Draft Genome Sequence of Diplodia seriata F98.1, a Fungal Species Involved in Grapevine Trunk Diseases

ABSTRACT

The ascomycete Diplodia seriata is a causal agent of grapevine trunk diseases. Here, we present the draft genome sequence of D. seriata isolate F98.1 (37.27 Mb, 512 contigs, 112 scaffolds, and 8,087 predicted protein-coding genes).

GENOME ANNOUNCEMENT

Diplodia seriata (1, 2) is one of the most common species in the family Botryosphaeriaceae that is associated with grapevine trunk diseases (3, 4). In grapevine, D. seriata is frequently isolated from necrotic tissues (black spots or sectors) localized in the wood of infected trunks or arms (3–5). This species is also frequently isolated from woody tissues of trees such as Acer sp., Prunus sp., and Quercus sp. (2). Pycnidia are produced on infected grapevine wood or pruning shoots, and liberate pycnidiospores dispersed by rainfall or sprinkler irrigation (6, 7). On grapevine surfaces, pycnidiospores germinate and infectious hyphae penetrate into the plant tissues through pruning wounds (4, 5). Inoculation of D. seriata on wounded stems from grafted grapevines of the highly susceptible cultivar tempranillo induces a local brown necrosis in all plants and foliar symptoms in 50% of plants (8). D. seriata is known to secrete several plant polymers degrading enzymes such as cellulases, xylanases, lipases, and laccases (9, 10). This fungal species also produces phytotoxic secondary metabolites such as (−)-mellein and its derivates (11, 12).

D. seriata F98.1 was isolated in 1998 at Perpignan, France, from the trunk of a grapevine exhibiting foliar symptoms typical of Syrah decline (13). D. seriata F98.1 is pathogenic on grapevine (8, 13). Sequencing was performed by BGI-Tech (China) using Illumina HiSeq 2500 at a coverage of 270× (170-, 500-, and 6,000-bp libraries). After quality filtering, a total of 88,596,792 paired-end reads of 125 bp were obtained. Assembly with SOAPdenovo version 1.05 (14) led to 512 contigs and 112 scaffolds (37.27 Mb; G+C%: 56.8). This high-quality genome (scaffold N₅₀: 2.9 Mb; minimum scaffold length: 1,007 bp; gaps: 250 kb) has 13 scaffolds with a size greater than 1 Mb (90% of the total sequence), likely corresponding to chromosomes. Using GLEAN (15), 8,087 coding sequences (CDSs) were identified, 93% being supported by RNAseq (mycelium on potato dextrose broth or minimal medium for 4 days). Recently, the genome sequence of D. seriata DS831, isolated from an infected grapevine (United States, 2011), was released (16). The genome size of DS831 (37.13 Mb) is similar to the genome size of F98.1, but its assembly is five times more fragmented (1,391 contigs; 695 scaffolds), and it carries 9,398 CDSs. Bidirectional best BLAST hit (BDBH) analysis revealed that 82% of F98.1’s and DS831’s CDSs are similar. OrthoFinder (17) identified 5,935 orthologous single-copy gene families shared between the two genomes. According to BDBH analysis, 1,507 genes are specific to strain F98.1, and 2,763 are specific to strain DS831. Using BLASTN, we found that 2,686 (97.2%) of the genes thought to be specific to strain DS831 were present in the F98.1 genome sequence, and 1,440 (95.6%) of the genes thought to be specific to strain F98.1 are present in the DS831 genome sequence. The difference in CDS numbers between DS831 and F98.1 is likely a consequence of using different annotation software (GLEAN versus Augustus). Fusing the two annotations produces a set of 10,773 CDSs (8,087 from F98.1 and 2,686 from DS831).

Accession number(s).

This whole-genome project has been deposited at NCBI GenBank under the accession number MSZU00000000. The version described in this paper is the first version, MSZU01000000.