Genome Sequence Resource of Fusarium oxysporum f. sp. vanillae IXF41 and IXF50 Alongside the Endophyte F. oxysporum IXF53, Isolated from Vanilla Root Rot

HomePlant DiseaseVol. 107, No. 3Genome Sequence Resource of Fusarium oxysporum f. sp. vanillae IXF41 and IXF50 Alongside the Endophyte F. oxysporum IXF53, Isolated from Vanilla Root Rot PreviousNext RESOURCE ANNOUNCEMENT OPENOpen Access licenseGenome Sequence Resource of Fusarium oxysporum f. sp. vanillae IXF41 and IXF50 Alongside the Endophyte F. oxysporum IXF53, Isolated from Vanilla Root RotRicardo Santillán-Mendoza, Humberto J. Estrella-Maldonado, Cristian Matilde-Hernández, Mauricio Luna-Rodríguez, Cynthia G. Rodríguez-Quibrera, Carlos González-Cruz, Monserrat Torres-Olaya, and Felipe R. Flores-de la RosaRicardo Santillán-Mendoza†Corresponding authors: R. Santillán-Mendoza; E-mail Address: [email protected], and F. R. Flores-de la Rosa; E-mail Address: [email protected]https://orcid.org/0000-0003-2387-0810Campo Experimental Ixtacuaco, CIR-Golfo Centro, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Tlapacoyan, Veracruz 93650, MéxicoSearch for more papers by this author, Humberto J. Estrella-MaldonadoCampo Experimental Ixtacuaco, CIR-Golfo Centro, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Tlapacoyan, Veracruz 93650, MéxicoSearch for more papers by this author, Cristian Matilde-HernándezCampo Experimental Ixtacuaco, CIR-Golfo Centro, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Tlapacoyan, Veracruz 93650, MéxicoSearch for more papers by this author, Mauricio Luna-RodríguezLaboratorio de Genética, Facultad de Ciencias Agrícolas, Universidad Veracruzana, Xalapa, Veracruz 91090, MéxicoSearch for more papers by this author, Cynthia G. Rodríguez-QuibreraCampo Experimental Ixtacuaco, CIR-Golfo Centro, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Tlapacoyan, Veracruz 93650, MéxicoSearch for more papers by this author, Carlos González-CruzCampo Experimental Ixtacuaco, CIR-Golfo Centro, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Tlapacoyan, Veracruz 93650, MéxicoSearch for more papers by this author, Monserrat Torres-OlayaCampo Experimental Ixtacuaco, CIR-Golfo Centro, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Tlapacoyan, Veracruz 93650, MéxicoSearch for more papers by this author, and Felipe R. Flores-de la Rosa†Corresponding authors: R. Santillán-Mendoza; E-mail Address: [email protected], and F. R. Flores-de la Rosa; E-mail Address: [email protected]Campo Experimental Ixtacuaco, CIR-Golfo Centro, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Tlapacoyan, Veracruz 93650, MéxicoSearch for more papers by this authorAffiliationsAuthors and Affiliations Ricardo Santillán-Mendoza1 † Humberto J. Estrella-Maldonado1 Cristian Matilde-Hernández1 Mauricio Luna-Rodríguez2 Cynthia G. Rodríguez-Quibrera1 Carlos González-Cruz1 Monserrat Torres-Olaya1 Felipe R. Flores-de la Rosa1 † 1Campo Experimental Ixtacuaco, CIR-Golfo Centro, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Tlapacoyan, Veracruz 93650, México 2Laboratorio de Genética, Facultad de Ciencias Agrícolas, Universidad Veracruzana, Xalapa, Veracruz 91090, México Published Online:31 Dec 2022https://doi.org/10.1094/PDIS-07-22-1543-AAboutSectionsPDF ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Fusarium is a filamentous fungal genus, which is ubiquitous with more than 200 species grouped into 22 species complexes, distributed in soil, air, water, and organic substrates, and associated with animals, plants, insects, and humans (Al-Hatmi et al. 2016). It is of great importance in agriculture because it is responsible for devastating diseases, causing billions of dollars in losses annually; standouts among these diseases include head blights, malformations, sudden death, vascular wilts, and root rots (Sharma and Marques 2018). Two species of Fusarium are classified among the top 10 fungal pathogens of plants, Fusarium graminearum and F. oxysporum (Dean et al. 2012). F. oxysporum is also an important saprophyte and endophyte, but research efforts discarded strains with these ecological roles, causing a loss of very relevant genetic information (Magdama et al. 2019).The F. oxysporum species complex comprise fungi found in cultivated and noncultivated soils with worldwide distribution. Plant pathologists have studied F. oxysporum for more than a century. The narrow host specificity of pathogenic strains has led to the concept of formae speciales. Pathogenic strains with the same host range are grouped in the same forma specialis (Edel-Hermann and Lecomte 2019; O’Donnell et al. 2009). The current record indicates 143 formae speciales, of which 106 are well characterized and 37 remain to be well documented (Edel-Hermann and Lecomte 2019). One of the last ones is Fusarium oxysporum f. sp. vanillae (Fov), due to the lack of knowledge of its molecular mechanisms for infection.The ascomycete fungus Fov causes Fusarium root rot, which is the most important and serious disease affecting vanilla (Vanilla planifolia) production around the world. However, despite its importance, the genomic information of this F. oxysporum forma specialis is not yet available, which limits the knowledge about the molecular mechanisms of pathogenicity.Vanilla is the second most important spice in the food industry worldwide. However, Fov threatens global vanilla production, causing symptoms of root and stem rot (Pinaria et al. 2015). Fov strongly limits vanilla production in major vanilla-producing countries such as French Polynesia, Reunion Island, Madagascar (Benezet et al. 2000; Koyyappurath et al. 2016), and Mexico (Flores-de la Rosa et al. 2018), where it is considered the main disease. There are reports of high pathogenic diversity in this fungal organism associated with the crop (Adame-García et al. 2015), suggesting that the pathogenic mechanisms are limited to the superficial layer of the vanilla root (Koyyappurath et al. 2016).Here we announce the complete genome of two Fov strains and the genome of one nonpathogenic endophytic strain of F. oxysporum, isolated from infected vanilla roots, collected in 2021 from the Totonacapan region in Veracruz State, Mexico, the main center of origin and dispersion of the crop. We sequenced the whole genome of IXF41, IXF50, and IXF53 strains in the Illumina NextSeq platform. Pathogenicity of the strains was evaluated in three independent assays on vanilla leaves as described previously (Adame-García et al. 2015). The pathogenicity tests showed that strains IXF41 and IXF50 were highly and moderately virulent, respectively, while strain IXF53 was not pathogenic. As the IXF53 strain was isolated from internal root tissue, this strain is considered an endophyte (Brader et al. 2017). Koch’s postulates were completed by isolating the same strains from the pathogenicity tests, which were molecularly identified by TEF1 amplification and sequencing (O’Donnell et al. 1998). The three isolates were grown statically on potato dextrose broth at 25 ± 1°C for 7 days prior to DNA extraction using a CTAB protocol (Santillán-Mendoza et al. 2018). The fresh mycelium of the pathogenic strains IXF41, IXF50, and endophyte IXF53 strain was sent to the University Unit of Bioinformatics and Massive Sequencing (UUSMB) of the Institute of Biotechnology of the National Autonomous University of Mexico for sequencing.Whole-genome sequencing from three strains and library preparation was conducted through the IDT-ILMN (Illumina DNA prep [M] Tagmentation) Nextera DNA UD (unique dual index adapters) Library Prep kit, according to the manufacturer’s protocol at 100× coverage, using the Ilumina NextSeq 500 platform, into 75-bp paired-end reads. The average base quality of Illumina reads was 34.7, 34.5, and 34.4 with a 72-bp read length for IXF41, IXF50, and IXF53, respectively. Genome sequences were assembled using SPAdes v3.14.1 (Nurk et al. 2013) and RAMPART v0.12.2 (Mapleson et al. 2015). The genome was automatically annotated using the PAT v0.3 pipeline and the MAKER pipeline (Campbell et al. 2014). Functional analysis was done through different approaches: clusters of orthologous groups (COGs) of proteins (Tatusov 2000), gene ontology (GO) (Gene Ontology Consortium 2004), Enzyme Commission number (EC) (Boyce and Tipton 2001), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways annotation (Kanehisa et al. 2016). The completeness of genome was evaluated using benchmarking universal single-copy orthologs (BUSCO v5.2.2) software (Mann et al. 2021), with F. oxysporum f. sp. lycopersici Fol4287 (GCF_000271745.1) as reference genome database with default parameters (Ayhan et al. 2018; Ma et al. 2010).The final assembly for the highly pathogenic IXF41 strain is 47.3 Mb with 18,139 CDS (coding sequence), 312 scaffolds, and an N50 (scaffold length at which 50% of the total assembly length is covered) value of 0.93 Mb. The largest scaffold size is 2.22 Mb. The GC (guanine and cytosine) content is 48%. The assembly includes two rRNA-coding sequences. The final assembly for the moderately pathogenic IXF50 strain is 47.25 Mb with 18,143 CDS, 290 scaffolds, and an N50 value of 0.93 Mb. The largest scaffold size is 1.82 Mb. The GC content is 48%. The assembly includes two rRNA-coding sequences. Finally, the assembly for the nonpathogenic endophytic strain IXF53 is 47.2 Mb with 18,136 CDS, 260 scaffolds, and an N50 value of 1 Mb. The largest scaffold size is 2.59 Mb. The GC content is 48%. The assembly includes one rRNA-coding sequences. By using functional protein alignments, 4,881 proteins were assigned to the COG database, 11,158 proteins were assigned to GO terms, 5,573 EC numbers were assigned to the EC database, and 6,597 proteins were mapped to KEGG pathways. Table 1 summarizes the characteristics of the sequenced genomes and results of the corresponding BUSCO evaluation.Table 1. Genome features of Fusarium oxysporum strainsFeaturesaIXF41IXF50IXF53Genome size (bp)47,307,58347,255,00947,202,656Scaffolds312290260Scaffold N50 (Mb)b0.9300.9351.007Scaffold L50191818Maximum scaffold length (pb)2,229,5171,828,2812,591,969Minimum scaffold length (pb)1,0081,0101,011GC content (%)484848Predicted CDS number18,13918,14318,136Total gene length (bp)23,475,28223,477,02823,487,959CDS in genome (%)49.6249.6849.76Ribosomal RNA number221Hypothetical proteins18,13918,14318,136Proteins with COG assignments4,8814,8714,868Proteins with KEGG assignments6,5976,5876,585Proteins with GO assignments11,15811,14411,143Proteins with Pfam and BLASTP assignments12,80612,80112,805Proteins with EC assignments5,5735,5555,557BUSCOcComplete BUSCOs754 (99.5)754 (99.5)753 (99.4)Complete and single-copy BUSCOs752 (99.2)752 (99.2)751 (99.1)Complete and duplicated BUSCOs2 (0.3)2 (0.3)2 (0.3)Fragmented BUSCOs0 (0)0 (0)1 (0.1)Missing BUSCOs4 (0.5)4 (0.5)4 (0.5)Total BUSCO groups searched758758758aCDS = coding sequence; COG = cluster of orthologous groups; KEGG = Kyoto Encyclopedia of Genes and Genomes; GO = gene ontology; Pfam = protein families database; BLASTP = Basic Local Alignment Search Tool; EC = Enzyme Commission number; BUSCO = benchmarking universal single-copy ortholog.bN50 indicates the scaffold or contig length at which 50% of the total assembly length is covered.cParentheses indicate percentages.Table 1. Genome features of Fusarium oxysporum strainsView as image HTML This report represents the first complete genome sequence resource of F. oxysporum f. sp. vanillae (IXF41, IXF50), and the first of a nonpathogenic vanilla endophyte, F. oxysporum (IXF53), isolated from Mexico. The genomic resources provide a reference for in-depth analysis of pathogenicity, contribute to our comprehension of Fov-vanilla interactions, and help develop new strategies to prevent and control the disease.Data AvailabilityThe complete genomic data of Mexican Fov strains IXF41 and IXF50, along with the vanilla nonpathogenic endophytic F. oxysporum strain IXF53 have been deposited in the NCBI GenBank database under the Bioproject number PRJNA855480 with the BioSample accession numbers SAMN29493395 (IXF41), SAMN29493396 (IXF50), and SAMN29493397 (IXF53).AcknowledgmentsThe authors appreciate the skilled technical assistance of Charín Martínez Gendrón in microbiological methods.The author(s) declare no conflict of interest.Literature CitedAdame-García, J., Rodríguez-Guerra, R., Iglesias-Andreu, L. G., Ramos-Prado, J. M., and Luna-Rodríguez, M. 2015. Molecular identification and pathogenic variation of Fusarium species isolated from Vanilla planifolia in Papantla, Mexico. Bot. 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Nucleic Acids Res. 28:33‐36. https://doi.org/10.1093/nar/28.1.33 Crossref, ISI, Google ScholarFunding: The authors want to thank the Consejo Veracruzano de Investigación Científica y Desarrollo Tecnológico for the grant to the project 15 1755/2021 “Diseño y validación de marcadores moleculares para la detección del agente causal de la fusariosis en vainilla mediante genómica comparativa”.The author(s) declare no conflict of interest.DetailsFiguresLiterature CitedRelated Vol. 107, No. 3 March 2023SubscribeISSN:0191-2917e-ISSN:1943-7692 Download Metrics Article History Issue Date: 3 Apr 2023Published: 31 Dec 2022Accepted: 15 Aug 2022 Pages: 899-902 Information© 2022 The American Phytopathological SocietyFundingConsejo Veracruzano de Investigación Científica y Desarrollo TecnológicoGrant/Award Number: 15 1755/2021Keywordscomparative genomicsF. oxysporum f. sp. radicis-vanillaefungipathogen diversitytropical plantsVanilla planifoliaThe author(s) declare no conflict of interest.PDF download