Draft Genome Sequence and Annotation of the Lichen- Forming Fungus Arthonia radiata Ellie E. Armstrong, a Stefan Prost, a,b Damien Ertz, c,d Martin Westberg, e Andreas Frisch, f Mika Bendiksby f a Department of Biology, Stanford University, Stanford, California, USA b Department of Integrative Biology, University of California, Berkeley, California, USA c Department of Research, Botanic Garden Meise, Meise, Belgium d Fédération Wallonie-Bruxelles, Direction Générale de l’Enseignement non Obligatoire et de la Recherche Scientifique, Brussels, Belgium e Museum of Evolution, Uppsala University, Uppsala, Sweden f NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway ABSTRACT We report here the draft de novo genome assembly, transcriptome as- sembly, and annotation of the lichen-forming fungus Arthonia radiata (Pers.) Ach., the type species for Arthoniomycetes, a class of lichen-forming, lichenicolous, and saprobic Ascomycota. The genome was assembled using overlapping paired-end and mate pair libraries and sequenced on an Illumina HiSeq 2500 instrument. H ere, we report the draft de novo genome assembly, transcriptome assembly, and annotation of Arthonia radiata (Pers.) Ach. (strain EZ20314). This lichen-forming fungus is the type species of Arthonia (Ach.) Ach., on which the Arthoniaceae Rchb. (Arthoniales, Arthoniomycetes), a large family of about 800 lichen-forming, licheni- colous, and saprobic Ascomycota, are based. Arthonia radiata is a common and polymorphic epiphyte on mainly smooth-barked deciduous trees throughout the Holarctic. It has also been reported in Africa and New Zealand (1). It has played a key role in recent efforts to develop a new classification of the Arthoniomycetes based on phylogenetic principles (2–4). The genome was assembled using overlapping paired-end (PE) and mate pair (MP) libraries (with an average insert size of 5 to 8 kb) and sequenced with Illumina HiSeq 2500 v4 chemistry (2  125 bp). Assemblies were created using AllPaths-LG (5) and SPAdes (6). The best assembly was chosen based on assembly continuity and Bench- marking Universal Single-Copy Orthologs 2 (BUSCO2) (7) scores (using OrthoDB v9 data sets for fungi and ascomycetes, downloaded from http://busco.ezlab.org). AllPaths-LG provided the best assembly, with a contig N 50 value of 1.2 Mb (46 contigs), a scaffold N 50 value of 2.25 Mb (17 scaffolds), and a total sequence length of 33.5 Mb. Of all BUSCO2 genes, 99% for fungi (out of 290, none of which show duplication) and 94.8% for ascomycetes (out of 1,315, none of which show duplication) were present as complete genes in the assembly. This indicates the high quality of the presented genome. Transcriptome assembly was performed using Trinity (8) and a combination of Hierarchical Indexing for Spliced Alignment of Transcripts v2 (HISAT2) (9) and StringTie (10). The best assembly was chosen based on assembly statistics and BUSCO2 scores. We further used different cleaning filters for read assembly with Trinity. First, we ran Trinity on the raw reads. Then, we filtered and removed only adapter sequences and low-quality bases. Last, we performed a full filtering for contaminants, adapter se- quences, and low-quality bases. The combination of AdapterRemoval (11) and Trinity resulted in the best transcriptome assembly, with 27,220 contigs and an N 50 value of 6.8 kb. BUSCO2 scores indicated the presence of 94% complete and 5.5% fragmented Received 19 March 2018 Accepted 20 March 2018 Published 5 April 2018 Citation Armstrong EE, Prost S, Ertz D, Westberg M, Frisch A, Bendiksby M. 2018. Draft genome sequence and annotation of the lichen-forming fungus Arthonia radiata. Genome Announc 6:e00281-18. https://doi .org/10.1128/genomeA.00281-18. Copyright © 2018 Armstrong et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Mika Bendiksby, mika.bendiksby@ntnu.no. E.E.A. and S.P. contributed equally to this work. EUKARYOTES crossm Volume 6 Issue 14 e00281-18 genomea.asm.org 1