Eimad Dine Tariq Bouhlali, Benamar Houria, Youssef El Hilali Alaoui, Sajeet Haridas, Jie Guo, Anna Lipzen, Catalina Vega Hurtado, Sravanthi Tejomurthula, Kerrie Barry, Igor V. Grigoriev, Jeffrey J. Coleman, Dilay Hazal Ayhan, Li-Jun Ma, and Adil EssariouiSiham KhoulassaNational Institute of Agricultural Research (INRA), Errachidia, MoroccoMoulay Ismail University (FSTE/UMI), Errachidia, MoroccoSearch for more papers by this author, Benaissa ElmoualijMoulay Ismail University (FSTE/UMI), Errachidia, MoroccoSearch for more papers by this author, Mohamed BenlyasMoulay Ismail University (FSTE/UMI), Errachidia, MoroccoSearch for more papers by this author, Reda MezianiNational Institute of Agricultural Research (INRA), Errachidia, MoroccoSearch for more papers by this author, Eimad Dine Tariq BouhlaliNational Institute of Agricultural Research (INRA), Errachidia, MoroccoSearch for more papers by this author, Benamar HouriaNational Institute of Agricultural Research (INRA), Errachidia, MoroccoSearch for more papers by this author, Youssef El Hilali AlaouiUniversity Sultan Moulay Slimane, Beni Mellal, MoroccoSearch for more papers by this author, Sajeet HaridasUnited States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A.Search for more papers by this author, Jie GuoUnited States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A.Search for more papers by this author, Anna LipzenUnited States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A.Search for more papers by this author, Catalina Vega HurtadoUnited States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A.Search for more papers by this author, Sravanthi TejomurthulaUnited States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A.Search for more papers by this author, Kerrie BarryUnited States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A.Search for more papers by this author, Igor V. GrigorievUnited States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A.Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, U.S.A.Search for more papers by this author, Jeffrey J. Colemanhttps://orcid.org/0000-0001-8579-1996Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, U.S.A.Search for more papers by this author, Dilay Hazal AyhanUniversity of Massachusetts, Amherst, MA, U.S.A.Search for more papers by this author, Li-Jun MaUniversity of Massachusetts, Amherst, MA, U.S.A.Search for more papers by this author, and Adil Essarioui†Corresponding author: A. Essarioui; E-mail Address: adil.essarioui@inra.mahttps://orcid.org/0000-0002-3643-3196National Institute of Agricultural Research (INRA), Errachidia, MoroccoSearch for more papers by this author AffiliationsAuthors and Affiliations Siham Khoulassa1 2 Benaissa Elmoualij2 Mohamed Benlyas2 Reda Meziani1 Eimad Dine Tariq Bouhlali1 Benamar Houria1 Youssef El Hilali Alaoui3 Sajeet Haridas4 Jie Guo4 Anna Lipzen4 Catalina Vega Hurtado4 Sravanthi Tejomurthula4 Kerrie Barry4 Igor V. Grigoriev4 5 Jeffrey J. Coleman6 Dilay Hazal Ayhan7 Li-Jun Ma7 Adil Essarioui1 † 1National Institute of Agricultural Research (INRA), Errachidia, Morocco 2Moulay Ismail University (FSTE/UMI), Errachidia, Morocco 3University Sultan Moulay Slimane, Beni Mellal, Morocco 4United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A. 5Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, U.S.A. 6Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, U.S.A. 7University of Massachusetts, Amherst, MA, U.S.A. Published Online:10 May 2022https://doi.org/10.1094/PDIS-01-22-0245-AAboutSectionsPDF ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Genome AnnouncementFusarium oxysporum f. sp. albedinis is the causal agent of date palm vascular wilt, also known as Bayoud disease. The infection by this soilborne fungus occurs through the root system and the pathogen subsequently establishes in the vascular tissue where growth and sporulation take place, leading to the blocking of conducting vessels and, ultimately, to palm death. The disease has constituted a veritable threat to date industry, killing more than 10 million palm trees since it was first reported in Morocco in the late 19th century (Sedra 2003). The pathogen has expanded its geographical range and was found in the neighboring countries of Algeria and Northern Mauritania (Sedra 2003). Like any other vascular plant wilt, the use of resistant varieties remains the most effective and sustainable control method against Bayoud. One major hurdle to breeding for resistant cultivars is a lack of understanding of the molecular basis that underlies the interactions between date palm and F. oxysporum f. sp. albedinis. Because of the geographic confinement of the disease, only a few molecular-based studies on pathogen characterization and pathogenicity have been conducted at the international level (Fernandez and Tantaoui 1994; Fernandez et al. 1997, 1998; Freeman and Maymon 2000; Tantaoui and Boisson 1991; Tantaoui and Fernandez 1993; Tantaoui et al. 1996). Thus, the genetic underpinnings of pathogenicity are completely unknown. However, advances in new-generation DNA sequencing technologies offer great opportunities for exploring fungal phytopathogens through generating high-quality whole-genome sequences (Ayhan et al. 2018; Ma et al. 2010; Shu et al. 2021). In a recent study, the whole genome of F. oxysporum f. sp. albedinis strain 33 was sequenced (Khayi et al. 2020) but, due to the quality of sequencing data and technology in this investigation, assembly remained restricted to contig level. In this article, we report a high-quality draft genome sequence of F. oxysporum f. sp. albedinis strain 9 v1.0 isolated from an infected date palm tree in the Tafilalet Valley, Morocco.Genomic DNA of strain 9 was extracted from fresh hyphae grown in liquid potato dextrose broth using cetyltrimethylammonium bromide (Kim et al. 2010). The genome was sequenced using the PacBio Sequel II system, as described by Hagestad et al. (2021). Filtered subread data were processed to remove artifacts and assembled with Flye assembler (Kolmogorov et al. 2019). The assembly yielded 114 contigs with a total assembly size of 65,559,131 bp (47.73% GC, maximum contig size = 5.6 Mbp, and N50 contig length = 2,949,549 bp), 19,411 gene models, and 54,130 expressed sequence tags. The mitochondrial genome consists of a contig of 51,600 bp.In addition, RNA was extracted from mycelium grown in two distinct media, potato dextrose broth and minimum medium, to allow differential gene expression analysis using Illumina sequencing. RNA sample prep and sequencing was carried out as previously reported (Hagestad et al. 2021). Filtered fastq files were used as input for de novo assembly of RNA contigs. Reads filtered and trimmed for quality and contamination were assembled into consensus sequences using Trinity v2.8.5 (Grabherr et al. 2011). In all, 88.7% of the transcriptome sequences were mapped to the genome. The genome annotation was conducted using the Joint Genome Institute (JGI) Annotation Pipeline (Grigoriev et al. 2014) and resulted in 19,411 gene models with an average length of 1,742 bp.The mitochondrial genome was assembled separately with the circular consensus sequencing (CCS) reads. An in-house tool (assemblemito.py) was first used to filter the CCS reads. The mitochondria-filtered CCS reads were then assembled with Flye version 2.3.6-release (https://github.com/fenderglass/Flye) to generate an assembly and polished with the gcpp tool using the Arrow algorithm included in the SMRT LINK software v8.0.0.80529. The assembly resulted in a single scaffold of 51,600 bp in length.Data AvailabilityThe data described in this work can be accessed on the JGI Genome Portal (https://genome.jgi.doe.gov/portal/pages/accessDenied.jsf?state=%27anonDownload%27) and the JGI MycoCosm (Grigoriev et al. 2014) (https://mycocosm.jgi.doe.gov/Fusoxalb1/Fusoxalb1.info.html), or can be obtained through NCBI with the accession number PRJNA677031. Data were generated for JGI CSP Proposal ID 1408 (Coleman et al. 2013). This Whole Genome Shotgun project has been deposited at DNA Data Bank of Japan/European Nucleotide Archive/GenBank under the accession JAKELM000000000. The version described in this article is version JAKELM010000000.AcknowledgmentsWe thank the Moroccan-American Commission for Educational & Cultural Exchange (MACECE) for supporting A. Essarioui under the Fulbright grant program.The author(s) declare no conflict of interest.Literature CitedAyhan, D. H., López-Díaz, C., Di Pietro, A., and Ma, L. J. 2018. Improved assembly of reference genome Fusarium oxysporum f. sp. lycopersici strain Fol4287. Microbiol. Resour. Announce. 7:e00910-18. https://doi.org/10.1128/MRA.00910-18 Crossref, ISI, Google ScholarColeman, J., Freitag, M., Geiser, D., Epstein, L., Kistler, H. C., Ma, L.-J., O’Donnell, K., Rep, M., VanEtten, H., Essarioui, A., and Marman, J. 2013. Exploring the supernumerary chromosomes of the Fusarium solani and Fusarium oxysporum species complexes: Reservoirs for functional genetic diversity. U.S. Department of Energy Office of Scientific and Technical Information. https://doi.org/10.46936/10.25585/60001402 Google ScholarFernandez, D., Ouinten, M., Tantaoui, A., and Geiger, J.-P. 1997. Molecular records of micro-evolution within the Algerian population of Fusarium oxysporum f. sp. albedinis during its spread to new oases. Eur. J. Plant Pathol. 103:485-490. https://doi.org/10.1023/A:1008644515046 Crossref, ISI, Google ScholarFernandez, D., Ouinten, M., Tantaoui, A., Geiger, J.-P., Daboussi, M.-J., and Langin, T. 1998. Fot1 insertions in the Fusarium oxysporum f. sp. albedinis genome provide diagnostic PCR targets for detection of the date palm pathogen. Appl. Environ. Microbiol. 64:633-636. https://doi.org/10.1128/AEM.64.2.633-636.1998 Crossref, ISI, Google ScholarFernandez, D., and Tantaoui, A. 1994. Random amplified polymorphic DNA (RAPD) analysis for rapid characterization of Fusarium oxysporum f. sp. albedinis isolates. Phytopathol. Mediterr. 33:223-229. Google ScholarFreeman, S., and Maymon, M. 2000. Reliable detection of the fungal pathogen fusarium oxysporum f. sp. albedinis, causal agent of Bayoud disease of date palm, using molecular techniques. Phytoparasitica 28:341-348. https://doi.org/10.1007/BF02981829 Crossref, ISI, Google ScholarGrabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., Chen, Z., Mauceli, E., Hacohen, N., Gnirke, A., Rhind, N., di Palma, F., Birren, B. W., Nusbaum, C., Lindblad-Toh, K., Friedman, N., and Regev, A. 2011. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat. Biotechnol. 29:644-652. https://doi.org/10.1038/nbt.1883 Crossref, ISI, Google ScholarGrigoriev, I. V., Nikitin, R., Haridas, S., Kuo, A., Ohm, R., Otillar, R., Riley, R., Salamov, A., Zhao, X., Korzeniewski, F., Smirnova, T., Nordberg, H., Dubchak, I., and Shabalov, I. 2014. MycoCosm portal: Gearing up for 1000 fungal genomes. Nucleic Acids Res. 42:D699-D704. https://doi.org/10.1093/nar/gkt1183 Crossref, ISI, Google ScholarHagestad, O. C., Hou, L., Andersen, J. H., Hansen, E. H., Altermark, B., Li, C., Kuhnert, E., Cox, R. J., Crous, P. W., Spatafora, J. W., Lail, K., Amirebrahimi, M., Lipzen, A., Pangilinan, J., Andreopoulos, W., Hayes, R. D., Ng, V., Grigoriev, I. V., Jackson, S. A., Sutton, T. D. S., Dobson, A. D. W., and Rämä, T. 2021. Genomic characterization of three marine fungi, including Emericellopsis atlantica sp. nov. with signatures of a generalist lifestyle and marine biomass degradation. IMA Fungus 12:21. https://doi.org/10.1186/s43008-021-00072-0 Crossref, ISI, Google ScholarKhayi, S., Khoulassa, S., Gaboun, F., Abdelwahd, R., Diria, G., Labhilili, M., Iraqi, D., El Guilli, M., Fokar, M., and Mentag, R. 2020. Draft genome sequence of Fusarium oxysporum f. sp. albedinis strain Foa 133, the causal agent of Bayoud disease on date palm. Microbiol. Resour. Announce. 9:e00462-20. https://doi.org/10.1128/MRA.00462-20 Crossref, ISI, Google ScholarKim, J. S., Seo, S. G., Jun, B. K., Kim, J. W., and Kim, S. H. 2010. Simple and reliable DNA extraction method for the dark pigmented fungus, Cercospora sojina. Plant Pathol. J. 26:289-292. https://doi.org/10.5423/PPJ.2010.26.3.289 Crossref, ISI, Google ScholarKolmogorov, M., Yuan, J., Lin, Y., and Pevzner, P. A. 2019. Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37:540-546. https://doi.org/10.1038/s41587-019-0072-8 Crossref, ISI, Google ScholarMa, L.-J., van der Does, H. C., Borkovich, K. A., Coleman, J. J., Daboussi, M.-J., Di Pietro, A., Dufresne, M., Freitag, M., Grabherr, M., Henrissat, B., Houterman, P. M., Kang, S., Shim, W.-B., Woloshuk, C., Xie, X., Xu, J.-R., Antoniw, J., Baker, S. E., Bluhm, B. H., Breakspear, A., Brown, D. W., Butchko, A. E., Chapman, S., Coulson, R., Coutinho, P. M., Danchin, E. G. J., Diener, A., Gale, L. R., Gardiner, D. M., Goff, S., Hammond-Kosack, K. E., Hilburn, K., Hua-Van, A., Jonkers, W., Kazan, K., Kodira, C. D., Koehrsen, M., Kumar, L., Lee, Y.-H., Li, L., Manners, J. M., Miranda-Saavedra, D., Mukherjee, M., Park, G., Park, J., Park, S.-Y., Proctor, R. H., Regev, A., Ruiz-Roldan, M. C., Sain, D., Sakthikumar, S., Sykes, S., Schwartz, D. C., Turgeon, B. G., Wapinski, I., Yoder, O., Young, S., Zeng, Q., Zhou, S., Galagan, J., Cuomo, C. A., Kistler, H. C., and Rep, M. 2010. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 464:367-373. https://doi.org/10.1038/nature08850 Crossref, ISI, Google ScholarSedra, M. H. 2003. Le Bayoud du palmier dattier en Afrique du Nord. Food and Agriculture Organization of the United Nations (FAO), SNEA, Tunis, Tunisia. https://agris.fao.org/agris-search/search.do?recordID=XF2015042672 Google ScholarShu, Y., Luo, M., and Dong, Z. 2021. Whole genome sequence resource for Fusarium oxysporum f. sp. capsici 14003, the causative agent of pepper wilt. Plant Dis. 105:1183-1186. https://doi.org/10.1094/PDIS-10-20-2294-A Link, ISI, Google ScholarTantaoui, A., and Boisson, C. 1991. Compatibilité végétative d’isolats du Fusarium oxysporum f. sp. albedinis et de Fusarium oxysporum de la rhizosphère du palmier dattier et des sols de palmeraies. Phytopathol. Mediterr. 30:155-163. Google ScholarTantaoui, A., and Fernandez, D. 1993. Comparaison entre Fusarium oxysporum f. sp. albedinis et Fusarium oxysporum des sols de palmeraies par l0 étude du polymorphisme de longueur des fragments de restriction (RFLP). Phytopathol. Mediterr. 32:235-244. Google ScholarTantaoui, A., Ouinten, M., Geiger, J. P., and Fernandez, D. 1996. Characterization of a single clonal lineage of Fusarium oxysporum f. sp. albedinis causing Bayoud disease of date palm in Morocco. Phytopathology 86:787-792. https://doi.org/10.1094/Phyto-86-787 Crossref, ISI, Google ScholarFunding: This work was conducted by the U.S. Department of Energy (DOE) Joint Genome Institute, a DOE Office of Science User Facility, under contract number DE-AC02-05CH11231. D. H. Ayhan and L.-J. Ma are supported by the National Institute of Health (R01EY030150), National Institute of Food and Agriculture (MASR-2009-04374) and the National Science Foundation (IOS-1652641).The author(s) declare no conflict of interest.DetailsFiguresLiterature CitedRelated Vol. 106, No. 7 July 2022SubscribeISSN:0191-2917e-ISSN:1943-7692 Download Metrics Downloaded 658 times Article History Issue Date: 8 Jul 2022Published: 10 May 2022Accepted: 2 Mar 2022 Pages: 1974-1976 Information© 2022 The American Phytopathological SocietyFundingU.S. Department of EnergyGrant/Award Number: DE-AC02-05CH11231National Institute of HealthGrant/Award Number: R01EY030150National Institute of Food and AgricultureGrant/Award Number: MASR-2009-04374National Science FoundationGrant/Award Number: IOS-1652641KeywordsannotationBayoud diseaseFusarium oxysporum f. sp. albedinisgenome assemblymitochondrial genomeThe author(s) declare no conflict of interest.PDF download