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ARS Home » Southeast Area » Byron, Georgia » Fruit and Tree Nut Research » Research » Publications at this Location » Publication #346965

Research Project: Mitigating Alternate Bearing of Pecan

Location: Fruit and Tree Nut Research

Title: High-quality genome of the peach scab pathogen, Venturia carpophila

Author
item Chen, Chunxian
item Bock, Clive
item WOOD, BRUCE - Retired ARS Employee

Submitted to: American Phytopathological Society Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 5/17/2017
Publication Date: 12/1/2017
Citation: Chen, C., Bock, C.H., Wood, B.W. 2017. High-quality genome of the peach scab pathogen, Venturia carpophila. American Phytopathological Society Annual Meeting. 107:S5.134.

Interpretive Summary:

Technical Abstract: Venturia carpophila causes peach scab, a disease that renders peach (Prunus persica) fruit unmarketable. We report a high-quality draft genome (36.9 Mb) of V. carpophila from an isolate collected from a peach tree in central Georgia. The genome was sequenced by MiSeq using an Illumina paired-end library (a V3 kit, 2 × 300 cycles), which generated 40,041,052 raw reads consisting of 12,052,356,652 raw nucleotides. After trimming adaptors and removing low-quality reads, a total of 39,057,608 reads (~97.54%), containing 10,111,608,273 nucleotides (83.90%) passed robust error correction (EC) algorithms. The final assembly of the genome from EC reads included 657 scaffolds, accounting for 36,917,822bp. The average depth of each nucleotide was 263.47 and about 98.58% of the assembled bases had a PHRED-scale quality score >= 40, indicating it is a very high-quality assembly. The longest contig is 1,454,817bp and the N50 length is 292,586bp. BLASTN suggested 107 of the 657 scaffolds (144,247bp long) were the mitochondrial sequences. The actual genome size of V. carpophila is unknown but estimated ~38.9 Mb (typical in the phylum Ascomycota), assuming this assembly has 95% genome coverage. The annotated genome sequence will be a useful resource for various studies of the pathogen and it’s interaction with the host.