Genome Sequence Resource of Colletotrichum horii, an Important Pathogenic Fungus Threatening Persimmon Production

HomePlant DiseaseVol. 106, No. 3Genome Sequence Resource of Colletotrichum horii, an Important Pathogenic Fungus Threatening Persimmon Production PreviousNext RESOURCE ANNOUNCEMENT OPENOpen Access licenseGenome Sequence Resource of Colletotrichum horii, an Important Pathogenic Fungus Threatening Persimmon ProductionHanyue Fan, Yongkuan Li, Sadaruddin Chachar, Yong Yang, and Changfei GuanHanyue FanState Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, ChinaSearch for more papers by this author, Yongkuan LiState Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, ChinaSearch for more papers by this author, Sadaruddin ChacharState Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, ChinaSearch for more papers by this author, Yong YangState Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, ChinaSearch for more papers by this author, and Changfei Guan†Corresponding author: C. Guan; E-mail Address: guanchangfei@nwafu.edu.cnhttps://orcid.org/0000-0002-0486-1321State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, ChinaSearch for more papers by this author AffiliationsAuthors and Affiliations Hanyue Fan Yongkuan Li Sadaruddin Chachar Yong Yang Changfei Guan † State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China Published Online:8 Mar 2022https://doi.org/10.1094/PDIS-11-21-2417-AAboutSectionsView articlePDFSupplemental ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat View articleGenome AnnouncementColletotrichum horii causes anthracnose disease on persimmon. It is an important fungus that seriously threatens persimmon production worldwide. To date, the genome of C. horii has not been reported, although various genomic sequences are available for the C. gloeosporioides species complex to which the pathogen belongs. Here, we isolated C. horii FJ-1 from persimmon in China and presented the high-quality and completed genome of C. horii with a total size of 74.32 Mb by using Nanopore sequencing technology. The genome of C. horii FJ-1 was assembled into 42 contigs with an N50 of 3.1 Mb. In total, 15,529 genes were predicted, among which 358 genes encoded the candidate effector proteins. Our results provide the first genome resource for determining the pathogenic mechanism of C. horii to plant and identifying potential resistant candidates for persimmon-breeding programs.The genus Colletotrichum comprises nine major clades (Cannon et al. 2012) and includes 252 species and 15 complexes (Talhinhas and Baroncelli 2021). Colletotrichum spp. are important plant pathogens that can cause anthracnose in economic crops such as persimmon (Zhang and Xu 2003), banana (Chillet et al. 2006), mango (Li et al. 2019), chili (Than et al. 2008), tomato (Barksdale 1972), and strawberry (Xiao et al. 2004). The genus has been voted as one of the top 10 fungal plant pathogens in molecular plant pathology (Dean et al. 2012).Persimmon (Diospyros kaki Thunb.), one of the most important fruit trees in the world, is primarily cultivated in East Asia (Kanzaki and Nara 2016; Luo and Wang 2008). Persimmon anthracnose is a serious disease occurring in many countries where persimmon is cultivated. Based on molecular and morphological analyses, the pathogen of persimmon anthracnose was renamed C. horii by Weir and Johnston (2010) and belongs to the C. gloeosporioides species complex. Anthracnose symptoms first appear in the spring as spots; then, the spots develop into dark lesions. Under favorable conditions, adjacent lesions may coalesce, increasing in size until the entire twig is infected (Xie et al. 2010). As a destructive disease of persimmon trees, C. horii can cause leaf defoliation, fruit rot, and even the death of the whole plant (Zhang and Xu 2005). In some growing areas of persimmon in China, the anthracnose could reduce the yield of persimmon by more than 50% (Deng et al. 2019). However, due to a lack of the reference genome, the molecular pathogenic mechanism of C. horii to the plant remains unknown. Hence, the genome analysis of C. horii is a significant step to understand its pathogenic mechanism and persimmon–C. horii interactions, thereby providing a reference for the study of effective management strategies.The strain FJ-1 was isolated from diseased persimmon branches (D. kaki L. ‘Fuping Jianshi’) from the National Field Genebank for Persimmon, Yangling, Shaanxi, China (34°17′42.80″ N, 108°04′8.21″ E). Genomic DNA was extracted from 7-day-old cultures grown on potato dextrose agar (PDA) using the E.Z.N.A. fungal DNA kit (Omega Bio-Tek). Based on the concatenated dataset of actin, chalcone synthase, glyceraldehyde 3-phosphate dehydrogenase, and β-tubulin-2 gene sequences of C. horii and those of other C. gloeosporioides species complex members (Talhinhas and Baroncelli 2021), a maximum-likelihood phylogenetic tree was constructed with MEGA v7.0 (Kumar et al. 2016), and the bootstrap value was set as 1,000. The phylogenetic tree showed that the isolate FJ-1 clustered with the C. horii strain with high bootstrap support (Supplementary Fig. S1). The genome of C. horii strain FJ-1 was sequenced using Oxford Nanopore Technologies and sequencing was performed at the Beijing Biomarker Technologies Co., Ltd. (Beijing, China). The purity, concentration, and integrity of genomic DNA were examined by Nanodrop, Qubit, and 0.35% agarose gel electrophoresis, respectively. The BluePippin automatic nucleic acid recovery system was used to recover large fragments of DNA. The library was constructed with an SQK-LSK109 kit and sequenced with a Nanopore III sequencer. After filtering out low-quality and short-length subreads (<2,000 bp), the remaining subreads were assembled to contigs without gaps by using NECAT v0.0.1 (https://github.com/xiaochuanle/NECAT) software.In total, 6.9 GB of raw data (92.84× genome coverage) was obtained, and a complete genome was assembled with a total length of 74.32 Mb. The genome contained 42 contigs, with an N50 of 3.1 Mb, a maximum length of 8.8 Mb, and a GC content of 46.79% (Table 1; Supplementary Tables S1 and S2). The completeness of the genome assembly was assessed using BUSCO v4.0 (Manni et al. 2021), resulting in a coverage rate of 97.93% (Supplementary Fig. S2). With the help of LTR_FINDER v1.05 (Xu and Wang 2007), MITE-Hunter (v 2010-09-29) (Han and Wessler 2010), RepeatScout v1.0.5 (Price et al. 2005), and PILER-DF v2.4 (Edgar and Myers 2005), the repetitive sequence database of the fungal genome was constructed based on the principles of structural prediction and de novo prediction. The database was classified by PASTEClassifier v2.0 (Wicker et al. 2007) and then merged with Repbase v14.02 (Jurka et al. 2005) database as the final repetitive sequence database. Based on the constructed repetitive sequence database, the repetitive sequence of this fungus was predicted using RepeatMasker v4.0.6 (Smit et al. 2013-2015) software, and a repetitive sequence of 15.83 Mb with a repetitive sequence ratio of 21.30% was obtained. Genscan v1.0 (Burge and Karlin 1997), Augustus v2.4 (Stanke and Waack 2003), GlimmerHMM v3.0.4 (Majoros et al. 2004), GeneID v1.4 (Blanco et al. 2007), and SNAP (v 2006-07-28) (Korf 2004) were used to predict the gene structure from scratch. GeMoMa v1.3.1 (Keilwagen et al. 2016) was used for prediction based on homologous protein, and EVM v1.1.1 (Haas et al. 2008) was adopted to integrate the prediction results obtained with the above two methods. Consequently, 15,529 genes were obtained, with an average length of 1,863.38 bp. For the prediction of noncoding RNAs, tRNAscan-SE v1.3 software (Lowe and Eddy 1997) was used to predict transfer RNA in the genome, and Infenal1.1 (Nawrocki and Eddy 2013) was used to predict ribosomal RNA in the genome based on the Rfam (Nawrocki et al. 2014) database. By comparing the predicted protein sequences with those in the Swiss-Prot database and using GenBlastA v1.0.4 software (She et al. 2009), we searched the genome for homologous gene sequences (possible genes). Then, GeneWise v2.4.1 (Birney et al. 2004) was used to search for early termination codons and frameshift mutations in the gene sequences; thus, two pseudogenes were obtained (Table 1).Table 1. Statistical features of the Colletotrichum horii FJ-1 genomeFeaturesStatisticsGenome size (bp)74,324,508Genome coverage92.84×Contig number42Contig N50 (bp)3,135,412Maximum contig length (bp)8,827,220GC content (%)46.79Complete BUSCOs (%)97.93Gene number15,529Average gene length (bp)1,863.38Repetitive sequence (%)21.30Ribosomal RNA101Transfer RNA413Pseudogene2Signal peptide2,111Secreted proteins1,613Candidate effectors358Table 1. Statistical features of the Colletotrichum horii FJ-1 genomeView as image HTML Genome function annotation includes general database annotation and proprietary database annotation. The general annotation results were obtained by comparing the predicted gene sequences with functional databases such as EuKaryotic Orthologous Groups (KOG) (Tatusov et al. 2000), Kyoto Encyclopedia of Genes and Genomes (KEGG) (Kanehisa et al. 2004), Swiss-Prot (Boeckmann et al. 2003), TREMBL (Boeckmann et al. 2003), and nonredundant (NR) (Deng et al. 2006). Among all coding genes, 15,449 (99%) genes were annotated by the NR database, 7,218 (46%) were classified using the gene ontology database, 3,620 (23%) were assigned to the KEGG database, and 7,080 (45%) were mapped to the KOG database (Supplementary Figs. S3, S4, and S5; Supplementary Table S3). The functional annotation of 1,034 carbohydrate-active enzyme (CAZy) genes was obtained using HMMER v2.2.1 software (Eddy 1998) in the CAZy database (Cantarel et al. 2009) (Supplementary Fig. S5). In total, 141 transport proteins and 4,964 pathogen–host interaction proteins were annotated by the TCDB (Saier et al. 2006) and PHI (Winnenburg et al. 2006) databases, respectively. Based on the protein sequences of all predicted genes, 2,111 proteins containing signal peptides were predicted using SignalP 4.0 software (Petersen et al. 2011). The remaining 1,613 proteins after removing the protein containing a transmembrane helix from the predicted protein containing a signal peptide are secretory proteins. Then, we predicted 358 fungal candidate effector proteins after further analysis of secreted proteins by EffectorP v1.0 software (Sperschneider et al. 2015).Additionally, we compared the FJ-1 genome assembly statistics with those of seven strains (Cg56, ICMP18580, HC540, CgLH19, Cg01, hn1205-1, and CF75) belonging to C. gloeosporioides complexes in the NCBI database (Supplementary Table S4). The genome assembly statistics of C. horii strain FJ-1 were comparable with those of other C. gloeosporioides species complex.Taken together, these findings provide a significant discovery for the genome analysis of C. horii, which can help us to better understand its pathogenic mechanism and persimmon–C. horii interactions. In turn, such understanding can contribute to the effective control methods of this disease. 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Google ScholarFunding: This research was supported by National Key Research and Development Program of China (2019YFD1000600) and Special Project of Science and Technology Innovation Plan of Shaanxi Academy of Forestry (SXLK2020-0212).The author(s) declare no conflict of interest.DetailsFiguresLiterature CitedRelated Vol. 106, No. 3 March 2022SubscribeISSN:0191-2917e-ISSN:1943-7692 Download Metrics Downloaded 638 times Article History Issue Date: 30 Mar 2022Published: 8 Mar 2022Accepted: 2 Jan 2022 Pages: 1052-1055 Information© 2022 The American Phytopathological SocietyFundingNational Key Research and Development ProgramGrant/Award Number: 2019YFD1000600Special Project of Science and Technology Innovation Plan of Shaanxi Academy of ForestryGrant/Award Number: SXLK2020-0212KeywordsColletotrichum horiidisease managementfungal pathogengenomepersimmontree fruitsThe author(s) declare no conflict of interest.PDF download