Colletotrichum fructicola is a causal agent of strawberry anthracnose and a major economic pathogen of horticultural and ornamental crops worldwide. Here, we present an annotated draft genome sequence for a C. fructicola isolate previously used for transcriptomic analysis. The assembly totals 58.0 Mb in 477 contigs with 18,143 predicted genes

Armitage, Andrew D.

Bates, Helen J.

Gao, Qing-Hua

Harrison, Richard J.

Nellist, Charlotte F.

Rokas, Antonis

Zhang, Liqing

Zou, Xiaohua

English

Gao, Qing Hua

NARCIS 

Draft Genome Sequence of the Strawberry Anthracnose Pathogen Colletotrichum fructicola

Greenwich Academic Literature Archive

Draft Genome Sequence of the Strawberry AnthracnosePathogen Colletotrichum fructicolaAndrew D. Armitage,a,b Charlotte F. Nellist,a Helen J. Bates,a Liqing Zhang,c Xiaohua Zou,c Qing-Hua Gao,cRichard J. Harrisona,daDepartment of Genetics, Genomics and Breeding, NIAB EMR, Kent, United KingdombNatural Resources Institute, University of Greenwich, Chatham, Kent, United KingdomcShanghai Key Laboratory of Protected Horticultural Technology, Forestry and Fruit Tree Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, ChinadNIAB Cambridge Crop Research, NIAB, Cambridge, United KingdomABSTRACT Colletotrichum fructicola is a causal agent of strawberry anthracnose anda major economic pathogen of horticultural and ornamental crops worldwide. Here,we present an annotated draft genome sequence for a C. fructicola isolate previouslyused for transcriptomic analysis. The assembly totals 58.0 Mb in 477 contigs with18,143 predicted genes.Colletotrichum fructicola (phylum Ascomycota, class Sordariomycetes) is a fungalpathogen of a wide range of horticultural crops, including strawberry, avocado, apple,Asian pear, yam, cacao, coffee, and ornamentals such as statice (1). The fungus is thecausative agent of anthracnose on cultivated strawberry in Asia, which leads to severeeconomic losses (2–4). The hemibiotrophic nature of the fungus has led to recent investi-gation into gene expression at spore germination, biotrophic and necrotrophic infection (5),and response of the host to infection (6). We provide expansion of the genomic resourcesavailable for the anthracnose pathogen C. fructicola through assembly and annotation ofthe same strain used for published transcriptomic work (5).C. fructicola isolate CGMCC3.17371 was isolated in 2007 from an infected strawberryplant displaying strawberry anthracnose symptoms in Feng Xian District, Shanghai.Freeze-dried mycelium, grown in potato dextrose broth (Fluka, Sigma-Aldrich), wasused for genomic DNA (gDNA) extraction with a Macherey-Nagel NucleoSpin plant II kit(catalog number 11912262, Fisher). Paired-end PCR-free genomic libraries were pre-pared for Illumina sequencing using New England Biolabs Next End Repair (catalog numberE6050S), dA-tailing (catalog number E6053S), and Blunt T/A ligase (catalog numberM0367S) module reagents. For MinION sequencing, library preparation was performedusing a 1D genomic DNA ligation sequencing kit (catalog number SQK-LSK108; OxfordNanopore Technologies), with shearing performed using a g-TUBE (Covaris) and sizeselection on a BluePippin system (4 kbp). Genomic libraries were sequenced usingIllumina MiSeq v.3 2  300-bp paired-end (PE) reads (catalog number MS-102-3003) andMinION FLO-MIN106 R9.4 flow cells, generating 75.49-fold (7,426,411 reads) and 13.57-fold(155,413 reads) coverage of sequence data, respectively.Illumina reads were trimmed and adapters removed using fastq-mcf v.1.04.676 (7),while MinION reads were trimmed using Porechop v.0.2.0 (https://github.com/rrwick/Porechop). Genome assembly was performed with SPAdes v.3.5.0 (hybridSPAdes) (8),generating a 58-Mb assembly in 447 contigs, with 308 contigs larger than 1,000 bp(Table 1). A total of 2.11 Mb of the genome was repeat masked using RepeatMaskerv.4.0.3 (http://www.repeatmasker.org) and TransposonPSI (http://transposonpsi.source-forge.net; 2013-03-05 release). Genome completeness was assessed using BUSCO v.3(9), identifying 3,685 of 3,725 (98.9%) genes from the Sodariomycota_odb9 data set asCitation Armitage AD, Nellist CF, Bates HJ,Zhang L, Zou X, Gao Q-H, Harrison RJ. 2020.Draft genome sequence of the strawberryanthracnose pathogen Colletotrichumfructicola. Microbiol Resour Announc 9:e01598-19. https://doi.org/10.1128/MRA.01598-19.Editor Antonis Rokas, Vanderbilt UniversityCopyright © 2020 Armitage et al. This is anopen-access article distributed under the termsof the Creative Commons Attribution 4.0International license.Address correspondence to Andrew D.Armitage, A.D.Armitage@gre.ac.uk.Received 6 January 2020Accepted 22 February 2020Published 19 March 2020GENOME SEQUENCEScrossmVolume 9 Issue 12 e01598-19 mra.asm.org 1 on April 2, 2020 by guesthttp://mra.asm.org/Downloaded from both present and complete in the assembly. Published RNAseq data from differentstages of plant infection (GenBank accession numbers SRR5194993, SRR5194994, andSRR5194995) (5) were aligned to the genome using STAR v.2.5.3a (10). These align-ments were used to train prediction of gene models using BRAKER1 v.2.0 using thefungal option and CodingQuarry v.2.0 run in pathogen mode (11, 12). A total of 18,143genes were predicted, encoding 18,447 proteins, with 16,459 of these proteins pre-dicted from BRAKER1 and supplemented with a further 1,684 genes predicted byCodingQuarry that were located in intergenic regions of BRAKER1 gene models.Functional annotation was performed using InterProScan v.5.18-57.0 (13) and withBLASTp (E 1  10100) searches against the March 2018 release of the SWISS-PROTdatabase (14, 15).Genes that play a putative role in pathogenicity were identified from predicted genemodels. SignalP v.4.1 and TMHMM v.2 were used to predict genes encoding secretedproteins (16, 17), from which carbohydrate-active enzymes were predicted usingdbCAN and the CAZy database classification system (18, 19). Furthermore, proteins withan effector-like structure were predicted using EffectorP v.1.0 (20) (Table 1). Defaultparameters were used for software unless otherwise noted.Data availability. This whole-genome shotgun project has been deposited atDDBJ/ENA/GenBank under the accession number SSNE00000000 (BioProject numberPRJNA532407). This version of the project has the accession number SSNE01000000 andconsists of sequences deposited under the GenBank accession numbers SSNE01000001 toSSNE01000447. The raw reads are available on the NCBI SRA database under accessionnumber PRJNA532407.ACKNOWLEDGMENTSWe thank DEFRA for permitting work to be performed in the United Kingdom underplant health license 6996/221427 held by R.J.H.This collaboration was enabled by a BBSRC China partnering award for “aUK-China partnership to understand the genetic architecture of the Colletotrichumgloeosporioides-Fragaria  ananassa interaction” (BB/N022289/1) and was reliant uponbioinformatic pipelines developed as part of the BBSRC-LINK project “Improving DiseaseResistance in Strawberry” (BB/K017071/1 and BB/K017071/2), both awarded to R.J.H.REFERENCES1. Weir BS, Johnston PR, Damm U. 2012. 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Comparative genomic and transcriptomicTABLE 1 Genome statistics for Colletotrichum fructicola isolate CGMCC3.17371Statistic ValueAssemblySize (bp) 58,056,435No. of contigs 447Largest contig (bp) 2,278,540GC content (%) 53.20N50 (bp) 90,947Repeat masked (%) 3.63Gene modelsTotal no. of genes 18,143Total no. of proteins 18,447No. of encoding secreted proteins 2,070No. of proteins encoding effector candidatesSecreted carbohydrate active enzymes 516Secreted with effector-like structure 612Armitage et al.Volume 9 Issue 12 e01598-19 mra.asm.org 2 on April 2, 2020 by guesthttp://mra.asm.org/Downloaded from analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi.New Phytol 197:1236–1249. https://doi.org/10.1111/nph.12085.5. Zhang L, Huang X, He C, Zhang Q-Y, Zou X, Duan K, Gao Q. 2018. Novelfungal pathogenicity and leaf defense strategies are revealed by simul-taneous transcriptome analysis of Colletotrichum fructicola and straw-berry infected by this fungus. 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Draft genome sequence of the strawberry anthracnose pathogen colletotrichum fructicola

http://gala.gre.ac.uk/id/eprint/27564/7/27564%20ARMITAGE_Draft_Genome_Sequence_of_the_Strawberry_Anthracnose_Pathogen_%28OA%29_2020.pdf

Draft genome sequence of the strawberry anthracnose pathogen colletotrichum fructicola

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