Cameroonian fruit bats harbor divergent viruses, including rotavirus H, bastroviruses, and picobirnaviruses using an alternative genetic code

Yinda, Claude Kwe; Ghogomu, Stephen Mbigha; Conceição-Neto, Nádia; Beller, Leen; Deboutte, Ward; Vanhulle, Emiel; Maes, Piet; Van Ranst, Marc; Matthijnssens, Jelle

For identification of bacteriophages, scaffolds >1 kb were classified using VirSorter (decontamination mode; Roux et al. 2015) . Only scaffolds assigned to Categories 1 and 2 were considered bacteriophage contigs and were filtered for redundancy at 95% nt identity over 70% of the length using Cluster Genomes (Dios et al. 2014) . Then, trimmed reads from each bat sample were mapped using Bowtie 2 (Langmead and Salzberg 2012) to the bacteriophage contigs and the generated BAM files were filtered to remove reads that aligned at <95% identity using BamM (http:// ecogenomics.github.io/BamM/). Abundance tables were obtained and normalized for total number of reads. For the richness comparison, Mann-Whitney tests were used and for the clustering, an Adonis test was performed. All downstream analysis were done in R Core Team (2016) using the vegan package (Oksanen et al. 2017) . Furthermore, to identify the potential corresponding bacterial species of the bacteriophage contigs identified by VirSorter, a database of this contigs was made to which a nucleotide BLASTn search (100% identity without gaps) was performed using a fasta file of CRISPR sequences (Grissa et al. 2007 ) as query.