The draft genome sequence of the ascomycete fungus Penicillium subrubescens reveals a highly enriched content of plant biomass related CAZymes compared to related fungi
Résumé
Here we report the genome sequence of the ascomycete saprobic fungus Penicillium subrubescens FBCC1632/CBS132785 isolated from a Jerusalem artichoke field in Finland. The 39.75 Mb genome containing 14,188 gene models is highly similar for that reported for other Penicillitun species, but contains a significantly higher number of putative carbohydrate active enzyme (CAZyme) encoding genes. Here we report the genome sequence of the ascomycete saprobic fungus Penicillium subrubescens FBCC1632/CBS132785 isolated from a Jerusalem artichoke field in Finland. The 39.75 Mb genome containing 14,188 gene models is highly similar for that reported for other Penicillium species, but contains a significantly higher number of putative carbohydrate active enzyme (CAZyme) encoding genes.Penicillium subrubescens is a saprobic species and the strain sequenced here, FBCC1632/CBS132785, was originally isolated from soil of a Jerusalem artichoke field in Helsinki, Finland. It has been placed in section Lanata-diversicata of the genus Penicillium, which has several distinctive morphological features ( Mansouri et al., 2013). The species has a high potential for the production of plant biomass degrading enzyme mixtures (Mäkelä et al., 2016).The fungus was cultivated on complete medium (de Vries et al., 2004) and genomic DNA from 3-day old mycelium was extracted using CTAB-based extraction buffer (Hildén et al., 2005). The RNA was extracted using TRIzol reagent (Invitrogen/Thermo Fischer Scientific, Carlsbad, CA) and purified by NucleoSpin RNAII (Macherey-Nagel, Düren, Germany) from 3-day old cultures grown on wheat bran and sugar beet pulp in minimal medium (de Vries et al., 2004). Concentration and quality of the DNA were determined using the Life Technology Qubit and 0.6% agarose gel, respectively while the RNA samples quality was checked using Fragment Analyser (Advanced Analytical Technologies). Genome and transcriptome sequencing were performed in GenomeScan facilities. The DNA was fragmented using the Covaris Focused-ultrasonicator. NEBNext® Ultra DNA Library Prep kit for Illumina (cat# NEB #E7370S/L) and NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7420S/L) were used according to manual for library preparation. Quality and yield after sample preparation was measured with Lab-on-a-Chip analysis or Fragment Analyzer. Clustering and DNA sequencing using the Illumina cBot and HiSeq 2500 was performed according to manufacturer’s protocols using concentration of 8.0 pM of DNA and 16.0 pM of cDNA, standard Illumina primers and HiSeq control software HCS v2.2.58. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA v1.18.64 and Bcl2fastq v1.8.4. Adapter trimming and quality filtering were performed using GenomeScan in-house tool FASTQFilter v2.05. Briefly: adapter sequences were removed from the read. Reads were then filtered and clipped: bases with phred scores below Q22 were removed and their reads were split; reads shorter than 36 bp were removed. Abyss v1.3.7 (Simpson et al., 2009) was employed for the assembly, using k-mer length of 64. Scaffolds shorter than 500 bp were removed. The 39.75 Mb genome was obtained by assembly of 776 contigs (Table 1). The GC content was 49.21% as assessed by QUAST (Gurevich et al., 2013). The HMM-based algorithm Glimmer (version 3.02) (Majoros et al., 2004) was trained for gene finding using the genome of Penicillium oxalicum ( Liu et al., 2013). Furthermore, an evidence-based method of gene finding was performed using the CodingQuarry (Testa et al., 2015) software tool and the mapped mRNA-Seq reads. The output of both methods was combined into a single gene model of 14,188 genes.
