Objectives: The fungal pathogen Thecaphora frezii Carranza & Lindquist causes peanut smut, a severe disease currently endemic in Argentina. To study the ecology of T. frezii and to understand the mechanisms of smut resistance in peanut plants, it is crucial to know the genetics of this pathogen. The objective of this work was to isolate the pathogen and generate the first draft genome of T. frezii that will be the basis for analyzing its potential genetic diversity and its interaction with peanut cultivars. Our research group is working to identify peanut germplasm with smut resistance and to understand the genetics of the pathogen. Knowing the genome of T. frezii will help analyze potential variants of this pathogen and contribute to develop enhanced peanut germplasm with broader and long-lasting resistance. Data description: Thecaphora frezii isolate IPAVE 0401 (here referred as T.f.B7) was obtained from a single hyphal-tip culture, its DNA was sequenced using Pacific Biosciences Sequel II (PacBio) and Illumina NovaSeq6000 (Nova). Data from both sequencing platforms were combined and the de novo assembling estimated a 29.3 Mb genome size. Completeness of the genome examined using Benchmarking Universal Single-Copy Orthologs (BUSCO) showed the assembly had 84.6% of the 758 genes in fungi_odb10

Arias, Renee S.

Bernardi-Lima, Nelson

Carloni, Edgardo J.

Conforto, Cinthia

Lamb, Marshall C.

Massa, Alicia N.

Orner, Valerie A.

Rago, Alejandro M.

Soave, Juan H.

English

DigitalCommons@University of Nebraska

University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Publications from USDA-ARS / UNL Faculty U.S. Department of Agriculture: Agricultural Research Service, Lincoln, Nebraska 12-1-2023 First draft genome of Thecaphora frezii, causal agent of peanut smut disease Renee S. Arias USDA ARS National Peanut Research Laboratory, renee.arias@usda.gov Cinthia Conforto Instituto Nacional de Tecnologia Agropecuaria Buenos Aires Valerie A. Orner USDA ARS National Peanut Research Laboratory Edgardo J. Carloni Instituto Nacional de Tecnologia Agropecuaria Buenos Aires Juan H. Soave Criadero El Carmen See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/usdaarsfacpub  Part of the Agriculture Commons Arias, Renee S.; Conforto, Cinthia; Orner, Valerie A.; Carloni, Edgardo J.; Soave, Juan H.; Massa, Alicia N.; Lamb, Marshall C.; Bernardi-Lima, Nelson; and Rago, Alejandro M., "First draft genome of Thecaphora frezii, causal agent of peanut smut disease" (2023). Publications from USDA-ARS / UNL Faculty. 2562. https://digitalcommons.unl.edu/usdaarsfacpub/2562 This Article is brought to you for free and open access by the U.S. Department of Agriculture: Agricultural Research Service, Lincoln, Nebraska at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Publications from USDA-ARS / UNL Faculty by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Renee S. Arias, Cinthia Conforto, Valerie A. Orner, Edgardo J. Carloni, Juan H. Soave, Alicia N. Massa, Marshall C. Lamb, Nelson Bernardi-Lima, and Alejandro M. Rago This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/usdaarsfacpub/2562 Arias et al. BMC Genomic Data            (2023) 24:9  https://doi.org/10.1186/s12863-023-01113-wDATA NOTEThis is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2023. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http:// creat iveco mmons. org/ licen ses/ by/4. 0/. The Creative Commons Public Domain Dedication waiver (http:// creat iveco mmons. org/ publi cdoma in/ zero/1. 0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.Open AccessBMC Genomic DataFirst draft genome of Thecaphora frezii, causal agent of peanut smut diseaseRenee S. Arias1*  , Cinthia Conforto2,3, Valerie A. Orner1, Edgardo J. Carloni4, Juan H. Soave5, Alicia N. Massa1, Marshall C. Lamb1, Nelson Bernardi‑Lima2,3 and Alejandro M. Rago3,6 Abstract Objectives The fungal pathogen Thecaphora frezii Carranza & Lindquist causes peanut smut, a severe disease cur‑rently endemic in Argentina. To study the ecology of T. frezii and to understand the mechanisms of smut resistance in peanut plants, it is crucial to know the genetics of this pathogen. The objective of this work was to isolate the patho‑gen and generate the first draft genome of T. frezii that will be the basis for analyzing its potential genetic diversity and its interaction with peanut cultivars. Our research group is working to identify peanut germplasm with smut resistance and to understand the genetics of the pathogen. Knowing the genome of T. frezii will help analyze poten‑tial variants of this pathogen and contribute to develop enhanced peanut germplasm with broader and long‑lasting resistance.Data description Thecaphora frezii isolate IPAVE 0401 (here referred as T.f.B7) was obtained from a single hyphal‑tip culture, its DNA was sequenced using Pacific Biosciences Sequel II (PacBio) and Illumina NovaSeq6000 (Nova). Data from both sequencing platforms were combined and the de novo assembling estimated a 29.3 Mb genome size. Completeness of the genome examined using Benchmarking Universal Single‑Copy Orthologs (BUSCO) showed the assembly had 84.6% of the 758 genes in fungi_odb10.Keywords PacBio, Genome, Pathogen, Groundnut, Smut disease, FungiObjectivePeanut smut disease converts the peanut seed into a brown/black powder of fungal teliospores, example shown in Data File 1, Table 1 [1]. The disease is currently endemic to Argentina [2], where the pathogen Theca-phora frezii [1] has been reported to cause up to 51% disease incidence [3] and crop losses up to 35% [2, 4]. Global trade could potentially spread the disease to other areas. For example, United States is a major exporter of peanuts [5], but it also imports peanuts from other countries [6] including Argentina [7]. Scientists from the U.S. and Argentina are working in collaboration to bet-ter understand the disease and to identify resistant pea-nut germplasm [8–11]. Part of that effort is to know the genetics of the pathogen. Previously, we have sequenced the 123  kb mitochondrial genome of T. frezii based on DNA obtained from teliospores [12]. Other than that, the *Correspondence:Renee S. Ariasrenee.arias@usda.gov1 USDA‑ARS National Peanut Research Laboratory (NPRL), Dawson, GA, USA2 Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, IPAVE‑CIAP‑INTA, X5020 Córdoba, Argentina3 Unidad de Fitopatología y Modelización Agrícola, Consejo Nacional de Investigaciones Científicas y Técnicas, UFYMA‑CONICET, X5020 Córdoba, Argentina4 Instituto de Fisiología y Recursos Genéticos Vegetales, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, IFRG‑CIAP‑INTA, X5020 Córdoba, Argentina5 El Carmen S.A., General Cabrera, Córdoba, Argentina6 Centro de Investigaciones Agropecuarias ‑ INTA, Córdoba, ArgentinaPage 2 of 4Arias et al. BMC Genomic Data            (2023) 24:9 National Center for Biotechnology Information (NCBI) has only 170 entries for this species, those sequences are under 2,500  bp, and more than half correspond to microsatellites and ribosomal RNA. We have found that working with teliospores had its own constraints, thus, the current work aimed to sequence the genome of a hyphal tip culture of this fungus. The isolate referred as T.f.B7 was obtained from peanuts in Argentina and is now stored in the IPAVE culture collection as IPAVE 0401, both, the hyphal tip culture and the original telio-spores are kept in the collection. Overall, BLAST analysis performed on assembled T. frezii contigs showed high-est similarity (~ 78%) to Anthracocystis flocculosa (Syn. Pseudozyma flocculosa), followed by (~ 76%) similarity to Sporisorium spp. and lower similarity (~ 73%) to Ustilago spp. Given the limited information available about this pathogen, the data are very useful.Data descriptionThecaphora frezii isolate IPAVE 0401 (here referred as T.f.B7), was obtained as a hyphal culture from teli-ospores of a smut-affected peanut plant collected in 2018 from Hernando city, in Tercero Arriba, Cordoba (32° 24′ 30.5028″ S, 63° 42′ 18.9468″ W). Genomic DNA was extracted from T.f.B7, a culture expected to be haploid monokaryotic as shown by HCL-Giemsa and Propidium iodide nuclear staining, Data File 1, Table 1 [1], and was sequenced as paired end 150 base pairs (bp) using Illu-mina NovaSeq6000 which resulted in 114,541,382 reads, Data set 1, Table  1 [15]. After trimming for potential presence of adapters and removal of sequences shorter than 140  bp, 112,980,831 clean reads were available. A summary of read length and quality is listed in Data File 2, Table 1 [13]. A second DNA extraction of isolate T.f.B7 was processed following HiFi low DNA input library preparation with Single Molecule Real Time (SMRT) bell Express Template Prep Kit 2.0 and sequenced using PacBio Sequel II (Pacific Biosciences, San Diego, CA) at the Genome Center, University of California Davis, CA. This generated 1,201,967 subreads, Data set 2, Table  1 [16], with average length 4,086 bases, N50 = 6,011, N90 = 2,669, and HiFi read count = 17,988. Nova reads were mapped to the 123  kb mitochondrial DNA of T. frezii [12], the mapping had a 119,373 X coverage and the assembled consensus contig had two single nucleo-tide polymorphisms (SNPs) compared to the published mitogenome of T. frezii, contig_7166_TF_mitochondrion Data set 3, Table 1 [17]. Nova reads that did not map to the mitochondrial DNA comprised 2.3 Gb that were de novo assembled using CLC Workbench. For the assem-bly, corrected PacBio Subreads were used as “guidance only”, application where guidance only reads are not used to create the de Bruijn graph but to resolve ambi-guities in the graph. This resulted in 7,165 contigs with average coverage 80 X, and an estimated genome size of 29,333,160  bp when adding the mitochondrial DNA (contig number 7,166), Data set 3 [17] and Data file 3, Table  1 [14]. The assembly was performed with word size 23, bubble size 50, and resulted in N75 = 3,838, N50 = 9,027, N25 = 16,027, max length = 60,190 bp, min length = 377  bp, average = 4,094  bp. As a comparison, a genome size of the related species, Thecaphora thlas-peos, is 20,591,600 bp [18]. The 9,012 bp Contig_22 [17] contains the ribosomal RNA (rRNA) cistron; alignment of the 615  bp partial rRNA sequence of T. frezii (Sa-EM1) accession JX041638.1 [19] to Contig_22 showed 100% identity. Further assessment of genome complete-ness was done using BUSCO [20] v.5.2.2, with the fungi_odb10 database, which consists of 549 genomes (www. ortho db. org). The results showed 641 of the 758 BUSCO genes (84.6%) were complete, with 632 complete sin-gle copy (83.4%), 9 complete duplicates (1.2%), 48 genes were fragmented (6.3%), and 69 BUSCO genes were missing (9.1%). Mapping and assembly were performed Table 1 Overview of data files/data setsLabel Name of data file/data set File types(File extension)Data repository and identifier (DOI or accession number)Data file 1 Peanut smut in shellThecaphora_frezii_cultureTag Image File Format (.tiff ) https:// doi. org/ 10. 7910/ DVN/ EOYLUX [1] at Harvard DataverseData file 2 QC_140bp Excel (.xlsx) https:// doi. org/ 10. 7910/ DVN/ I338KA [13] at Harvard DataverseData file 3 Contig_Length_&_Cumulative Length_TF Portable Document Format (.PDF) https:// doi. org/ 10. 7910/ DVN/ SOFHRR [14] at Harvard DataverseData set 1 B7_S113_L004_R1_001B7_S113_L004_R2_001Illumina NovaSeq 6000 data; Fastq file (fastq.gz)SRR18840655 [15] at NCBI GenBank DatabaseData set 2 M64069_211005_200549 PacBio, Binary alignment map (.BAM) SRR18837637 [16] at NCBI GenBank DatabaseData set 3 T. frezii Genome Assembly: 7166_Con‑tigs_TF_B7_GenomeFasta (.fasta) JALNIF000000000 [17] at NCBI GeneBank DatabasePage 3 of 4Arias et al. BMC Genomic Data            (2023) 24:9  in CLC_Genomics Workbench 20.0.4 (Qiagen, Aarhus, Denmark), using CLC Genome Finishing Module for pro-cessing PacBio data. The data were deposited in NCBI, Bioproject PRJNA828173, Biosample SAMN27642199, Data sets 1, 2 and 3, Table 1 [15–17].LimitationsThecaphora frezii isolation and DNA extraction proved very challenging since teliospores after  germination form a very thin layer of budding-yeast phase, without aerial mycelium. A first whole genome sequencing of T. frezii as paired end 150 bases using NovaSeq 6000 and de novo assembly resulted in a relatively fragmented genome. Additional sequencing of a small amount of DNA of suboptimal quality was performed by PacBio resulting in 95% of reads shorter than 10  Kb, thus, the reads were corrected to keep only long sequences that were supported by multiple reads. A de novo assembly of data obtained from both platforms combined was still fragmented. Since the genetic information of T. frezii is very limited, the draft genome we obtained by combin-ing both sequencing platforms and reported here, will allow mining for genes of interest, and perform studies on genetic diversity of this pathogen.AbbreviationsNova  Illumina NovaSeq 6000PacBio  Pacific Biosciences Sequel IINCBI  National Center for Biotechnology InformationIPAVE  Instituto de Patologia VegetalSMRT  Single Molecule Real TimeSNP  Single Nucleotide PolymorphismAcknowledgementsNot applicable.Authors’ contributionsRSA, AMR, JHS, MCL: Conceptualization. JHS, MCL, BES, AMR: Funding acquisi‑tion and resources. RSA, VAO: Formal analysis, data curation and uploading. CEC, NBL: Fungal isolation, DNA extractions, photographs. RSA: Writing original draft. EJC: nuclear staining, microscopy. RSA, CEC, AMR, ANM, JHS, MCL: Review and editing. All authors reviewed and approved the manuscript.Authors’ informationNot applicable.FundingThis work was funded by the United States Department of Agriculture, Agricultural Research Service, Project Number: 6604–21000‑005‑00D; and by Instituto Nacional de Tecnologia Agropecuaria (INTA), Cordoba, Argentina. The funding bodies played no role in the design of the study, collection, analysis, and interpretation of data and in writing the manuscript.Availability of data and materialsThe data described in this Data note can be freely and openly accessed on NCBI Bioproject PRJNA828173, Biosample SAMN27642199 (Data sets 1–3), Harvard Dataverse under https:// doi. org/ 10. 7910/ DVN/ EOYLUX; https:// doi. org/ 10. 7910/ DVN/ I338KA (Data files 1–3); and NCBI Accession numbers: SRR18840655, SRR18837637, JALNIF000000000. Please see Table 1 and refer‑ences [1, 13, 14, 15, 16, 17] for details and links to the data.DeclarationsEthics approval and consent to participateNot applicable.Consent for publicationNot applicable.Competing interestsThe authors declare having no competing interest.Received: 17 May 2022   Accepted: 9 February 2023References 1. Data file 1: Photograph of peanut smut disease and Thecaphora frezii culture, by Conforto EC. Harvard Dataverse. (2022). https:// doi. org/ 10. 7910/ DVN/ EOYLUX. 2. Rago AM, Cazón LI, Paredes JA, Molina JPE, Conforto EC, Bisonard EM, Oddino C. Peanut smut: from an emerging disease to an actual threat to Argentine peanut production. Plant Dis. 2017;101(3):400–8. 3. Oddino C, Marinelli A, March G, Garcia JDJ, Tarditi L, D’Eramo L, Ferrari S. Relation between potential inoculum of Thecaphora frezii, smut disease intensity and crop yield. Cordoba: XXV National Peanut Congress; 2010. 1–2 (#6). 4. Paredes JA, Cazón LI, Osella A, Peralta V, Alcalde M, Kearney MI, Zuza MS, Rago AM, Oddino C. Regional survey of peanut smut and estimated losses caused by the disease. Cordoba: XXXI National Peanut Congress; 2016. 21–2 (#21). 5. American Peanut Council, United States Exports to World [https:// www. peanu tsusa. com/ phoca downl oad/ Export_ Stati stics/ USAnn ualEx ports/ Thru2 020/U. S.% 20Ann ual% 20Exp orts‑% 20All% 20Pro ducts. pdf ] 6. American Peanut Council, Global Imports from World [https:// www. peanu tsusa. com/ phoca downl oad/ Export_ Stati stics/ Globa lImpo rts/ World% 20Pea nut% 20Imp orts% 202015‑ 2020. pdf ] 7. Arias SL, Mary VS, Velez PA, Rodriguez MG, Otaiza‑Gonzalez SN, Theumer MG. Where does the peanut smut pathogen, Thecaphora frezii, fit in the spectrum of smut diseases? Plant Dis. 2021;105(9):2268–80. 8. de Blas FJ, Bruno CI, Arias RS, Ballen‑Taborda C, Mamani E, Oddino C, Rosso M, Costero BP, Bressano M, Soave JH, et al. Genetic mapping and QTL analysis for peanut smut resistance. BMC Plant Biol. 2021;21(1):312. 9. Massa AN, Bressano M, Soave JH, Buteler MI, Seijo G, Sobolev VS, Orner VA, Oddino C, Soave SJ, Faustinelli PC, et al. Genotyping tools and resources to assess peanut germplasm: smut‑resistant landraces as a case study. PeerJ. 2021;9:e10581. 10. Bressano M, Massa AN, Arias RS, de Blas F, Oddino C, Faustinelli PC, Soave S, Soave JH, Perez MA, Sobolev VS, et al. Introgression of peanut smut resistance from landraces to elite peanut cultivars (Arachis hypogaea L.). Plos One. 2019;14(2):e0211920. 11. de Blas FJ, Bressano M, Teich I, Balzarini MG, Arias RS, Manifesto MM, Costero BP, Oddino C, Soave SJ, Soave JA, et al. Identification of smut resistance in wild Arachis species and its introgression into peanut elite lines. Crop Sci. 2019;59(4):1657–65. 12. Arias RS, Cazon LI, Massa AN, Scheffler BE, Sobolev VS, Lamb MC, Duke MV, Simpson SA, Conforto C, Paredes JA, et al. Mitogenome and nuclear‑encoded fungicide‑target genes of Thecaphora frezii ‑ causal agent of peanut smut. Fungal Genom Biol. 2019;9(1):160–8. https:// www. longd om. org/ archi ve/ fgb‑ volume‑ 9‑ issue‑1‑ year‑ 2019. html 13. Data file 2: Length and quality of Illumina sequencing reads. Harvard Dataverse. (2022). https:// doi. org/ 10. 7910/ DVN/ I338KA. 14. Data file 3: Contig length and cumulative length of assembled Theca-phora frezii genome. Harvard Dataverse. (2022). https:// doi. org/ 10. 7910/ DVN/ SOFHRR. 15. National Center for Biotechnology Information. Illumina sequenc‑ing reads of Thecaphora frezii. Sequence Read Archive. SRR18840655. (2022). https:// www. ncbi. nlm. nih. gov/ sra/ SRR18 840655.Page 4 of 4Arias et al. BMC Genomic Data            (2023) 24:9 • fast, convenient online submission •  thorough peer review by experienced researchers in your field•  rapid publication on acceptance•  support for research data, including large and complex data types•  gold Open Access which fosters wider collaboration and increased citations  maximum visibility for your research: over 100M website views per year •  At BMC, research is always in progress.Learn more biomedcentral.com/submissionsReady to submit your research ?  Choose BMC and benefit from:  16. National Center for Biotechnology Information. PacBio sequencing reads of Thecaphora frezii. Sequence Read Archive: SRR18837637. (2022). https:// www. ncbi. nlm. nih. gov/ sra/ SRR18 837637. 17. National Center for Biotechnology Information. Genome Assembly Bio‑project PRJNA828173. (2022). https:// www. ncbi. nlm. nih. gov/ biopr oject/ PRJNA 828173. 18. Courville KJ, Frantzeskakis L, Gul S, Haeger N, Kellner R, Hessler N, Day B, Usadel B, Gupta YK, van Esse HP, et al. Smut infection of perennial hosts: the genome and the transcriptome of the Brassicaceae smut fungus Thecaphora thlaspeos reveal functionally conserved and novel effectors. New Phytol. 2019;222(3):1474–92. 19. Conforto C, Cazón I, Fernández FD, Marinelli A, Oddino C, Rago AM. Molecular sequence data of Thecaphora frezii affecting peanut crops in Argentina. Eur J Plant Pathol. 2013;137(4):663–6. 20. Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single‑copy orthologs. Bioinformatics. 2015;31(19):3210–2.Publisher’s NoteSpringer Nature remains neutral with regard to jurisdictional claims in pub‑lished maps and institutional affiliations.

First draft genome of \u3ci\u3eThecaphora frezii\u3c/i\u3e, causal agent of peanut smut disease

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First draft genome of \u3ci\u3eThecaphora frezii\u3c/i\u3e, causal agent of peanut smut disease

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