HomePlant DiseaseVol. 106, No. 9Genome Sequence Resource of Albifimbria verrucaria Causing the Leaf Spot Disease of the Spinach Plant Spinacia oleracea PreviousNext RESOURCE ANNOUNCEMENT OPENOpen Access licenseGenome Sequence Resource of Albifimbria verrucaria Causing the Leaf Spot Disease of the Spinach Plant Spinacia oleraceaChunyue Chai, Chongyi Chen, Lulu Zhu, Jinli Liu, and Fengli HuiChunyue Chaihttps://orcid.org/0000-0003-2486-5810School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, 473061, ChinaResearch Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Nanyang, 473061, ChinaSearch for more papers by this author, Chongyi ChenSchool of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, 473061, ChinaSearch for more papers by this author, Lulu ZhuSchool of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, 473061, ChinaSearch for more papers by this author, Jinli LiuSchool of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, 473061, ChinaSearch for more papers by this author, and Fengli Hui†Corresponding author: F. Hui; E-mail Address: fenglihui@yeah.netSchool of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, 473061, ChinaSearch for more papers by this authorAffiliationsAuthors and Affiliations Chunyue Chai1 2 Chongyi Chen1 Lulu Zhu1 Jinli Liu1 Fengli Hui1 † 1School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, 473061, China 2Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Nanyang, 473061, China Published Online:26 Jul 2022https://doi.org/10.1094/PDIS-04-22-0843-AAboutSectionsPDF ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Genome AnnouncementAlbifimbria verrucaria (formerly in the genus Myrothecium) (Lombard et al. 2016) is a ubiquitous plant-pathogenic fungus, known for its broad host range and destructive diseases. A. verrucaria causes types of foliar spots in a large number of important crops, cultivated vegetables, and ornamental plants, including soybean (Nguyen et al. 1973), upland cotton (Heyn 1958), tomato (Stevenson and McColloch 1947), rice (Singh and Aujla 1967), corn (Yang and Jong 1995), potato, cucumber (Raymond et al. 1959), muskmelon (Belisario et al. 1999), melon, watermelon, cucurbits (Rennberger and Keinath 2020), pea (Farr and Rossman 2018), wild rocket (Garibaldi et al. 2016c), peanut, spinach (Matić et al. 2019), beet, birdsfoot trefoil (Farr et al. 1990), kudzu (Abbas et al. 2001), and sunflower (De Romano 1979). The genome sequences of A. verrucaria will support functional genetic studies into pathogenesis mechanisms and contribute to the development of an effective method to control this fungus.In this study, we sequenced the genome of A. verrucaria strain HC3, which was isolated from leaf spot of spinach (Spinacia oleracea L.) in the vegetable planting greenhouse of the HuaCheng farm of Henan Province, China. Total genomic DNA of strain HC3 was extracted from mycelia with a cetyltrimethylammonium bromide-based approach and sequenced using long-read PacBio platforms with single-molecule real-time (SMRT) technology (Beijing BerryGenomics Co., Ltd.), with an average insert size of 20 kb. In total, we obtained 7.09 Gb of raw reads, with 524,807 long reads, an average length of 13.52 kb, and an N50 length of 14.14 kb, representing 155× coverage of the A. verrucaria genome generated after sequencing. Sequence error polishing with Pilon v1.22 (Walker et al. 2014) corrected 10,621 base substitutions, 1,550 insertions, and 1,339 deletions, resulting in the final assembly. The genome of A. verrucaria strain HC3 was de novo assembled with MECAT (Xiao et al. 2017). Removing organelle-originating contigs, the final genome assembly comprised 45.90 Mb containing 24 contigs, with an N50 length of 3.20 Mb and a GC content of 49.54%. The longest contig was 6.07 Mb (Table 1). Genome completeness was assessed using benchmarking universal single-copy ortholog (BUSCO) v4.1.4 with the lineage-specific dataset helotiales_odb10 (Seppey et al. 2019). The result showed that the genome assembly contains a high overall completeness of 95.69%, 2.33% of BUSCOs were present as fragments, and only 1.98% were missing. GenomeScope (Vurture et al. 2017) estimated genome sizes ranging from 45,687,391 to 45,693,687 bp. The repetitive component of the genome was estimated to be between 1,631,109 and 1,631,333 bp, and the heterozygosity was estimated to be 1.44 to 1.74%. Repeat sequences of the genome were assessed with RepeatMasker v4.0.7 (http://www.repeatmasker.org), using a de novo repeats library generated by RepeatModeler v1.08 (http://www.repeatmasker.org/RepeatModeler/). Approximately 6.53% of sequences were identified as repetitive sequences.Table 1. Summary of Albifimbria verrucaria HC3 genome assemblyFeaturesStrain HC3Sequencing platformPacBio RSIITotal reads (Gb)7.09Assembly size (Mb)45.90Number of contigs24Average reads length (kb)13.52N50 length (Mb)3.20BUSCO completeness (%)a95.68Coverage155×Repeat sequence rate (%)6.53Predicated protein-coding genes13,121Candidate secreted proteins1,449Candidate effectors470Carbohydrate-active enzymes2,441Secondary metabolite gene clusters84Pathogen–host interaction proteins3,709Fungal virulence factors2315aBenchmarking universal single-copy ortholog.Table 1. Summary of Albifimbria verrucaria HC3 genome assemblyView as image HTML After repeat masking, the sequences were used for ab initio gene prediction. Overall, 13,121 protein-coding genes were identified by GeneMark-ES v1.48, with an average length of 1,439 bp and 53.05% GC content, constituting 41.12% of the total genome. By analyzing with tRNAscan-SE 2.0 (Chan et al. 2021), 285 transfer RNA genes were identified. The gene annotation mapped 12,578 genes to the NCBI nonredundant protein database, 6,883 genes to the Swiss-Prot database, and 3,979 genes to the Kyoto Encyclopedia of Genes and Genomes database, and 7,284 genes were assigned gene ontology terms. Using classical secreted protein analysis conducted with SignalP v4.1 (Petersen et al. 2011), in total, 1,449 secreted proteins were identified. Among them, 470 proteins were identified as effector candidates by EffectorP v3.0 (Sperschneider and Dodds 2022). In addition, 84 secondary metabolite gene clusters were predicted by antismash 4.1.0 (Blin et al. 2017), 2,441 putative carbohydrate-active enzymes were predicted using the CAZy database (Cantarel et al. 2009), 3,709 pathogen–host interaction proteins were predicted using the PHI database (Urban et al. 2020) (E values were all < 1e-5), and 2,315 fungal virulence factors were predicted using DFVF: the database of fungal virulence factors (Lu et al. 2012).In summary, we reported a long-read sequencing-based genome assembly of A. verrucaria strain HC3. This high-quality genome sequence provides a valuable resource to mitigate future losses by facilitating our subsequent study of its infection mechanism and developing effective control strategies against leaf spot disease.Data AvailabilityThis genome is the first available genome sequence of A. verrucaria. 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Plant Dis. 79:994-997. https://doi.org/10.1094/PD-79-0994 Crossref, ISI, Google ScholarFunding: This project was supported by the Key Specialized Research and Development Breakthrough Program in Henan Province (grant number 212102110261) and an open-ended project of the Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture and Rural Affairs, P.R. China (grant number 2021ZTSJJ5).The author(s) declare no conflict of interest.DetailsFiguresLiterature CitedRelated Vol. 106, No. 9 September 2022SubscribeISSN:0191-2917e-ISSN:1943-7692 Download Metrics Article History Issue Date: 30 Aug 2022Published: 26 Jul 2022Accepted: 18 May 2022 Pages: 2511-2513 Information© 2022 The American Phytopathological SocietyFundingKey Specialized Research and Development Breakthrough Program in Henan ProvinceGrant/Award Number: 212102110261Ministry of Agriculture and Rural Affairs, P.R. ChinaGrant/Award Number: 2021ZTSJJ5KeywordsAlbifimbria verrucariafungal pathogengenomeleaf spot diseaseThe author(s) declare no conflict of interest.PDF download