Data in Brief 57 (2024) 110951 Contents lists available at ScienceDirect Data in Brief journal homepage: www.elsevier.com/locate/dib Data Article Draft genome sequence data of Fusarium verticillioides strain REC01, a phytopathogen isolated from a Peruvian maize Richard Estradaa , ∗ , Liliana Aragónb, Wendy E. Pérezc , Yolanda Romeroa, Gabriel Martíneza, Karina Garciaa, Juancarlos c Cruz , Carlos I. Arbizud , ∗ a Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru b Facultad de Agronomía, Universidad Nacional Agraria La Molina (UNALM), Av. La Molina s/n, Lima 15024, Peru c Dirección de Supervisión y Monitoreo en las Estaciones Experimentales Agrarias, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru d Facultad de Ingeniería y Ciencias Agrarias, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas (UNTRM), Cl. Higos Urco 342, Amazonas 01001, Peru a r t i c l e i a b s t r a c t n f o Article history: Fusarium verticillioides represents a major phytopathogenic Received 20 April 2024 threat to maize crops worldwide. In this study, we present Revised 11 September 2024 genomic sequence data of a phytopathogen isolated from a Accepted 12 September 2024 maize stem that shows obvious signs of vascular rot. Using Available online 23 September 2024 rigorous microbiological identification techniques, we corre- lated the disease symptoms observed in an affected maize Dataset link: WGS of Fusarium verticillioides isolated from peruvian root region with the presence of the pathogen. Subsequently, corn (Original data) the pathogen was cultured in a suitable fungal growth medium and extensive morphological characterization was Keywords: performed. In addition, a pathogenicity test was carried out Genome sequencing in a DCA model with three treatments and seven repetitions. Vascular rot De novo assembly from Illumina Novaseq 60 0 0 sequencing SSR data mining yielded 456 contigs, which together constitute a 42.8 Mb genome assembly with a GC % content of 48.26. Subsequent ∗ Corresponding authors. E-mail addresses: richard.estrada.bioinfo@gmail.com (R. Estrada), carlos.arbizu@untrm.edu.pe (C.I. Arbizu). Social media: @arbizu_carlos (C.I. Arbizu) https://doi.org/10.1016/j.dib.2024.110951 2352-3409/© 2024 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY-NC license ( http://creativecommons.org/licenses/by-nc/4.0/ ) 2 R. Estrada, L. Aragón and W.E. Pérez et al. / Data in Brief 57 (2024) 110951 comparative analyses were performed with other Fusarium genomes available in the NCBI database. © 2024 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY-NC license ( http://creativecommons.org/licenses/by-nc/4.0/ ) S 1 2 p m a i e pecifications Table Subject Biology Specific subject area Genomics, Microbiology, Bioinformatics . Data format Raw sequence reads (fastq) Analyzed Filtered Type of data Genomic sequence, Table, Figure Data collection The strain was collected from a rotten stem of Peruvian maize and subsequently isolated on Potato Dextrose Agar (PDA). Then a microscopic inspection was carried out to observe morphological characteristics of the pathogen. The pathogenicity analysis was performed in a complete randomised design (CRD) model with three treatments; T1 (substrate without inoculum), T2 (1 g.kg-1 of substrate) and T3 (5 g.kg-1 of substrate) with 7 repetitions. Genomic DNA was extracted using the E.Z.N.A kit. Sequencing was performed using the Illumina Novaseq 60 0 0 platform and de novo assembly MaSuRCA version 4.0.6. To evaluate the quality and integrity of the genome assembly, BUSCO version 5.4.2 was used. Additionally, identification of Simple Sequence Repeats (SSR) regions was performed using MISA software. Data source location Institution: EEA Vista Florida, Instituto Nacional de Innovación Agraria City/Town/Region: Chiclayo (6.72 °S, 79.77 °W) Country: Perú Data accessibility Repository name: NCBI (National Center for Biotechnology Information) Data identification number: SRR21935339 Direct URL to data: https://www.ncbi.nlm.nih.gov/sra/?term=SRR21935339 The Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JAWRVJ0 0 0 0 0 0 0 0 0.1 . Value of the Data • The genomic sequence data provide valuable information for conducting comparative ge- nomic studies aimed at exploring the core genome of the Fusarium genus. • The genomic sequence data allows a detailed examination of genes related to pathogenicity in the affected plant, paving the way for the development of genetic engineering strategies aimed at reducing the pathogen’s virulence toward the host plant. • The genome data is essential for advancing our understanding of the phylogeny of the Fusar- ium genus , contributing to the analysis of evolutionary relationships within this group of phy- topathogenic fungi. . Background The incidence of Fusarium verticillioides as a phytopathogen poses a substantial threat to the roduction and quality of maize, with significant economic repercussions [ 1 ]. The presence of ycotoxins in this crop adversely impacts human and animal health, leading to economic losses nd affecting international trade relations [ 2 ]. F. verticillioides has multiple routes of infection, ncluding systemic infection in seedlings, entry through the stigma, and infection of stems and ars due to mechanical damage [ 3 ]. R. Estrada, L. Aragón and W.E. Pérez et al. / Data in Brief 57 (2024) 110951 3 In this study, F. verticillioides was isolated from maize samples (INIA 627 - Pátapo variety) collected in Lambayeque, Peru, which exhibited symptoms of pink vascular rot. The tissues were disinfected and cultured on PDA medium, where a change in mycelial morphology from white to violet was observed, along with the presence of macroconidia and microconidia. The phytopathogenic activity was confirmed by a reduction in seed germination and the number of seedlings as the inoculum concentration increased, demonstrating the pathogen’s negative impact. Sequencing of F. verticillioides was conducted using the Illumina Novaseq 60 0 0 platform, with de novo assembly performed using MaSuRCA v. 4.0.6. The quality and integrity of the as- sembled genome were assessed using BUSCO v 5.4.2, and Simple Sequence Repeat (SSR) re- gions were identified with MISA software. This genomic analysis is crucial for characterising local strains and understanding their genetic variability, which can influence the pathogen’s vir- ulence and resistance. Such comparisons are essential for identifying regional differences and developing targeted management strategies to protect local agriculture. 3. Data Description 3.1. Sample collection Maize samples of crop season 2022 were taken from a plot at Experimental Station Vista Florida in Lambayeque, Peru (6 °43′ 33"S 79 °46′ 44"W). Then, the samples were placed in paper envelopes and maintained at room temperature. Sample characterization and analysis was car- ried out within the next 10 days. 3.2. Microbiological identification The pieces of plant tissues (stems and roots) exhibiting symptoms of vascular lesion were processed to detect infection by Fusarium sp. A characterization of affected tissues of Peruvian maize (INIA 627 - Pátapo variety) was conducted, involving segments of stems and roots dis- playing a pinkish vascular rot ( Fig. 1 A-B). The stem tissue samples were disinfected with 1.0 % sodium hypochlorite, washed with sterilised distilled water, and aseptically transferred to Petri dishes containing Potato Dextrose Agar (PDA) medium. The plates were incubated for 7 days at 28 °C, then purified on new Petri dishes with PDA medium [ 4 ]. Initially, the strain exhibited white mycelial morphology ( Fig. 1C ) that transitioned to a violet hue ( Fig. 1D ) with age. Mi- croscopic examination facilitated the observation of detailed morphological features, including macroconidia ( Fig. 1E ), microconidia ( Fig. 1F ) and conidiogenous cells ( Fig. 1G ). 3.3. Strain phytopathogenic assay The phytopathogenic activity was verified through the germination of seeds inoculated with this strain. Table 1 shows the result of the germination percentage for each treatment 15 daysTable 1 Germination percentage of maize seeds in substrate inoculated with F. verticillioides isolated from maize, 15 days after sowing under semi-controlled mesh house conditions. Treatment Inoculum concentration Phytopathogenic activity T1 0g.Kg-1 100 % T2 1g.Kg-1 57.10 ∗ % T3 5g.Kg-1 33.30 ∗ % ∗ significance p < 0.05 4 R. Estrada, L. Aragón and W.E. Pérez et al. / Data in Brief 57 (2024) 110951 Fig. 1. A-B Maize stems and roots with vascular rot caused by F. verticillioides , the injured tissue was pink (red arrows). C. Colonies 6 days after inoculation on sterile petri dish. D. Colonies 10 days after inoculation. E. Macroconidia with 5 septa (red arrows). F. Microconidia in chains. G. Conidiogenous cell in monophyalid (red circle). a p t g m 3 ( 4 S r fter sowing the maize seeds. Fig. 2 compares the reaction of the treatments during the ex- eriment. Because it was necessary to define the behaviour of the pathogenicity with respect o the inoculum concentration, two doses were carried out. In both inoculation treatments, the ermination reaction was reduced by the pathogen; and therefore, there was a lower number of aize seedlings, as the inoculum concentration increased. .4. Genomic survey Low heterozygosity and repetition (0.7 %) were obtained and the estimated genome size 41.73 Mb) was close to the reported F. verticillioides genome references (7600: 41.9 Mb, HN2: 2.8 Mb, BRIP53590: 42.2 Mb, BRIP53263: 42.3 Mb, BRIP14953: 42.3 Mb, Fv10027_t1: 44.6 Mb, 1123A: 43.1 Mb and NRRL 20984: 41.9 Mb). ( Fig. 3 ). Before quality control, a total of 23,102,402 eads were generated, which were reduced to 22,481,566 reads after trimming and filtering. The R. Estrada, L. Aragón and W.E. Pérez et al. / Data in Brief 57 (2024) 110951 5 Fig. 2. Maize seedlings 15 days after germination in a substrate inoculated with F. verticillioides isolated from maize, under semi-controlled screen house conditions. T1 = 0 g.Kg-1 , T2 = 1 g.Kg-1 and T3 = 5 g.Kg-1 . Fig. 3. Distribution of k-mers in the draft REC01 genome. low heterozygosity and repetition rate suggest a relatively homogeneous genome with limited genetic variation. Furthermore, the genome size aligns closely with the reported sizes of other F. verticillioides genomes. 3.5. Assembly de novo , reference-assisted scaffolding, and validation The scaffold assembled using MaSuRCA has a total length of 42.8 Mb, consisting of 42,796,516 contigs ( ≥10 0 0 bp) with a GC content of 48.26 %. The longest contig was 1,769,758 bp ( Table 2 ). Additionally, BUSCO was obtained: 4384 complete (S), 4377 simple copies, 7 complete and du- plicates (D), 27 fragmented and 3 missing ( Table 2 ). However, when compared to other F. verticillioides assemblies at different levels—such as scaffold level (S1123A, NRRL20984), whole genome level (7600), chromosome level (HN2, 6 R. Estrada, L. Aragón and W.E. Pérez et al. / Data in Brief 57 (2024) 110951 Table 2 Statistics of the completeness of the de novo assembly and summary of the BUSCO approach in the F. verticillioides . Statistic Value N50 462380 N75 263483 L50 30 L75 75 Largest contig 1769758 Total length 42866930 GC (%) 48.26 # contigs ( ≥ 10 0 0 bp) 42796516 # contigs ( ≥ 50 0 0 bp) 42674077 # contigs ( ≥ 10,0 0 0 bp) 42549820 # contigs ( ≥ 25,0 0 0 bp) 42224523 # contigs ( ≥ 50,0 0 0 bp) 41728895 # N’s per 100 kbp 2.51 Complete BUSCOs 4384 Complete and single-copy BUSCOs 4377 Complete and duplicated BUSCOs 7 Fragmented BUSCOs 27 Missing BUSCOs 83 B t t 9 a 3 a 1 c B g RIP53590, BRIP53263, and BRIP14953), and contig level (Fv10027_t1)—the assembly we ob- ained for REC01 had an N50 of 462 kb ( Table 3 ). Additionally, the assemblage has 97.55 % complete BUSCOs (C) (S: 97.4 % + D: 0.16 %), similar o the BRIP53590 type with 97.60 % C (S: 97.49 % + D:0.11 %) and the NRRL 20984 type with 7.64 % C (S: 97.33 % + D:0.31 %) ( Fig. 4 ). The genome has been deposited in GenBank with the ccession number JAWRVJ0 0 0 0 0 0 0 0 0.1. Fig. 4. Comparison of the BUSCO analysis of F. verticillioides REC01 with other types. .6. SSR data mining The most abundant microsatellite motif type of REC01 was mononucleotide repeats, which ccounted for 47.25 % of total Simple Sequence Repeats (SSRs), followed by dinucleotide repeats 8.98 %, trinucleotide 18.09 %, tetranucleotide 8.03 %, of pentanucleotides 4.34 % and hexanu- leotides 3.31 %. Similar to the distribution of microsatellite motifs of other types 7600, HN2, RIP53590, BRIP53263, BRIP14953, Fv10027_t1, S1123A and NRRL 20984 ( Fig. 5 ). A total of 3113 microsatellite loci were identified based on the assembled REC01 draft enome sequence, with a frequency of 72.62 SSR/Mb, which is almost the same as BRIP53263 R. Estrada, L. Aragón and W.E. Pérez et al. / Data in Brief 57 (2024) 110951 7 Table 3 Comparison of the assembly of F. verticillioides REC01 with other types. Type F. verticillioides 7600 HN2 BRIP53590 BRIP53263 BRIP14953 Fv10027_t1 S1123A NRRL 20984 REC01 Level Assembly Genome Chromosome Chromosome Chromosome Chromosome Contig Scaffold Scaffold Scaffold complete Total sequence length 41994356 42814391 42294396 42398840 4235067 44652197 43183040 41924634 42866930 Gaps per 100 kbp 0 0 177.56 183.5 189.26 0.02 6.09 1.88 2.51 Number of scaffolds 11 12 258 153 255 21 94 857 404 Scaffold N50 4 mb 4 mb 4 mb 4 mb 4 mb 2 mb 1 mb 104 kb 462 kb Scaffold L50 5 5 5 5 5 5 10 118 30 Number of contigs 11 12 1009 931 1060 21 147 866 456 Contig N50 4 mb 4 mb 105 kb 101 kb 97 kb 2 mb 856 kb 104 kb 347 kb 8 R. Estrada, L. Aragón and W.E. Pérez et al. / Data in Brief 57 (2024) 110951 Fig. 5. Distribution of SSRs in types. Percentage of RSS by reason in REC01 compared to other types. ( S S n ( 4 4 t t m I s 4 I r N 72.17 SSR/Mb), lower than HN2 (3355 SSR/Mb), BRIP5359 (3146 SSR/Mb), BRIP14953 (3244 SR/Mb), Fv100257_t1 (3339 SSR/Mb) and S1123A (3344 SSR/Mb) but higher than 7600 (2925 SR/Mb), BRIP53263 (3060 SSR/Mb) and NRRL 20984 (2700 SSR/Mb) ( Table 4 ). Furthermore, the umber of SSRs present in the composite matrix of REC01 (202) is similar to the type of HN2 203), greater than 7600 (162), Fv10027_t1 (194) and NRRL 20984 (165). Table 4 Summary of RSS distribution in REC01 and other types. F. verticillioides genomes Type 7600 HN2 BRIP BRIP BRIP Fv10027_t1 S1123A NRRL REC01 53590 53263 14953 20984 Total number of 2925 3355 3146 3060 3244 3339 3344 2700 3113 identified SSRs Frequency (SSR/kb) 69.65 78.36 74.38 72.17 76.6 74.78 77.44 64.4 72.62 Number of SSRs 162 203 274 283 278 194 233 165 202 present in compound formation . Experimental Design, Materials, and Methods .1. Microbiological identification The microbiological analysis focused on the identification and characterization of the phy- opathogen F. verticillioides from collected tissues of Peruvian maize stems that showed symp- oms of rot. These fragments were subjected to an isolation and culture process in a PDA edium incubated at 28 °C, allowing controlled growth and development between 6 and 10 days. n addition, a thorough microscopic examination was carried out to observe the reproductive tructures, specifically macroconidia and microconidia. .2. Molecular identification To confirm the presence of F. verticillioides , PCR was performed to amplify ITS1-5.8S- TS2 region using the forward ITS-Fu-f (5′ -CAACTCCCAAACCCCTGTGA-3′ ) and reverse ITS-Fu- (5′ ) primers. -GCGACGATTACCAGTAACGA-3′ ) [ 5 ]. The sequence was first compared with the CBI database using the blastn program [ 6 ], ensuring the identity of Fusarium verticillioides. R. Estrada, L. Aragón and W.E. Pérez et al. / Data in Brief 57 (2024) 110951 9 Subsequently, taxonomic classification was performed using massBLASTer ( https://github.com/ TU-NHM/massblaster_plutof_pub ) available on the UNITE website ( https://unite.ut.ee/analysis. php ) v. 10.0, which offers a curated set of fungal ITS sequences [ 7 ]. The ITS1 region was ex- tracted using tools from UNITE to ensure accurate classification, following methods similar to those described in previous studies [ 8 , 9 ]. This approach, independent of sequence alignment, is effective in reducing redundancy and ensuring consistency in taxonomic information [ 9 ]. 4.3. Pathogenicity evaluation 4.3.1. Inoculation The increase in inoculum of F. verticillioides REC01 was through the development of mycelium on wheat grains (previously cooked and autoclaved in polypropylene bags). The inoculated wheat was incubated at 25 °C for 3 weeks; this was the methodology used at the Clínica de Di- agnosis de Fitopatologia – Universidad Nacional Agraria La Molina [ 10 ].. The inoculation method was by incorporating the inoculated wheat grains into the substrate according to the doses es- tablished in treatments 2 and 3. 4.3.2. Statistical design CRD was established with an absolute control (T1, substrate without inoculum), and 2 treat- ments with different levels of inoculum concentration: T2, 1 g/kg of substrate; and T3, 5 g/kg of substrate. 7 repetitions were established, each repetition with 2 pots; and each pot contain- ing 3 seeds of hard yellow maize (Dekalb-7500). Analysis of variance and Tukey’s comparison of means test were performed at an alpha of 0.05; using the statistical program Statistix version 9.0. 4.3.3. Parameters evaluated After 15 days from sowing, the number of corn seedlings was quantified for each experiment as a percentage value. Additionally, the incidence of the characteristic sign of the pathogen in root medullary rot was measured 60 days after sowing. The development of necrosis in the internal part of the root was assessed as a percentage for each repetition. 4.4. Sample collection and DNA extraction The strain isolated on the PDA medium was selected for the extraction of its genomic DNA; we used the E.Z.N.A. bacterial DNA isolation kit (Omega Bio-tek, USA) following the manufac- turer’s protocol. The genomic DNA was subjected to Illumina technology, specifically 150-bp paired-end (PE) sequencing, utilising the Illumina Nextera DNA Flex library preparation kit. The resulting PE Illumina library was loaded onto the NovaSeq 60 0 0 instrument for cluster genera- tion and subsequent sequencing, conducted by Novogene Co. Ltd. (CA, USA). 4.5. Genome sequencing and genomic survey DNA sequencing of pair ends was performed using the Illumina HiSeq 2500 platform. Raw reads were verified using FastQC v.0.11.9 software [ 11 ]. In addition, read quality trimming (phred Q > 25) and adapter removal were performed using the Trimmomatic v0.36 [ 12 ] and TrimGalore v.0.6.7 [ 13 ] programs, respectively. For the purpose of genomic investigation, we employed the Jellyfish v.2.0 software [ 14 ]. Furthermore, the Genome Scope v1.0.0 tool [ 15 ] (Cold Spring Harbor Laboratory, Laurel Hollow, US) was utilised to derive estimations regarding key genome features, including genome size, repetitive content, and heterozygosity rate. These estimations were based on the output generated by Jellyfish, in conjunction with the utilisation of 17-mer for K-mer 10 R. Estrada, L. Aragón and W.E. Pérez et al. / Data in Brief 57 (2024) 110951 a d 4 b t b v 4 P g v B ( G p t N L E h C s a d K C D nalysis. To identify a uniform pattern characterised by a single peak in the K-mer frequency istribution analysis, the depth of K was estimated. .6. De novo assembly and validation De novo assembly process was carried out using MaSuRCA v.4.0.6 [ 16 ]. Subsequently, assem- ly statistics were assessed using QUAST v.5.2.0 [ 17 ]. Furthermore, QUAST was employed with he scaffold output for further analysis. To evaluate the completeness of the genome assem- ly and identify any gene gaps, we employed the BUSCO v.5.4.2 [ 18 ] strategy utilising the F. erticillioides -specific profile. .7. Repeat annotation To identify repetitive elements, we employed de novo and peer-based methods. The MISA erl script [ 19 ] ( http://pgrc.ipk-gatersleben.de/misa/ ) was used to identify SSRs within the REC01 enome. In addition, for SSR analysis, we incorporated genomes from various strains of F. erticillioides , namely 7600 (GenBank: GCA_027571605.1), HN2 (GenBank: GCA_026119585.1), RIP53590 (GenBank: GCA_003316995.2), BRIP53263 (GenBank: GCA_003317015.2), BRIP14953 GenBank: GCA_0 03316975.2), Fv10 027_t1 (GenBank: GCA_020882315.1), S1123A (GenBank: CA_025503005.1), and NRRL 20984 (GenBank: GCA_013759275.1). The BUSCO tool was em- loyed to assess the assembly quality. To conduct a comparative analysis of BUSCO, we re- rieved eight types (7600, HN2, BRIP53590, BRIP53263, BRIP14953, Fv10027_t1, S1123A, and RRL 20984) from the NCBI database at the assembly level. imitations Not applicable. thics Statement Work did not include animal experiments or data collected from social media platforms or uman subjects. RediT Author Statement Conceptualization, R.E., W.P., Y.R., L.A. and G.M.; methodology, R.E., G.M., E.V., L.A. and C.A.; oftware, R.E., and Y.R.; validation, C.A.; formal analysis, R.E. and Y.R.; research, R.E., W.P., Z.A. nd C.A.; resources, Y.R. and C.A.; data curation, R.E., and Y.R.; writing: preparation of original raft, R.E., Y.R., W.P. and G.M.; writing: review and editing, W.P., L.A. and K.G.; visualisation, G.M., .G. and E.V.; supervision, Z.A. and E.V.; project management, R.A. and J.C.; acquisition funding, .A. and J.C. All authors have read and accepted the published version of the manuscript. ata Availability WGS of Fusarium verticillioides isolated from peruvian root corn (Original data) (NCBI). R. Estrada, L. Aragón and W.E. Pérez et al. / Data in Brief 57 (2024) 110951 11 Acknowledgments We thank Ivan Ucharima for image editing and Linda Arteaga for her collaboration in the laboratory. C.I.A. thanks Vicerrectorado de Investigación of UNTRM. Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal rela- tionships that could have appeared to influence the work reported in this paper. References [1] A .A . Blacutt, S.E. Gold, K.A. Voss, M. Gao, A.E. Glenn, Fusarium verticillioides: advancements in understanding the toxicity, virulence, and niche adaptations of a model mycotoxigenic pathogen of maize, Phytopathology 108 (2018) 312–326, doi: 10.1094/PHYTO- 06- 17- 0203- RVW . [2] N. Devanna, P.N. Achar, M.Y. 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