Draft Genome Sequence of the Fungus Associated with Oak Wilt Mortality in South Korea, Raffaelea quercus-mongolicae KACC44405

ABSTRACT

The fungus Raffaelea quercus-mongolicae is the causal agent of Korean oak wilt, a disease associated with mass mortality of oak trees (e.g., Quercus spp.). The fungus is vectored and dispersed by the ambrosia beetle, Platypus koryoensis. Here, we present the 27.0-Mb draft genome sequence of R. quercus-mongolicae strain KACC44405.

GENOME ANNOUNCEMENT

Oak wilt disease has emerged rapidly across South Korea since 2004, and the putative causal agent of the disease has been identified as a filamentous ascomycetous fungus, Raffaelea quercus-mongolicae (1). This fungus has a symbiotic relationship with an insect vector, Platypus koryoensis (ambrosia beetle), which attacks oak trees (e.g., Quercus mongolica, Q. aliena, and Q. serrata) (2). After the fungus has been vectored into a beetle gallery of an oak tree, it can cause sapwood discoloration and disrupt sap flow in the host. Thus, R. quercus-mongolicae is considered to be the putative cause of wilt and blight symptoms that subsequently cause tree mortality. Previously, to evaluate the cause of mass mortality of oak trees in South Korea, the virulence of R. quercus-mongolicae on oak trees was assessed; however, these previous pathogenicity tests were inconclusive (3). Molecular biological investigations on the pathogenicity of R. quercus-mongolicae have not been addressed, largely due to the need for genomic information. Here, we present the draft genome sequence to assist further genome-based analyses of R. quercus-mongolicae and its host interactions.

The isolate of R. quercus-mongolicae (KACC44405) originated from discolored sapwood of Platypus koryoensis-infested Q. mongolica that was displaying pronounced symptoms of oak wilt (collected by K. H. Kim at Gwangreung Experimental Forest, Pocheon, South Korea, 12 May 2005). The fungal isolate was cultured on potato dextrose agar, and genomic DNA was extracted using a standard phenol-chloroform method.

The draft genome was sequenced with the Illumina NextSeq and MiSeq systems for paired-end reads and the HiSeq 2000 system for mate pair reads. The short reads were assembled with the A5-miseq pipeline (4), and gaps were filled with the GapCloser module in SOAPdenovo2 (5). The estimated genome size of R. quercus-mongolicae was 27,005,990 bp with a 54.25% GC content, which was assembled to 43 scaffolds with an N₅₀ of 2.2 Mb obtained from 200 contigs. The protein-coding genes were predicted using the MAKER genome annotation pipeline (6). A total of 8,155 coding genes were predicted, and 147 genes were identified as tRNA genes by tRNAscan-SE software (7). Using the previously developed gene family prediction pipelines, six gene families that possibly contribute major roles in the physiology and pathogenicity of R. quercus-mongolicae were annotated (8–12). The numbers of transcription factor and cytochrome P450 coding genes were 425 and 52, respectively. The genome had 625 secreted protein-coding genes, and, of those, 118 were small secreted polypeptides of less than 300 amino acids. Plant cell wall-degrading enzymes were encoded by 28 genes, in addition to 11 genes encoding laccases and 14 genes encoding peroxidases that may be involved in lignin degradation. Also, 13 polyketide synthase and 18 nonribosomal peptide synthetase genes were identified with antiSMASH software (13). The genome sequence of R. quercus-mongolicae strain KACC44405, along with other Raffaelea spp., will provide valuable resources for comparative genomic analyses and identifying genes that contribute to a potential pathogenic relationship between the fungus and host, as well as a potential symbiotic relationship between the fungus and insect vector.

Accession number(s).

This genome sequence has been deposited in GenBank under the accession no. NIPS00000000.