The Completed Genome Data of the Pathogenic Fungus Exobasidium cylindrosporum

HomePlant DiseaseVol. 107, No. 1The Completed Genome Data of the Pathogenic Fungus Exobasidium cylindrosporum PreviousNext RESOURCE ANNOUNCEMENT OPENOpen Access licenseThe Completed Genome Data of the Pathogenic Fungus Exobasidium cylindrosporumFei Liu, Yao-Yao Li, Wei Li, and Qi-Ming WangFei Liuhttps://orcid.org/0000-0002-6350-261XSchool of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, ChinaSearch for more papers by this author, Yao-Yao LiSchool of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, ChinaSearch for more papers by this author, Wei LiState Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, ChinaSearch for more papers by this author, and Qi-Ming Wang†Corresponding author: Q.-M. Wang; E-mail Address: [email protected]https://orcid.org/0000-0002-2180-8135School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, ChinaEngineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding 071002, Hebei, ChinaKey Laboratory of Microbial Diversity Research and Application of Hebei Province, Hebei University, Baoding 071002, Hebei, ChinaSearch for more papers by this authorAffiliationsAuthors and Affiliations Fei Liu1 Yao-Yao Li1 Wei Li2 Qi-Ming Wang1 3 4 † 1School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China 2State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China 3Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding 071002, Hebei, China 4Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Hebei University, Baoding 071002, Hebei, China Published Online:29 Dec 2022https://doi.org/10.1094/PDIS-01-22-0208-AAboutSectionsView articlePDFSupplemental ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat View articleGenome AnnouncementThe genus Exobasidium (Exobasidiaceae, Exobasidiales, Exobasidiomycetes, Ustilaginomycotina, Basidiomycota) comprises 50 species, which are distributed worldwide and are important plant pathogenic fungi mainly parasitizing woody plants, such as Ericaceae, Theaceae, and Lauraceae (Begerow et al. 2014). Some species of Exobasidium can reduce the production and quality of tea crop by affecting volatile, photosynthetic, and biochemical responses (Ponmurugan et al. 2016) and also infect blueberry and cranberry (Ingram et al. 2019). Phylogenetic studies indicated that the monophyletic lineages are often restricted to monophyletic host groups in the Ustilaginomycotina, and Exobasidium has a coevolution with Ericales (Begerow et al. 2004). However, the absence of authentic genomic data for Exobasidium has hindered the taxonomy, genetic diversity, pathogensis, and evolution of this obligate, biotrophic, pathogenic fungus (Chaliha et al. 2021).A high-quality reference genome is a prerequisite to understanding the genomic characterization, mechanisms of plant interaction, and system evolution. Two species of Exobasidium deposited in JGI Mycocosm (Kijpornyongpan et al. 2018), E. maculosum A7-4 with genome size 22.22 Mbp (185 scaffolds) and E. vaccinii MPITM with genome size 16.99 Mbp (119 scaffolds), were sequenced with the PacBio and the Illumina platform, respectively. However, they do not have intact telomeres, which indicated that they are not chromosomal-level genome assembly. To better understand the genomic features of Exobasidium, we sequenced and reported the complete genome of E. cylindrosporum, which parasitizes Rhododendron species (Park et al. 2006).Strain E. cylindrosporum YG638 was isolated from the leaf of Rhododendron sp. collected from Lushan, Jiangxi Province (29°33′28″ N, 115°59′06″ E) (Li 2008). DNA of YG638 was extracted using the CTAB protocol (Doyle and Doyle 1987) and purified using a QIAamp DNA Kit (Qiagen, Hilden, Germany). Short insert DNA libraries were constructed using TruSeq Nano DNA library prep kit (Illumina, San Diego, CA) and sequenced on the Illumina HiSeq 2000 platform (2 × 150 bp) using TruSeq SBS Kit (Illumina). A total of 4.85 Gb raw data (32,340,534 reads and approximately 273×) were obtained after sequencing. Low-quality and adapter sequences were then filtered using fastp v0.20.1 with default parameters (Chen et al. 2018). Long DNA libraries was purified using SMRTbell Template prep kit and sequenced on the PacBio RS II platform. A total of 197,453 long reads were obtained after sequencing by PacBio with average read length of 7,090 bp, 1.4 Gb bases in total (approximately 79×). We carried out a de novo assembly of the PacBio data with Canu (Koren et al. 2017) and mapped Illumina clean sequences data to the PacBio contigs for two rounds of polishing using Pilon (Walker et al. 2014). BUSCO v5.3.2 (Manni et al. 2021) was applied to evaluate the completeness using the Basidiomycota database as a reference. RepeatMasker (Tarailo-Graovac and Chen 2009) was used to predict repeat sequences.The complete genome assembly of YG638 contains three nuclear scaffolds and one mitochondrial genome. The final nuclear genome assembly consisted of two contigs with telomeres (TTAGGG/CCCTAA) on both ends and one contig with telomere on a single end. The YG638 genome consists of 17,796,081 bp spread over four scaffolds, with an N50 value of 5,696,943 bp. Analyses of the predicted protein product sequences with BUSCO showed that the proteome contained 95.2% of the BUSCOs as complete proteins (Table 1).Table 1. Main features of the Exobasidium cylindrosporum YG638 genomesFeaturesYG638Sequencing platformIllumina HiSeq 2000PacBioCoverage (×)27379Sequenced bases (Gb)4.851.40Sequenced reads32,340,534197,453Average read length (bp)1507,090Assembly contigs4Assembly size (bp)17,796,081N50 (bp)5,696,943Largest contig (bp)6,927,134GC (%)40.93Mitochondrial genome contigs1Mitochondrial genome total length (bp)82,829Mitochondrial genome GC (%)31.39Complete BUSCOs (%)95.20Complete and single-copy BUSCOs (%)95.20Complete and duplicated BUSCOs (%)0.00Fragmented BUSCOs (%)1.00Missing BUSCOs (%)3.80Repeat length (bp)612,565Repeat region of genome (%)3.44Predicted protein-coding genes6,980Secretome538Effector357CAZyme373PHI-base2,260Table 1. Main features of the Exobasidium cylindrosporum YG638 genomesView as image HTML Augustus (Stanke et al. 2004) was used for gene prediction and 6,980 protein-coding genes were predicted. The Swiss-Prot, NR, and PFAM (Finn et al. 2014) databases were used for function annotation and integrated by Trinotate (https://github.com/Trinotate).The secreted protein of YG638 was predicted following the pipeline: i) SignalP v5.0b (Almagro Armenteros et al. 2019) was used to scan signal peptide, ii) exclude sequences with transmembrane domains by Phobius v1.04 (Käll et al. 2007) and TMHMM v2.0 (Krogh et al. 2001), iii) exclude GPI anchored membrane proteins by PredGPI (Pierleoni et al. 2008), and iv) exclude endoplasmic reticulum targeting sequences (PS00014) by PS-Scan (de Castro et al. 2006). From a total of 6,980 predicted proteins, 538 proteins defined the fungus predicted secretome. EffectorP (Sperschneider and Dodds 2022) was used to predict the candidate effectors from the secretome and 357 proteins were considered candidate effectors (Fig. 1). The size of effectors less than 300 amino acids (aa) accounted for 71.99% (257/357) of the total putative effector and most of them (88.24%, 315/357) lacked homology proteins against in the SwissProt database. CAZymes were identified using dbCAN2 (Zhang et al. 2018) for all CAZyme annotation. The YG638 genome had 373 genes encoding 110 different CAZyme families with GHs representing the most abundant class (representing 39.41% of the total CAZymes). In order to study the mechanism of interaction between pathogen and host, genes were selected through BlastP against PHI-Base (Urban et al. 2022). A total of 2,260 genes with homologs in the PHI-base were identified in YG638. Out of 2,260 genes in the mutant phenotype, 1,044 genes were associated with reduced virulence, 160 with loss of pathogenicity, 100 with lethal phenotype, nine with effector, 649 with unaffected pathogenicity, and others with mixed functions.Fig. 1. Exobasidium cylindrosporum YG638 genome assembly. From outside to inside, the genome image represents the following tracks: Length chromosomes of each chromosome; gene density of per 100 kb; GC content of per 50 kb; histogram with Illumina sequencing depth ranging from 110 to 250×; histogram with PacBio sequencing depth; predictions of secretomes; predictions of effectors.Download as PowerPointData and Code AvailabilityThe complete chromosome-scale genome sequence of strain E. cylindrosporum YG638 has been deposited in the National Microbiology Data Center (NMDC) with accession number NMDC60033901 (https://nmdc.cn/resource/genomics/genome/detail/NMDC60033901) and in NCBI with BioSample ID SAMN27967614. Additional scripts and commands used in Circos plot are available through GitHub (https://github.com/Liufei0823/EC_YG638_Circos).The author(s) declare no conflict of interest.Literature CitedAlmagro Armenteros, J. J., Tsirigos, K. D., Sønderby, C. K., Petersen, T. N., Winther, O., Brunak, S., von Heijne, G., and Nielsen, H. 2019. SignalP 5.0 improves signal peptide predictions using deep neural networks. Nat. Biotechnol. 37:420-423. https://doi.org/10.1038/s41587-019-0036-z Crossref, ISI, Google ScholarBegerow, D., Göker, M., Lutz, M., and Stoll, M. 2004. On the evolution of smut fungi on their host. Pages 81-98 in: Frontiers in Basidiomycote Mycology. R. Agerer, M. Piepenbring, and P. Blanz, eds. IHW-Verlag, Echingen, Germany. Google ScholarBegerow, D., Schäfer, A., Kellner, R., Yurkov, A., Kemler, M., Oberwinkler, F., and R, B. 2014. Ustilaginomycotina. Pages 295-329 in: The Mycota, Vol. VII, Part A: Systematics and Evolution, 2nd ed. D. J. McLaughlin and J. W. Spatafora, eds. Springer-Verlag, Berlin, Germany. Crossref, Google ScholarChaliha, C., Kaladhar, V. C., Doley, R., Verma, P. K., Kumar, A., and Kalita, E. 2021. Bipartite molecular approach for species delimitation and resolving cryptic speciation of Exobasidium vexans within the Exobasidium genus. Comput. Biol. Chem. 92:107496. https://doi.org/10.1016/j.compbiolchem.2021.107496 Crossref, ISI, Google ScholarChen, S., Zhou, Y., Chen, Y., and Gu, J. 2018. Fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884-i890. https://doi.org/10.1093/bioinformatics/bty560 Crossref, ISI, Google Scholarde Castro, E., Sigrist, C. J., Gattiker, A., Bulliard, V., Langendijk-Genevaux, P. S., Gasteiger, E., Bairoch, A., and Hulo, N. 2006. ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res. 34:W362-W365. https://doi.org/10.1093/nar/gkl124 Crossref, ISI, Google ScholarDoyle, J. J., and Doyle, J. L. 1987. A rapid DNA isolation procedure from small quantities of fresh leaf tissue. Phytochem. Bull. 19:11-15. Google ScholarFinn, R. D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Heger, A., Hetherington, K., Holm, L., Mistry, J., Sonnhammer, E. L. L., Tate, J., and Punta, M. 2014. Pfam: the protein families database. Nucleic Acids Res. 42:D222-D230. https://doi.org/10.1093/nar/gkt1223 Crossref, ISI, Google ScholarIngram, R. J., Ludwig, H. D., and Scherm, H. 2019. Epidemiology of Exobasidium leaf and fruit spot of rabbiteye blueberry: Pathogen overwintering, primary infection, and disease progression on leaves and fruit. Plant Dis. 103:1293-1301. https://doi.org/10.1094/PDIS-09-18-1534-RE Link, ISI, Google ScholarKäll, L., Krogh, A., and Sonnhammer, E. L. L. 2007. Advantages of combined transmembrane topology and signal peptide prediction–the Phobius web server. Nucleic Acids Res. 35:W429-W432. https://doi.org/10.1093/nar/gkm256 Crossref, ISI, Google ScholarKijpornyongpan, T., Mondo, S. J., Barry, K., Sandor, L., Lee, J., Lipzen, A., Pangilinan, J., LaButti, K., Hainaut, M., Henrissat, B., Grigoriev, I. V., Spatafora, J. W., and Aime, M. C. 2018. Broad genomic sampling reveals a smut pathogenic ancestry of the fungal clade Ustilaginomycotina. Mol. Biol. Evol. 35:1840-1854. https://doi.org/10.1093/molbev/msy072 Crossref, ISI, Google ScholarKoren, S., Walenz, B. P., Berlin, K., Miller, J. R., Bergman, N. H., and Phillippy, A. M. 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27:722-736. https://doi.org/10.1101/gr.215087.116 Crossref, ISI, Google ScholarKrogh, A., Larsson, B., von Heijne, G., and Sonnhammer, E. L. 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305:567-580. https://doi.org/10.1006/jmbi.2000.4315 Crossref, ISI, Google ScholarLi, Z. Y. 2008. Study on Systematics of Exobasidiales in China. Doctoral dissertation. Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. Google ScholarManni, M., Berkeley, M. R., Seppey, M., Simão, F. A., and Zdobnov, E. M. 2021. BUSCO update: Novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol. Biol. Evol. 38:4647-4654. https://doi.org/10.1093/molbev/msab199 Crossref, ISI, Google ScholarPark, J. H., Kim, K. H., Lee, K. J., and Lee, S. K. 2006. Four species of Exobasidium from Korea. Mycotaxon 96:21-29. ISI, Google ScholarPierleoni, A., Martelli, P. L., and Casadio, R. 2008. PredGPI: a GPI-anchor predictor. BMC Bioinformatics 9:392. https://doi.org/10.1186/1471-2105-9-392 Crossref, ISI, Google ScholarPonmurugan, P., Manjukarunambika, K., and Gnanamangai, B. M. 2016. Impact of various foliar diseases on the biochemical, volatile and quality constituents of green and black teas. Australas. Plant Pathol. 45:175-185. https://doi.org/10.1007/s13313-016-0402-y Crossref, ISI, Google ScholarSperschneider, J., and Dodds, P. 2022. EffectorP 3.0: prediction of apoplastic and cytoplasmic effectors in fungi and oomycetes. Mol. Plant-Microbe Interact. 35:146-156. https://doi.org/10.1094/MPMI-08-21-0201-R Link, ISI, Google ScholarStanke, M., Steinkamp, R., Waack, S., and Morgenstern, B. 2004. AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Res. 32:W309-W312. https://doi.org/10.1093/nar/gkh379 Crossref, ISI, Google ScholarTarailo-Graovac, M., and Chen, N. 2009. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinf. 5:4.10.1-4.10.14. https://doi.org/10.1002/0471250953.bi0410s25 Google ScholarUrban, M., Cuzick, A., Seager, J., Wood, V., Rutherford, K., Venkatesh, S. Y., Sahu, J., Iyer, S. V., Khamari, L., De Silva, N., Martinez, M. C., Pedro, H., Yates, A. D., and Hammond-Kosack, K. E. 2022. PHI-base in 2022: a multi-species phenotype database for pathogen–host interactions. Nucleic Acids Res. 50:D837-D847. https://doi.org/10.1093/nar/gkab1037 Crossref, ISI, Google ScholarWalker, B. J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C. A., Zeng, Q., Wortman, J., Young, S. K., and Earl, A. M. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9:e112963. https://doi.org/10.1371/journal.pone.0112963 Crossref, ISI, Google ScholarZhang, H., Yohe, T., Huang, L., Entwistle, S., Wu, P., Yang, Z., Busk, P. K., Xu, Y., and Yin, Y. 2018. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 46:W95-W101. https://doi.org/10.1093/nar/gky418 Crossref, ISI, Google ScholarFunding: This study was supported by the National Natural Science Foundation of China (NSFC) grant no. 31961133020 and the Ministry of Science and Technology of China grant no. 2021FY100905.The author(s) declare no conflict of interest.DetailsFiguresLiterature CitedRelated Vol. 107, No. 1 January 2023SubscribeISSN:0191-2917e-ISSN:1943-7692 Download Metrics Article History Issue Date: 1 Feb 2023Published: 29 Dec 2022Accepted: 28 Jun 2022 Pages: 201-204 Information© 2022 The American Phytopathological SocietyFundingNational Natural Science Foundation of China (NSFC)Grant/Award Number: 31961133020Ministry of Science and Technology of ChinaGrant/Award Number: 2021FY100905Keywordscomplete genomeExobasidiumpathogen-host genespathogenic fungussecretomeThe author(s) declare no conflict of interest.PDF download