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Genome Sequence Resource for Cercospora rodmanii J1, a Potential Biological Control Agent for Water Hyacinth

2022; American Phytopathological Society; Volume: 112; Issue: 11 Linguagem: Inglês

10.1094/phyto-04-22-0119-a

1943-7684

Zhenyue Lin, Wei Wang, Jianming Chen,

Genomics and Phylogenetic Studies

HomePhytopathology®Vol. 112, No. 11Genome Sequence Resource for Cercospora rodmanii J1, a Potential Biological Control Agent for Water Hyacinth PreviousNext Resource Announcement OPENOpen Access licenseGenome Sequence Resource for Cercospora rodmanii J1, a Potential Biological Control Agent for Water HyacinthZhenyue Lin, Wei Wang, and Jianming ChenZhenyue Lin†Corresponding authors: Z. Lin; E-mail Address: [email protected], and J. Chen; E-mail Address: [email protected]https://orcid.org/0000-0002-6367-2459Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, ChinaFujian Provincial Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Minjiang University, Fuzhou, 350108, ChinaTechnology Innovation Center for Monitoring and Restoration Engineering of Ecological Fragile Zone in Southeast China, Ministry of Natural Resources, Fuzhou, 350108, China, Wei WangInstitute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, ChinaFujian Provincial Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Minjiang University, Fuzhou, 350108, China, and Jianming Chen†Corresponding authors: Z. Lin; E-mail Address: [email protected], and J. Chen; E-mail Address: [email protected]Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, ChinaFujian Provincial Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Minjiang University, Fuzhou, 350108, ChinaTechnology Innovation Center for Monitoring and Restoration Engineering of Ecological Fragile Zone in Southeast China, Ministry of Natural Resources, Fuzhou, 350108, ChinaAffiliationsAuthors and Affiliations Zhenyue Lin1 2 3 † Wei Wang1 2 Jianming Chen1 2 3 † 1Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China 2Fujian Provincial Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Minjiang University, Fuzhou, 350108, China 3Technology Innovation Center for Monitoring and Restoration Engineering of Ecological Fragile Zone in Southeast China, Ministry of Natural Resources, Fuzhou, 350108, China Published Online:22 Nov 2022https://doi.org/10.1094/PHYTO-04-22-0119-AAboutSectionsView articlePDFSupplemental ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat View articleGenome AnnouncementWater hyacinth, one of the world's worst invasive aquatic weeds, has a rapid growth rate and spreadability, causing a serious ecoenvironmental hazard for water bodies (Villamagna and Murphy 2010). Biological control agents based on plant pathogens and insects have been highly successful in the integrated control of water hyacinth, despite some limitations (Charudattan and Dinoor 2000). There are a number of controlled studies that have reported the roles of Cercospora rodmanii in causing water hyacinth populations to decline (Tessmann et al. 2008). C. rodmanii J1 (CDMCC number 62031) is patented in China and has gained much attention as a promising alternative as a biocontrol agent for controlling water hyacinth. Strain J1 is highly virulent toward water hyacinth, with high host mortality and infectivity. Field symptoms of the diseased plant appear as irregular necrotic lesions on leaves, stems, and crown, and petiole rots (Lin et al. 2022), which could effectively suppress water hyacinth populations. Therefore, mining the genome information of C. rodmanii J1 is of great significance for understanding its biocontrol mechanism to gain a better application in aquatic weed management.C. rodmanii J1 was originally recovered from symptomatic leaf tissue of water hyacinth in Fujian, China, and was confirmed by Koch's postulates (Supplementary Fig. S1). The fungal species have been formally identified by symptomology, morphological characteristics, and multigene phylogenetic analyses of the internal transcribed spacer (ITS), calmodulin (CAL), translation elongation factor (TEF), actin (ACT), H3, and chalcone synthase (CHS) (Lin et al. 2022), with the GenBank accession numbers ITS, MZ436974; CAL, MZ519385; TEF, OK340826; ACT, OK340824; H3, OK340828; and CHS, MZ519387. Young mycelia of C. rodmanii J1 were inoculated on 100 ml of potato dextrose broth, grown in shake culture at 25°C for 5 days, then harvested as the source material for genome sequencing. Freeze-dried mycelium was ground to a fine powder, and genomic DNA was extracted with a modified DNA Midi Kit (Tiangen, Inc., Beijing, China). The yield and integrity of DNA were determined by spectrophotometry (Thermo Scientific NanoDrop 2000) and 0.2% agarose gel electrophoresis. Genome sequencing was performed using two sequencing platforms: PacBio RSII (277× coverage) and Illumina HiSeq 3000 (84× coverage). Illumina sequences were trimmed with Fastp (Chen et al. 2018). PacBio long-read sequence data were assembled by overlap using MECAT (v.1.0) with parameters (corrected error rate 0.02) (Xiao et al. 2017), and the assembled sequence was then polished using Illumina reads by Quiver (SMRT Analysis version 2.3.0). The coding sequence in the fungal genome was predicted by GeneMarkS software (Besemer et al. 2001). The completeness of the assembly was assessed using benchmarking universal single-copy orthologs (BUSCO) v3.1 (Simão et al. 2015), while statistics were evaluated with Fungi_odb10 (Zdobnov et al. 2021). The transfer RNA (tRNA) and ribosomal RNA (rRNA) were predicted by tRNAscan-SE v2.0 (Lowe and Eddy 1997) and RNAmmer (Lagesen et al. 2007), respectively. Genome-wide localization of repeated sequences was identified using Tandem Repeats Finder (Benson 1999). Gene function annotation was performed using Blast2go and was searched against four databases—NCBI nonredundant proteins (Nr), eukaryotic orthologous groups (KOG), Kyoto Encyclopedia of Genes and Genomes (KEGG orthologue database), and Swiss-Prot—using BLAST with an E-value cut-off set to 10−5 (Boeckmann et al. 2003; Buchfink et al. 2015; Conesa et al. 2005; Kanehisa et al. 2004).The genome of C. rodmanii J1 is 33.17 Mb, divided into 10 nuclear chromosomes and 1 circular mitochondrial DNA. All 10 nuclear chromosomes have telomeric repeats (TTAGGG) on both ends. The N50 of the final assembly was 4,109,232 bp, while the average G+C content was 52.67%. BUSCO assessment showed 98.15% (single-copy genes: 98.15%, duplicated genes: 0%), 0.40%, and 1.45% of the 758 expected proteins, which were identified as complete, fragmented, and missing sequences, respectively. The genome was found to contain 119 tRNAs, 43 rRNAs (including 13 18s-rRNA, 16 5s-rRNA, and 14 28s-rRNA) and 3 noncoding small RNAs. Further chromosomal information can be found in Table 1. We predicted 11,913 protein-coding genes in the C. rodmanii J1 genome, of which 11,675 (98%) were revealed to have significant matches in at least one of the Nr, KEGG, KOG, and Swiss-Prot public databases. In addition, 1,086 secretory proteins, 1,656 carbohydrate-active enzymes, 330 candidate effectors, and 53 secondary metabolite gene clusters were predicted in C. rodmanii J1 by the Signal P 4.1 (Petersen et al. 2011), CAZy database (Lombard et al. 2014), EffectorP 3.0 database (Sperschneider and Dodds 2022), and antiSMASH (Blin et al. 2017), respectively.Table 1. Summary of the Cercospora rodmanii J1 genome assembly and annotation statisticsaSequenceAccessionTopologyTelLength (bp)GC (%)PE genesrRNAtRNAChr_1CP095188Linear23,945,25652.901,418NA18Chr_2CP095189Linear25,277,18853.391,962NA20Chr_3CP095190Linear21,797,30352.53626132Chr_4CP095191Linear24,508,55552.651,645NA11Chr_5CP095192Linear24,899,07152.321,732NA12Chr_6CP095193Linear22,918,90652.541,016NA9Chr_7CP095194Linear22,281,08752.7681416Chr_8CP095195Linear24,109,23252.511,518NA7Chr_9CP095196Linear22,840,32652.261,026NA10Chr_10CP095197Linear2566,95653.13145294Genomeb−−−33,143,88052.7011,9024399Chr_mtCP095198CircularNA27,34227.4711NA20aTel = telomeric repeat, PE genes = protein-encoding genes, rRNA = ribosomal RNA, tRNA = transfer RNA, and NA = not available.bWhole nuclear genome.Table 1. Summary of the Cercospora rodmanii J1 genome assembly and annotation statisticsaView as image HTML Cercospora is a species-rich genus that includes at least 281 distinct species (Bakhshi et al. 2015) and contains numerous important plant-pathogenic fungi from a diverse range of hosts (Groenewald et al. 2013). To date, limited genomic data have been available for the Cercospora genus, with only two chromosome-level reference-quality assemblies, C. sojina (assembly ASM429982v1) (Gu et al. 2020) and C. beticola (assembly CB0940_V2) (de Jonge et al. 2018), available in NCBI genomes. By comparison, the C. rodmanii genome is approximately 15% smaller than that of its most closely related species, C. beticola (37.06 Mb), and 21% smaller than that of C. sojina (40.12 Mb). The number of chromosomes and plasmids of the C. rodmanii assembly was 11 but the C. beticola assembly was 10 and the C. sojina assembly was 12 (Table 2). These results reveal a significant genome-phenotype difference within the Cercospora genus.Table 2. Comparative genome statisticsVariableCercospora rodmaniiC. sojinaC. beticolaAssembly accessionGCA_022965775.1GCA_004299825.1GCA_002742065.1StrainJ1RACE1509-40Total sequence length (bp)33,171,22240,115,97637,057,033Total number of chromosomes and plasmids111210Contig N50 (bp)4,109,2324,908,8234,173,231GC content (%)52.6753.4051.30Genome coverage250.0×150.0×70×Assembly methodMECAT v.1.0SMRT Link v5.0.1SOAPdenovo v. 2.04Sequencing technologyPacBio RSII + IlluminaPacBio RSIIIllumina + Optical MappingReferenceThis studyGu et al. 2020De Jonge et al. 2018Number of protein-coding genes11,91312,60712,271Table 2. Comparative genome statisticsView as image HTML Herein, for the first time, we provide a complete, high-quality genome sequence of C. rodmanii J1, a valuable resource for the biocontrol of water hyacinth. 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Wang contributed equally to this work.Funding: This research was financially supported by the Fujian Provincial Science and Technology Project (grant number 2020N5011), the Fujian Province Natural Resources Science and Technology Innovation Project, and the Funds for Quanzhou Water Ecological Protection and Restoration Innovation Center.The author(s) declare no conflict of interest.DetailsFiguresLiterature CitedRelated Vol. 112, No. 11 November 2022SubscribeISSN:0031-949Xe-ISSN:1943-7684 DownloadCaptionPierce's disease symptoms on grapevine (Vitis vinifera) mechanically inoculated with Xylella fastidiosa subsp. fastidiosa. Photograph was taken two and a half months after inoculation (Zecharia et al.). Photo credit: Ofir Bahar Metrics Article History Issue Date: 2 Dec 2022 Published: 22 Nov 2022 Accepted: 1 Jun 2022 Pages: 2462-2465 Information© 2022 The American Phytopathological SocietyFunding Fujian Provincial Science and Technology ProjectGrant/Award Number: 2020N5011 Fujian Province Natural Resources Science and Technology Innovation Project Funds for Quanzhou Water Ecological Protection and Restoration Innovation Center KeywordsbiocontrolCercospora rodmaniigenome assemblywater hyacinthThe author(s) declare no conflict of interest.PDF download