Nanopore Hybrid Assembly of Biscogniauxia mediterranea Isolated from Quercus cerris Affected by Charcoal Disease in an Endangered Coastal Wood

ABSTRACT Biscogniauxia mediterranea is the causal agent of charcoal disease, affecting oak decline under the trigger of various biotic and abiotic factors, including climate change. Here, we report the genome assembly of an Italian B. mediterranea strain obtained using hybrid sequencing technologies combining long and short reads.

T he causal agent of charcoal disease is the fungal pathogen Biscogniauxia mediterranea. B. mediterranea spends part of its life cycle endophytically in twigs, bark, and leaves and less in the wood until environmental stresses induce rapid colonization of the xylem and cortex, causing the formation of cankers that accelerate the decline of oak, possibly provoking its death (1). B. mediterranea is widespread in Italy, as well as in other Mediterranean Basin countries and in central-western Europe (2). The Palo Laziale Wood (Latium, Italy) has suffered a serious oak decline in the last decades (1), caused by various critical factors such as the abandonment of sylvicultural practices, the rise in temperatures, the increase in edaphic salinity due to the depositions of sea winds, and the changing precipitation regimes; these factors are correlated with climate change and have triggered widespread B. mediterranea infection (3,4). Here, we report the genome assembly of an Italian B. mediterranea strain obtained by combining hybrid data derived from long-and short-read sequencing approaches.
B. mediterranea strain FBL658 was isolated from stomata present on oak trunks sampled in Palo Laziale Wood. A monosporic culture was selected and plated on oatmeal agar (HiMedia). The plates were maintained in the dark at 25°C for 1 week. DNA was extracted from 30 mg of freeze-dried mycelium grown in potato dextrose broth (HiMedia) in the dark at 250 rpm for 5 days. Genomic DNA (gDNA) was extracted from B. mediterranea using the cetyltrimethylammonium bromide (CTAB) method (5).
Data availability. This whole-genome assembly project has been deposited at the NCBI under BioProject accession number PRJNA727443; the Nanopore and DNBseq reads are deposited at the SRA database under accession numbers SRR14425514 and SRR14425513, respectively. This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number JAGXTR000000000. The version described in this paper is version JAGXTR010000000.

ACKNOWLEDGMENTS
This work was supported by the EU funding program LIFE PRIMED-Restoration, Management and Valorisation of Priority Habitats of Mediterranean Coastal Areas (LIFE17 NAT/GR/000511).
The strain was deposited in the fungal collection of Anna Maria Persiani (Department of Environmental Biology, Sapienza University of Rome).