Draft genome sequence of Venturia carpophila, the causal agent of peach scab
© The Author(s). 2017
Received: 23 February 2017
Accepted: 20 November 2017
Published: 2 December 2017
Venturia carpophila causes peach scab, a disease that renders peach (Prunus persica) fruit unmarketable. We report a high-quality draft genome sequence (36.9 Mb) of V. carpophila from an isolate collected from a peach tree in central Georgia in the United States. The genome annotation is described and a phylogenetic analysis of the pathogen is presented. The genome sequence will be a useful resource for various studies on the pathogen, including the biology and ecology, taxonomy and phylogeny, host interaction and coevolution, isolation and characterization of genes of interest, and development of molecular markers for genotyping and mapping.
Besides peach, several economically important stone fruit crops, including apricot (P. armeniaca), almond (P. dulcis), and plum (P. domestica), can be infected by V. carpophila . Only recently has the taxonomic identity of the pathogens causing scab on stone fruit and other related genera begun to be clarified [6–8]. No complete genome sequence of V. carpophila has been reported, although some related species have now been sequenced [9–11]. As with these other species, an annotated genome of V. carpophila is a valuable resource for various genomic, genetic, and systematic studies. For example, various genes of interest and importance, such as those related to fungicide resistance, host recognition, or mating type, can be identified for further research to aid in management of the disease. Microsatellites can be developed as informative markers for genetic mapping and diversity studies. Also, the knowledge obtained from the genome can be useful in improving development of resistant cultivars.
In this report, we describe the first high-quality draft genome sequence of V. carpophila and provide a phylogenetic analysis of the fungus and other closely related species. The genome sequence will facilitate further genomic and phylogenetic exploration to understand the pathogen and its relationship with peach.
Classification and features
Classification and general features of Venturia carpophila
Evidence code a
Species Venturia carpophila
Conidia and ascospores
Mesophilic (15–25 °C)
pH range; Optimum
Rain splash and wind
Byron, Georgia, USA
Time of sample collection
83.739 o W
The fungus belongs in the Eukaryota, is a member of the Fungal kingdom, phylum Ascomycota, class Dothidiomycetes, and family Venturiaceae (Table 1). Several other economically important plant pathogens are members of the Dothidiomycetes, including apple scab ( V. inaequalis ), pear scab ( V. pyrina ), pecan scab ( F. effusum ), rice scald (Magnaprthe oryzae), and Septoria leaf blotch of wheat ( Zymoseptoria tritici syn. Mycosphaerella graminicola). V. carpophila has been classified based on its host range, morphology and some molecular characteristics . The sexual stage (pseudothecia that produce ascospores) of the fungus has been identified and described from Australia , but has not been described elsewhere at any time. Its role in the epidemiology of the disease is unknown.
Genome sequencing information
Genome project history
A paired-end library (average insert 518 bp for 2 × 300 cycles)
Gene calling method
Augustus using Saccharomyces as the species parameter, also COG and BLAST search NCBI NR (non-redundant) database
Genbank Date of Release
Source Material Identifier
Growth conditions and genomic DNA preparation
Culture of V. carpophila was on antibiotic-amended potato dextrose agar. The culture was incubated for 4 weeks at 25 °C (12 h light/12 h dark), when the DNA was extracted from the sample using a ZymoResearch DNA extraction kit (ZymoResearch, Irvine, CA), following a slightly modified protocol for DNA extraction from fungi . A Qiagen Tissue Lyser (Qiagen, Valencia, CA) was used to lyse the mycelium. Once obtained, the DNA was quantified using a Nanodrop spectrophotometer (Nanodrop Products, Wilmington, DE) and stored in TE buffer at −20 °C.
Genome sequencing and assembly
The genome was sequenced using an Illumina paired-end library (a V3 kit, 2 × 300 cycles) and a MiSeq machine, which generated 400,041,052 raw reads consisting of 12,052,356,652 raw nucleotides. The A5-Miseq assembly pipeline was used automatically to check quality, trim adaptors, filter low-quality reads, to correct sequencing errors using robust error correction (EC) parameters, and generate high-quality genome contigs with additional detection of assembly errors . About 97.54% raw reads and 83.90% nucleotides passed EC; thus a total of 39,057,608 EC reads, containing 10,111,608,273 EC nucleotides, were subject to the final assembly process. A total of 657 contigs, accounting for 36,917,822 bp, were assembled, representing the assembled genome size of the pathogen. Of the assembled nucleotides, 98.58% bases had a PHRED-scale score quality > = 40 (Q40) and the average depth of each nucleotide was 263.47, indicating it is a high-quality assembly. Additionally, the longest contig is 1,454,817 bp and the N50 length is 292,586 bp, suggesting the genome was covered mostly by larger contigs. The actual genome size is unknown at this stage, but the 263 × genome coverage likely covers more than 95% of the genome. Therefore we can estimate that the genome size of V. carpophila is ~38.9 Mb, which is in the typical size range of genomes in the phylum Ascomycota .
The draft genome was annotated using the MAKER pipeline . In summary, repeats were first found and masked using RepeatMasker and the RepBase database ; ab initio gene prediction was performed with AUGUSTUS under the parameter Saccharomyces ; these predicted genes were annotated by BLAST against the NCBI non-redundant (nr) nucleotide database and also by RPSBLAST (Reverse Position-Specific BLAST) batch search in conserved domain database (CDD v3.14) [21, 22]. The CCD is a superset including a total of 47,363 position-specific scoring matrix (PSSM) domains curated in the NCBI and imported from Pfam , SMART , COG , PRK , and TIGRFAM . The e-value for BLAST and RPSBLAST search in a database was 1e-50 and 0.01, respectively. In addition, CRISPR regions were identified using the CRISPR Recognition Tool (CRT) ; tRNAs were identified by tRNAScan-SE-1.23 ; rRNAs were identified by RNAmmer ; signal peptides and transmembrane helices were predicted using SignalP  and TMHMM , respectively. According to BLASTN, 107 of the 657 contigs, accounting for 144,247 bp, only had multiple hits of mitochondrial genome sequences at e-10, suggesting they belong to the organelle genome of the pathogen.
Nucleotide and gene count levels of the genome
% of Total a
Genome size (bp)
DNA coding (bp)
DNA G + C (bp)
Protein coding genes
Genes in internal clusters
Genes with function prediction
Genes assigned to COGs
Genes with Pfam domains
Genes with signal peptides
Genes with transmembrane helices
Number of genes associated with the 25 general COG functional categories
% of total a
RNA processing and modification
Replication, recombination and repair
Chromatin structure and dynamics
Cell cycle control, mitosis and meiosis
Signal transduction mechanisms
Cell wall/membrane biogenesis
Intracellular trafficking and secretion
Posttranslational modification, protein turnover, chaperones
Energy production and conversion
Carbohydrate transport and metabolism
Amino acid transport and metabolism
Nucleotide transport and metabolism
Coenzyme transport and metabolism
Lipid transport and metabolism
Inorganic ion transport and metabolism
Secondary metabolites biosynthesis, transport and catabolism
General function prediction only
Not in COGs
Insights from the genome sequence
The genome provides a useful resource for identifying genes of interest in V. carpophila . Furthermore, the phylogenetic analysis presented earlier confirms the relationship of V. carpophila to other members of the Venturiacae and confirms previous observations on the taxonomic relationships among these members of the Ascomycota. Based on the phylogenetic analysis using the sequence of the 18S rRNA gene (Fig. 2), V. carpophila is closely related to other scab-causing fungal pathogens of higher plants, including V. cerasi, causing scab on cherry, and also V. nashicola, cause of scab on Asian pear.
The predicted genes may represent most functional genes in the V. carpophila genome and can be used as a new resource for developing molecular markers for genetic diversity studies, and for other research into the biology, ecology, taxonomy and phylogeny of the pathogen, and for research into host/pathogen coevolution.
The authors thank Minling Zhang, Bryan Blackburn, and Wanda Evans for their technical support. This article reports the results of research only. Mention of a trademark or proprietary product is solely for the purpose of providing specific information and does not constitute a guarantee or warranty of the product by the USDA and does not imply its approval to the exclusion of other products that may also be suitable.
The research is partly supported by USDA-ARS projects (No. 6606–21,220-012-00D and No. 6606–21,000-004-00D).
CC, CB, and BW conceived the project and drafted the manuscript. CC performed genome bioinformatics and phylogenetic analysis. CB collected the isolate and extracted the DNA. Each author read and approved the final version of the manuscript.
The authors declare that they have no competing interests.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
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