Fungi are the causal agents of many of the world\u27s most serious plant diseases causing disastrous consequences for large-scale agricultural production. Pathogenicity genomic basis is complex in fungi as multicellular eukaryotic pathogens. The fungus Cercospora sojina is a plant pathogen that threatens global soybean supplies. Here, we report the genome sequence of C. sojina strain S9 and detect genome features and predicted genomic elements. The genome sequence of C. sojina is a valuable resource with potential in studying the fungal pathogenicity and soybean host resistance to frogeye leaf spot (FLS), which is caused by C. sojina. The C. sojina genome sequence has been deposited and available at DDBJ/EMBL/GenBank under the project accession number AHPQ00000000

Bradley, Carl A.

Ming, Ray

Wang, Chaofan

Wei, Junmei

Zeng, Fanchang

Zhang, Guirong

Genomics Data

English

PubMed

Fungi are the causal agents of many of the world's most serious plant diseases causing disastrous consequences for large-scale agricultural production. Pathogenicity genomic basis is complex in fungi as multicellular eukaryotic pathogens. The fungus Cercospora sojina is a plant pathogen that threatens global soybean supplies. Here, we report the genome sequence of C. sojina strain S9 and detect genome features and predicted genomic elements. The genome sequence of C. sojina is a valuable resource with potential in studying the fungal pathogenicity and soybean host resistance to frogeye leaf spot (FLS), which is caused by C. sojina. The C. sojina genome sequence has been deposited and available at DDBJ/EMBL/GenBank under the project accession number AHPQ00000000

Fanchang Zeng

Chaofan Wang

Guirong Zhang

Junmei Wei

Carl A. Bradley

Ray Ming

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Draft genome sequence of Cercospora sojina isolate S9, a fungus causing frogeye leaf spot (FLS) disease of soybean

University of Kentucky

University of KentuckyUKnowledgePlant Pathology Faculty Publications Plant Pathology3-15-2017Draft Genome Sequence of Cercospora sojina IsolateS9, a Fungus Causing Frogeye Leaf Spot (FLS)Disease of SoybeanFanchang ZengShandong Agricultural University, ChinaChaofan WangShandong Agricultural University, ChinaGuirong ZhangUniversity of Illinois at Urbana-ChampaignJunmei WeiShandong Agricultural University, ChinaCarl A. BradleyUniversity of Kentucky, carl.bradley@uky.eduSee next page for additional authorsRight click to open a feedback form in a new tab to let us know how this document benefits you.Follow this and additional works at: https://uknowledge.uky.edu/plantpath_facpubPart of the Diseases Commons, Fungi Commons, Genetics and Genomics Commons, and thePlant Pathology CommonsThis Article is brought to you for free and open access by the Plant Pathology at UKnowledge. It has been accepted for inclusion in Plant PathologyFaculty Publications by an authorized administrator of UKnowledge. For more information, please contact UKnowledge@lsv.uky.edu.Repository CitationZeng, Fanchang; Wang, Chaofan; Zhang, Guirong; Wei, Junmei; Bradley, Carl A.; and Ming, Ray, "Draft Genome Sequence ofCercospora sojina Isolate S9, a Fungus Causing Frogeye Leaf Spot (FLS) Disease of Soybean" (2017). Plant Pathology FacultyPublications. 74.https://uknowledge.uky.edu/plantpath_facpub/74AuthorsFanchang Zeng, Chaofan Wang, Guirong Zhang, Junmei Wei, Carl A. Bradley, and Ray MingDraft Genome Sequence of Cercospora sojina Isolate S9, a Fungus Causing Frogeye Leaf Spot (FLS) Disease ofSoybeanNotes/Citation InformationPublished in Genomics Data, v. 12, p. 79-80.© 2017 The Authors. Published by Elsevier Inc.This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).Digital Object Identifier (DOI)https://doi.org/10.1016/j.gdata.2017.02.014This article is available at UKnowledge: https://uknowledge.uky.edu/plantpath_facpub/74Data in BriefDraft genome sequence of Cercospora sojina isolate S9, a fungus causingfrogeye leaf spot (FLS) disease of soybeanFanchang Zeng a,b,1, Chaofan Wang a,1, Guirong Zhang b, Junmei Wei a, Carl A. Bradley c,d, Ray Ming b,e,⁎a State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, Chinab Department of Plant Biology, University of Illinois, Urbana, IL 61801, USAc Department of Plant Pathology, University of Kentucky, Princeton, KY 42445, USAd Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USAe FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, Chinaa b s t r a c ta r t i c l e i n f oArticle history:Received 17 February 2017Accepted 24 February 2017Available online 15 March 2017Fungi are the causal agents of many of the world's most serious plant diseases causing disastrous consequencesfor large-scale agricultural production. Pathogenicity genomic basis is complex in fungi as multicellular eukary-otic pathogens. The fungus Cercospora sojina is a plant pathogen that threatens global soybean supplies. Here, wereport the genome sequence of C. sojina strain S9 and detect genome features and predicted genomic elements.The genome sequence of C. sojina is a valuable resource with potential in studying the fungal pathogenicity andsoybean host resistance to frogeye leaf spot (FLS),which is caused by C. sojina. The C. sojina genome sequence hasbeen deposited and available at DDBJ/EMBL/GenBank under the project accession number AHPQ00000000.© 2017 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license(http://creativecommons.org/licenses/by-nc-nd/4.0/).SpecificationsOrganism/cell line/tissue Cercospora sojinaSex –Sequencer or array type Illumina GA IIxData format ProcessedExperimental factors DNA extracted from a field strain, no treatmentExperimental features Whole genome sequenceConsent n/aSample source location Soybean field from Georgia, USA1. Direct link to deposited datahttps://www.ncbi.nlm.nih.gov/nuccore/AHPQ00000000.2. Materials and methods2.1. C. sojina whole-genome sequencing and assemblyGenomeof C. sojina strain S9 [1], froma soybeanfield inGeorgia,wassequenced using the Illumina GA IIx next generation technology bypaired-end sequencing method to a depth of 239× at the Keck Centerat the University of Illinois Urbana-Champaign. The produced se-quences had a read length of 124 base pairs (bp). A total of 29,619,123reads from each end were produced for a total of 59,238,246 readsfrom one lane. C. sojina genomes were assembled using Velvet algo-rithm [2] to obtain optimized resultswith high quality assembly. The as-sembly contained 30,797,991 bases with 1804 scaffolds (N50 =37.690 bp) and the G + C content was 53.80%.2.2. C. sojina genome annotation.The C. sojina genes were predicted with ab initio gene finders(FGENESH, FGENESH+, and GENEWISE). We referred to the genemodels from Zymoseptoria tritici (Mycosphaerella graminicola) as themost closely related species with C. sojina to train the gene finding pro-grams. BlastX against publicly available non-redundant protein andBlastN against ESTs databases are used to validate and curate predictedcomplete coding regions of the gene models. The entire DNA sequencewas also compared against the nonredundant protein databases in allsix reading frames, using BlastX with threshold E b 1e−5 to identifyany possible coding sequences previously missed by using ARTEMIS tocollate data and facilitate annotation [3]. Finally, a non-redundant setof gene models is produced, in which a single best gene model perlocus is selected, preferring the candidate annotation with supportingevidence of homolog protein/EST sequence in public database and com-plete coding sequence region. rRNA genes were identified withRNAmmer [4]. And tRNA and ncRNA genes were identified by RFAMGenomics Data 12 (2017) 79–80⁎ Corresponding author.E-mail address: rming@life.illinois.edu (R. Ming).1 F. Z. and C. W. contributed equally to this work.http://dx.doi.org/10.1016/j.gdata.2017.02.0142213-5960/© 2017 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).Contents lists available at ScienceDirectGenomics Dataj ourna l homepage: www.e lsev ie r .com/ locate /gdataand TRNASCAN-SE [5,6] in JGI Annotation system. The complete ge-nome sequence contained 9099 protein-coding genes, 72rRNAs,63tRNAs, 9ncRNAs. The average size of a gene was 2742 bp and the av-erage CDS size was 1764 bp. The C. sojina sequencing and assembly sta-tistics are summarized in Table 1.2.3. Genomics functional annotation.All predicted genes are annotated for Gene Ontology (GO) usingBlast2Go function annotation system [7,8], according to sequence com-parison with BlastP and domains/motif identification with interProScan[7] and PFAM [9]. The C. sojina genome encoded predominant potentialgenomic elements involved in mycelium related development. It isthrough themycelium that a fungus absorbs nutrients from its environ-ment. The major set of genes involved in the C. sojina life cycle suggeststhe fundamental systems for life sustainment. Additionally, the C. sojinagenome contains extensive genetic factors involved in auxin biosyn-thetic process, and Ser/Thr protein kinases signal transduction and tran-scription factors regulation. It implies that considerable auxin regulationand signal transduction pathway involved in appropriate physiologyprocesses and pathogenesis. ABC transporters (ATP binding cassetteprotein) genes were highly redundant and assigned to the largest setof molecular function category in C. sojina genome. These results accordwith the report that ABC transporters act as an essential virulence fac-tors by mediating secretion of host-specific toxins compounds duringpathogenesis [10].AcknowledgmentsThis projectwas supported by a grant from theUSDA-CSREES as partof the SoybeanDisease Biotechnology Center at theUniversity of Illinois.This work was also supported by NSFC 31401428, National Key R& DProgram for Crop Breeding 2016YFD0100306, Fok Ying-Tong Founda-tion 151024 and Taishan Scholar Talent Project from PRC.References[1] M.A.R. Mian, A.M.Missaoui, D.R.Walker, D.V. Phillips, H.R. Boerma, Frogeye leaf spotof soybean: a review and proposed race designations for isolates of Cercospora sojinaHara. Crop Sci. 48 (2008) 14–24.[2] D.R. Zerbino, E. Birney, Velvet: algorithms for de novo short read assembly using deBruijn graphs. Genome Res. 18 (2008) 821–829.[3] K. Rutherford, J. Parkhill, J. Crook, T. Horsnell, P. Rice, M.A. Rajandream, B. Barrell, Ar-temis: sequence visualization and annotation. Bioinformatics 16 (2000) 944–945.[4] K. Lagesen, P. Hallin, E.A. Rodland, H.H. Staerfeldt, T. Rognes, D.W. Ussery,RNAmmer: consistent and rapid annotation of ribosomal RNA genes. NucleicAcids Res. 35 (2007) 3100–3108.[5] S. Griffiths-Jones, S. Moxon, M. Marshall, A. Khan-na, S.R. Eddy, A. Bateman, Rfam:annotating non-coding RNAs in complete genomes. Nucleic Acids Res. 33 (2005)D121–D124.[6] T.M. Lowe, S.R. Eddy, tRNAscan-SE: a program for improved detection of transferRNA genes in genomic sequence. Nucleic Acids Res. 25 (1997) 955–964.[7] S. Götz, J.M. García-Gómez, J. Terol, T.D. Williams, S.H. Nagaraj, M.J. Nueda, M.Robles, M. Talón, J. Dopazo, A. Conesa, High-throughput functional annotation anddata mining with the Blast2GO suite. Nucleic Acids Res. 36 (2008) 3420–3435.[8] A. Conesa, S. Götz, J.M. García-Gómez, J. Terol, M. Talón, M. Robles, Blast2GO: A uni-versal tool for annotation, visualization and analysis in functional genomics re-search. Bioinformatics 21 (2005) 3674–3676.[9] A. Bateman, E. Birney, L. Cerruti, R. Durbin, L. Etwiller, S.R. Eddy, S. Griffiths-Jones,K.L. Howe, M. Marshall, E.L. Sonnhammer, The Pfam protein families database.Nucleic Acids Res. 30 (2002) 276–280.[10] L.H. Zwiers, I. Stergiopoulos, J.G. Van Nistelrooy, M.A. De Waard, ABC transportersand azole susceptibility in laboratory strains of the wheat pathogen Mycosphaerellagraminicola. Antimicrob. Agents Chemother. 46 (2003) 3900–3906.Table 1C. sojina genome sequencing assembly and annotation statistics.Assembly and annotation No.Total no. paired-end reads 59,238,246Average depth-coverage of mapped reads 239Average read length (bp) 124Assembly size (bp) 30,797,991Total contigs (N500 bp) 1804N50 37,690Protein-coding genes 9099Protein coding genes N100 amino acids 8868Average CDS size (bp) 1764Average gene length (bp) 2742% coding 64Genes with known function 7542Genes with unknown function 1557rRNA 72ncRNA 9tRNA 6380 F. Zeng et al. / Genomics Data 12 (2017) 79–80

Draft Genome Sequence of \u3cem\u3eCercospora sojina\u3c/em\u3e Isolate S9, a Fungus Causing Frogeye Leaf Spot (FLS) Disease of Soybean

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Draft Genome Sequence of \u3cem\u3eCercospora sojina\u3c/em\u3e Isolate S9, a Fungus Causing Frogeye Leaf Spot (FLS) Disease of Soybean

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