Genome Sequence Resource of Ustilago crameri, a Fungal Pathogen Causing Millet Smut Disease of Foxtail Millet.

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HomePlant DiseaseVol. 107, No. 2Genome Sequence Resource of Ustilago crameri, a Fungal Pathogen Causing Millet Smut Disease of Foxtail Millet PreviousNext RESOURCE ANNOUNCEMENT OPENOpen Access licenseGenome Sequence Resource of Ustilago crameri, a Fungal Pathogen Causing Millet Smut Disease of Foxtail MilletYuwei Liu, Zhimin Hao, Hehe Sun, Jiayue Liu, Shen Shen, Cheng Zhou, and Zhiyong LiYuwei Liuhttps://orcid.org/0000-0002-9144-0014State Key Laboratory of North China Crop Improvement and Regulation, Baoding, ChinaHebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Baoding, ChinaSearch for more papers by this author, Zhimin HaoState Key Laboratory of North China Crop Improvement and Regulation, Baoding, ChinaHebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Baoding, ChinaSearch for more papers by this author, Hehe SunState Key Laboratory of North China Crop Improvement and Regulation, Baoding, ChinaSearch for more papers by this author, Jiayue LiuState Key Laboratory of North China Crop Improvement and Regulation, Baoding, ChinaSearch for more papers by this author, Shen ShenState Key Laboratory of North China Crop Improvement and Regulation, Baoding, ChinaSearch for more papers by this author, Cheng Zhou†Corresponding authors: C. Zhou; E-mail Address: [email protected], and Z. Y. Li; E-mail Address: [email protected]Affiliated Hospital of Hebei University, Baoding, ChinaSearch for more papers by this author, and Zhiyong Li†Corresponding authors: C. Zhou; E-mail Address: [email protected], and Z. Y. Li; E-mail Address: [email protected]https://orcid.org/0000-0001-6668-3009Institute of Millet Crops of Hebei Academy of Agriculture and Forestry Sciences, National Foxtail Millet Improvement Center, Minor Cereal Crops Laboratory of Hebei Province, Shijiazhuang, ChinaSearch for more papers by this authorAffiliationsAuthors and Affiliations Yuwei Liu1 4 Zhimin Hao1 4 Hehe Sun1 Jiayue Liu1 Shen Shen1 Cheng Zhou3 † Zhiyong Li2 † 1State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China 2Institute of Millet Crops of Hebei Academy of Agriculture and Forestry Sciences, National Foxtail Millet Improvement Center, Minor Cereal Crops Laboratory of Hebei Province, Shijiazhuang, China 3Affiliated Hospital of Hebei University, Baoding, China 4Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Baoding, China Published Online:4 Jan 2023https://doi.org/10.1094/PDIS-06-22-1439-AAboutSectionsPDF ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Genome AnnouncementUstilago crameri is a fungal pathogen that causes millet smut disease of foxtail millet (Fig. 1A) (Kumar 2011). U. crameri belongs to the division Basidiomycota, class Ustilaginomycetes, order Ustilaginales, family Ustilaginaceae, genus Ustilago. Millet smut disease is a serious disease caused by U. crameri, which infects the whole panicle or part of the grain of foxtail millet replacing plant tissues with fungal teliospores (Kumar 2011; Singh et al. 2004). Millet smut disease can seriously reduce the yield of foxtail millet, with a high incidence of 75% in severe years (Kumar 2011). To date, research on millet smut disease has focused on identifying candidate genes in foxtail millet to achieve resistance against smut and the rhizosphere bacterial community associated with smut disease (Han et al. 2017; Hao et al. 2020). There are few studies on the infection process and mechanism of pathogenicity in U. crameri.Fig. 1. Genome feature of Ustilago crameri Uc7 strain. A, Millet smut disease on foxtail millet. B, Circular representation of the genome of U. crameri Uc7. From outside to the center: the outermost circle are the scaffolds (>10 Kbp); the second and third circles are the density of genes and coding sequences; the fourth are the repeat sequences; the fifth and sixth circles show tRNA and rRNA. The image was created by Circos (http://circos.ca/).Download as PowerPointUp to now, genome information for U. crameri is still lacking. In our study, the PacBio and Illumina sequencing technologies were used to sequence the U. crameri genome, which will provide a preliminary understanding of its genetic information.U. crameri strain Uc7 was isolated from smut-diseased panicles of the foxtail millet variety Jingu21 in the field in Zhongguan (41.179°N, 117.966°E), Longhua, Chengde, Hebei, China. The single-spore culture of U. crameri was inoculated into potato dextrose broth medium and incubated for 5 days at 25°C on a rotary shaker at 120 rpm. The genomic DNA of U. crameri Uc7 was extracted by the CTAB method described previously (Möller et al. 1992). Genomic sequencing was performed at Majorbio (Shanghai Majorbio Co., Ltd., Shanghai, China). In total, 338,882 PacBio high quality subreads and 3,348,726,219 total bases were used for further assembly. For Illumina sequencing, a short insert library (495 bp) was constructed and sequenced on a Novaseq6000. In total, 18,140,741 × 2 high quality (150PE, paired-end) reads were obtained for further assembly.High-quality reads were de novo assembled using CANU (v 1.7) software (Koren et al. 2017). In total, 29 contigs were assembled, with an N50 length of 829,494 bp. The final genome assembly comprised 18.82 Mbp on 28 scaffolds with a 55.09% G+C content (Fig. 1B, Table 1). The N50 and N90 sizes of the scaffolds were 917,587 and 482,872 bp, respectively (Table 1). Further, the completeness of the genome assembly was assessed using Benchmarking Universal Single Copy Orthologs (BUSCO v3.0) with the lineage-specific profile library fungi_obd9 database (Waterhouse et al. 2018). The result showed that the genome was estimated to be 98.2% complete with 1.4% fragmented and 0.4% missing from the database.Table 1. Genome features of Ustilago crameri Uc7Genomic featuresStrain Uc7Genome size (Mb)18.82BUSCO completeness (%)98.2Number of scaffolds28N50 (bp)917,587N90 (bp)482,872GC content (%)55.09Repeat rate (%)0.1Predicted protein-coding genes6,228Annotated proteins with the nonredundant database5,586Annotated proteins with the Pfam motif4,507Secreted proteins686Table 1. Genome features of Ustilago crameri Uc7View as image HTML Maker2 (v 2.31.9) (Holt and Yandell 2011) was used for de novo gene prediction. In total, 6,228 genes were predicted as protein-coding genes and with an average length of 2,027.54 bp. In addition, 140 noncoding RNAs (116 transfer RNA and 24 ribosomal RNA) were predicted using tRNAscan-SE (v 2.0) (Lowe and Eddy 1997) and Barrnap (v 0.8) (https://github.com/tseemann/barrnap). Further, the repeat sequences were identified by Repeatmasker (v 4.0.7) (Tarailo-Graovac and Chen 2009). Results showed that the repetitive sequences account for about 0.1% of the assembled genome.Functional annotation of the predicted gene sequences was done using BLAST to search the nonredundant protein (NR) database, Swiss-Prot database, COG, and Kyoto encyclopedia of genes and genomes (KEGG), and the highest quality alignment was chosen as the gene annotation (Boeckmann et al. 2003; Kanehisa et al. 2004; Tatusov et al. 2000). Blast2GO was used for GO annotation (Conesa et al. 2005), and the software HMMER (v 3.3.1) was used to annotate the function of genes based on the Pfam database (Eddy 1998). Results showed that 5,586 genes aligned to the NR database, with 2,635 genes involved in metabolic pathways, 4,507 genes had at least one GO term, and 4,645 genes encoded protein sequences containing Pfam domains. In addition, the predicted gene sequences were also searched against the carbohydrate-active enzymes database (CAZymes) (Cantarel et al. 2009). Results showed that 176 genes were annotated as putative CAZymes genes, which included one carbohydrate-binding module, one polysaccharide lyase, 28 auxiliary activities, 28 carbohydrate esterases, 34 glycosyl transferases, and 84 glycoside hydrolases. To identify the genes associated with pathogenicity, the genes were aligned against the pathogen-host interactions (PHI) database (Winnenburg et al. 2006), the fungal virulence factors (DFVF, v6) database (Lu et al. 2012), and the transporter classification database (TCDB) (Saier et al. 2021). The strain was found to contain 1,460 genes encoding putative pathogen-host interaction proteins, 689 genes encoding virulence factor candidates, and 952 genes encoding transporters. Further, the signal peptides and transmembrane motifs were analyzed using SignalP (v4.1) (Petersen et al. 2011) and TMHMM (v 2.0) (Krogh et al. 2001), respectively, and a total of 686 secreted proteins were identified.In summary, we report the draft genome of U. crameri strain Uc7 from smut-diseased panicles of foxtail millet, which provide the foundation for future analyses of this phytopathogen from foxtail millet. 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Hao contributed equally to this work.Funding: Natural Science Foundation of Hebei (C2021301062), HAAFS Basic Science and Technology Contract Project (HBNKY-BGZ-02-ZDGG-07), Basic Research Funds of Hebei Academy of Agriculture and Forestry Sciences (2021030201), HAAFS Science and Technology Innovation Special Project (2022KJCXZX-GZS-4), Hebei Provincial Government Funding for Specialist Capacity Building and Junior College Leaders Training Project in 2018 (361007).The author(s) declare no conflict of interest.DetailsFiguresLiterature CitedRelated Vol. 107, No. 2 February 2023SubscribeISSN:0191-2917e-ISSN:1943-7692 Download Metrics Article History Issue Date: 28 Feb 2023Published: 4 Jan 2023Accepted: 28 Jul 2022 Pages: 546-548 Information© 2023 The American Phytopathological SocietyFundingNatural Science Foundation of HebeiGrant/Award Number: C2021301062HAAFS Basic Science and Technology Contract ProjectGrant/Award Number: HBNKY-BGZ-02-ZDGG-07Basic Research Funds of Hebei Academy of Agriculture and Forestry SciencesGrant/Award Number: 2021030201HAAFS Science and Technology Innovation Special ProjectGrant/Award Number: 2022KJCXZX-GZS-4Hebei Provincial Government Funding for Specialist Capacity Building and Junior College Leaders Training Project in 2018Grant/Award Number: 361007Keywordsfoxtail milletfungal pathogensgenome sequenceUstilago crameriThe author(s) declare no conflict of interest.PDF download