Program Book - 27th Fungal Genetics Conference

FULL POSTER SESSION ABSTRACTS286. Genome sequencing, assembly and annotation of three marine fungal isolates using different next generation DNA sequencing methods forpharmaceutically important secondary metabolites. Abhishek Kumar, Frank Kempken. Dept. of Genetics & Mol. Bio, Institute of Botany, CAU Kiel, KIEL,SH, Germany.Next-generation sequencing (NGS) techniques have changed the facets of genomics and its application. Until now marine fungal isolated are neglected infungal genetics, largely due to fact that fungi have enormous diversity on land itself. We aimed to explore marine fungal isolates and their encodingnatural products as drugs against cancer under the EU-funded project marine fungi (www.marinefungi.eu). We have taken three marine isolates namely,Scopulariopsis brevicaulis, Pestalotiopsis sp. and Calcarisporium sp. We have established the genomic sequences from these marine isolates of using threedifferent next-generation sequencing methods (Roche 454, Illumina and ion-torrent) and predicted genes are presently in process of validation usingillumina based RNA-seq. We are also comparing wild type phenotypes with higher -yielding mutants of these fungi with special interest on specific naturalcompound. The assembled genome of Scopulariopsis brevicaulis is ~32 Mb in size with N50 equals to 88 kb and 935 contigs containing 16298 genes withaverage intron length equals to 129.4. During annotation process, we were able to annotate 9340 genes (57.31 %) while 6958 genes (43.69 %) remainednon-annotated in Scopulariopsis brevicaulis genome. This genome has 17 genes encoding for non-ribosomal peptide synthetases (NRPSs), 18 polyketidesynthases (PKSs) and one gene is hybrid NRPS-PKS. Similarly, the genome size for Pestalotiopsis sp. is~46 Mb with N50 equals to 71.9 kb and 4186 contigscontaining 23492 genes, which is surprisingly very high for a fungus. The average intron length and the average intron per gene are 126.8 and 2.2,respectively. During annotation process, we annotated 60% genes of Pestalotiopsis genome with 44 NRPSs, 62 PKSs and 7 hybrid NRPS-PKS genes. Theassembled genome size of as Calcariosporium sp. is about 35 Mb genome with N50 equals to 91.9 kb and 2464 contigs containing 15459 genes. Thepercentage GC% for this genome is 50.7%. The average intron length and the average intron per gene are 121 and 2.1, respectively. During annotationprocess, we annotated 72% genes, while 28% genes remained non-annotated for Calcariosporium genome with 52 NRPSs, 66 PKSs and 7 hybrid NRPS-PKSgenes.287. From Shiitake genomics to comparative mushroom genomics: Mushroomics. Hoi Shan Kwan, Chun Hang Au, Man Chun Wong, Jing Qin, Yung YungLee, Kin Sing Wong, Lei Li, Qianli Huang, Wenyan Nong, Man Kit Cheung, Jinhui Chang, Xuanjin Cheng. School of Life Sciences, The Chinese University ofHong Kong, Hong Kong, China.The era of mushroom "omics" has come amongst the mushrooming of "omics" in all life science fields. I propose to name “omics” of mushrooms"Mushroomics". My laboratory has been working on the genomics and transcriptomics of the wood-degrading fungus Lentinula edodes, Shiitakemushroom, one of the most important cultivated mushrooms. We sequenced the genome of the monokaryon L54A using Roche 454 and ABI SOLiDsequencing platforms. Over 13,000 protein-coding genes were predicted. We constructed a high-density genetic linkage map that was useful to linkscaffolds into super-scaffolds. The L. edodes genome assembly revealed a genome size of about 40 Mb. We performed RNA-Seq of multiple stages of L.edodes. For comparison, we also analyzed the transcription profiles of different stages of the model mushroom Coprinopsis cinerea using NimbleGenmicroarrays. Genes differentially expressed during fruiting body initiation and development in these mushrooms were identified. We conductedcomparative analyses on publicly available genome sequences of basidiomycetes and ascomycetes, and revealed genes expanded in genomes ofmushroom-forming fungi. The expanded genes included specific types of regulators, ubiquitin ligases, protein-binding proteins, protein kinases, andtranscription factors. In particular, F-box and paracaspase domain proteins were significantly expanded. The cataloging of the unique composition of plantbiomass-degrading enzymes in L. edodes genome revealed lignin-degrading laccases and manganese peroxidases, and multiple polysaccharide-degradingenzyme families, such as glycoside hydrolase families that target beta-glucans and pectin. We compiled the genome sequences of L. edodes and otherfungi into an Ensembl-based platform, equipped with a battery of genomic analysis tools, for comparative mushroom genomic analysis. Our works havegenerated rich resources for the analysis of genomics and transcriptomics of mushroom-forming fungi. Our analysis also provided insights into themolecular mechanisms of fruiting body development in fungi and the evolution of fungal complex multicellularity. Indeed, our works showed that the eraof "Mushroomics" has arrived.288. Comparative genomics of Ceratocystis polonica and Ophiostoma bicolor, two bark beetle-associated pathogenic fungi. Ljerka Lah 1 , Tom Hsiang 2 ,Colette Breuil 3 , Joerg Bohlmann 4 , Radovan Komel 1,5 . 1) Lab. for Mol. Biol, National Inst. of Chemistry, Ljubjana, Slovenia; 2) School of EnvironmentalSciences, University of Guelph, Guelph, Canada; 3) Dept. of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, Canada; 4)Michael Smith Laboratories, University of British Columbia, Vancouver, Canada; 5) Institute of Biochemistry, Faculty of Medicine, University of Ljubljana,Slovenia.Outbreaks of bark beetles and their pathogenic fungal associates are responsible for killing conifer trees and destroying forests worldwide. For example,in British Columbia, the mountain pine beetle and its major associated fungal pathogen Grosmannia clavigera have destroyed over 17 million hectares ofpine forests. The sequenced genome of G. clavigera has provided insight into fungal mechanisms involved in resistance to conifer defense compounds, andinto population genomics of this species. In Europe, where outbreaks of the European spruce bark beetle (Ips typographus) threaten Norway spruce (Piceaabies), genomic resources are lacking for pathogenic fungal associates, Ceratocystis polonica and Ophiostoma bicolor. The aim of our work is to createthese resources and to compare the genomes of these species with the annotated G. clavigera genome. The sizes of C. polonica and O. bicolor genomes,sequenced using Illumina and assembled using Abyss ver. 1.3.4, are 34.7 and 27 Mb, respectively. We identified (with Augustus ver. 2.6.1) and functionallyannotated 6405 genes in C. polonica and 7746 in O. bicolor. We report results from preliminary analyses on gene family evolution, and on genes that codefor enzymes important in eliminating and modifying conifer defense compounds, and those involved in specialized metabolism. The number of genescoding for ABC-transporters is approximately the same in all three species, while G. clavigera has more cytochrome P450 genes, polyketide synthases andribosomal peptide synthases than either European bark beetle associate. Our results lead us to hypothesize that despite the fact that these species occupyapparently similar ecological niches, there are differences in their metabolism of host defense compounds and specialized metabolism.289. The largest fungal mitochondrial genome of a basidiomycete contains signs of genetic flexibility and recombination events. Taina K. Lundell 1 , HeikkiSalavirta 1 , Ilona Oksanen 1 , Jaana Kuuskeri 1 , Miia Mäkelä 1 , Pia Laine 2 , Lars Paulin 2 . 1) Microbiology and Biotechnology, Department of Food andEnvironmental Sciences, Viikki Campus, University of Helsinki, FI-00014 Helsinki, Finland; 2) Institute of Biotechnology, DNA Sequencing and GenomicsLaboratory, Viikki Campus, University of Helsinki, FI-00014 Helsinki, Finland.Background and results. As the first part of de novo genome sequencing of the biotechnologically important, wood-decaying enzyme producing whiterotBasidiomycota species Phlebia radiata, we first assembled and gene annotated its mitochondrial genome (mtDNA) using 454 sequencing. The P.radiata mtDNA of 157 kb in size is the largest mitochondrial genome among fungi sequenced and characterized so far. The genome assembled as a singlecircular dsDNA molecule containing over 100 open reading frames. However, almost 80% of the mt genome is comprised of non-coding, intergenic andintronic sequence regions. Genes for mt SSU and LSU rRNA, 28 tRNAs, and fifteen genes encoding the conserved protein subunits in the mitochondrial27th Fungal Genetics Conference | 191