Draft genome of the brown-rot fungus Fomitopsis pinicola GR9-4

Basidiomycete brown-rot fungi have a huge importance for wood decomposition and thus the global carbon cycle. Here, we present the genome sequence of Fomitopsis pinicola GR9-4 which represent different F. pinicola clade than the previously sequenced North American isolate FP-58527 SS1. The genome was sequenced by using a paired-end sequence library of Illumina and a 2.5k and 5k mate-pair library (ABI SOLiD). The final assembly adds up to a size of 45 Mb (including gaps between contigs), with a GC-content of 56%. The gene prediction resulted in 13,888 gene models. The genome sequence will be used as a basis for understanding population genomics, genome-wide association studies and wood decay mechanisms of this brown-rot fungus.


a b s t r a c t
Basidiomycete brown-rot fungi have a huge importance for wood decomposition and thus the global carbon cycle. Here, we present the genome sequence of Fomitopsis pinicola GR9-4 which represent different F. pinicola clade than the previously sequenced North American isolate FP-58527 SS1. The genome was sequenced by using a paired-end sequence library of Illumina and a 2.5k and 5k mate-pair library (ABI SOLiD). The final assembly adds up to a size of 45 Mb (including gaps between contigs), with a GC-content of 56%. The gene prediction resulted in 13,888 gene models. The genome sequence will be used as a basis for understanding population genomics, genome-wide association studies and wood decay mechanisms of this brown-rot fungus.
& Value of the data F. pinicola plays an important role in the carbon cycle of conifer forests as the species is one of the most prominent wood decayers in forest ecosystems, but the biology of this fungus is poorly studied at the population level.
Draft genome assembly of F. pinicola will increase the knowledge of the biochemical process of wood degradation and create an opportunity for comparative studies with other brown-rot fungi.

Data
We present the draft genome assembly and gene prediction of the fungus Fomitopsis pinicola, an important and ubiquitous brown-rot fungus of boreal forests causing a cubical brown-rot in both softwood and hardwood [1]. The broad host range and phenotypic differences with respect to color and form, already observed by Fries [2], led to speculation that cryptic species might be present. Early findings based on crossings of single spore isolates of F. pinicola confirmed intersterility among lineages within North America and between North America and Europe [3]. Recently a multi-locus phylogenetic study confirmed that F. pinicola is a species complex encompassed of four well-supported phylogenetic species, three in North America and one in Eurasia [4]. The genome of F. pinicola GR9-4 was sequenced in order to provide a basis for population genomics, transcriptomics and genome-wide association studies. The final assembly contained 1920 contigs larger than 1000 bp (an N 50 contig length of 69,460 bp a N 80 contig length of 18,102 bp), with a largest length of 788,230 bp, which were assembled into 1613 scaffolds larger than 1000 bp in size and the maximum length being of 1,100,126 bp. In total, the genome sequence adds up to a size of 45 Mb (including gaps between contigs), with a GC-content of 56%. The sequencing read coverage depth of the total assembly was 127-fold. The gene prediction resulted in 13,888 gene models ( Table 2). The draft genome assembly information of F. pinicola compares well to other sequenced genomes within the Agarimycotina [5]. Genes with predicted functions for plant polysaccharide (cellulose, hemicellulose and pectin) degradation involved in the breakdown or modification of glycoconjugates were identified in the genome. We found 403 carbohydrate-active enzymes (CAZymes) using the pipeline dbCAN [13] with E-values below 1e-4. These were divided into 209 Glycoside Hydrolases (GHs), 81 Glycosyl Transferases (GTs), 5 Polysaccharide Lyases (PLs) and 108 Carbohydrate Esterases (CEs). In addition to the CAZymes, 51 redox enzymes that act in conjunction with CAZymes (AAs) and 48 Carbohydrate-Binding Modules (CBMs) were found. The CAZymes-coding genes profiles for F. pinicola GR9-4 was similar to the profile of the North American isolate F. pinicola FP-58527 SS1, but their secondary metabolite profiles differed substantially as analyzed by the antiSMASH 3.0 genome mining of biosynthetic gene clusters [14]. The next generation sequencing data is available from the NCBI under GenBank assembly accession GCA_001931775.1. We also applied a maximum likelihood analysis (Fig. 1) to infer the phylogeny of the three nuclear genes ITS, EF1A and RPB2 respectively from a  representative collection of isolates within the species complex, using Daedalea quercina as an outgroup [3,5,6], analyzed in MEGA 7 [7]. This analysis was performed in order to reveal the phylogenetic position of the two sequenced F. pinicola genomes within the four well supported clades; European clade-C which is distinctly separated from North American clades-A, B & D. Our sequenced isolate, GR9-4, belongs to F. pinicola clade C while the previously sequenced North American isolate, F. pinicola FP-58527 SS1 belongs to the distinctly different F. pinicola clade D. This difference will permit future estimations of positive selection to the divergence between species. Furthermore, information about the draft genome sequence of F. pinicola GR9-4 will be helpful for future studies in population genomics and genome-wide association in order to reveal the wood decay mechanisms of this brown-rot fungus.

Library
Strategy: Whole-genome DNA sequencing. Library: Paired-end 100 bp reads and Mate-pair 2.5 kb and 5 kb reads.

Library construction protocol
Basidiospores were restrained on a glass slide placed below living sporocarps for overnight. Serially diluted spores were spread on Hagem-agar petri dishes -sterilized medium containing of 0.5 g each of NH 4 NO 3, KH 2 PO 4 and MgSO 4 ·7H 2 O, 5 g of glucose, 5 g of malt and 10 g of agar in 1 L of deionized water. Three to five days after inoculation, between 1 and 20 single germinated spores were collected under dissecting microscope and cultured on fresh media to produce single monokaryon isolates. Monokaryon isolates were cultured on liquid Hagem medium for 3 weeks. DNA was extracted by standard CTAB protocol. 3 μg DNA was used for sequencing on the Illumina platform and 5 μg was used for mate-pair library from ABI SOLiD (SNP&SEQ Technology Platform, Uppsala University). The raw sequencing data produced is shown in Table 1.