Virus genome sequences

The Tasmanian devil faecal virome was characterised using both metagenomics and meta-transcriptomics. For metagenomics, sequencing libraries were constructed using the Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturers instructions with the following modifications: (i) the tagmentation time was reduced to 4 min to increase fragment size, (ii) input DNA was increased to 1.2 ng/ l-1 and (iii) reagent quantities were halved to further increase the fragment size. Paired-end (100 bp) sequencing of each library was performed on a Hiseq2500 platform (Illumina).For meta-transcriptomics, the RNA pools were depleted of host and bacteria rRNA using a Ribo-Zero-Gold (Epidemiology) kit (Illumina) before constructing sequencing libraries using a TruSeq total RNA Library Preparation Kit (Illumina). Paired-end (75 bp) sequencing of each library was performed on a NextSeq500 HO platform (Illumina).Sequence reads were de-multiplexed and quality trimmed with Trimmomatic and assembled de novo using Trinity. Genome sequences for each virus was extended by merging related contigs. Gaps in the genome were filled either by mapping the reads against the existing scaffold or by RT-PCR and Sanger sequencing. Putative ORFs in viral genomes were predicted by the Geneious 8.1 software or NCBI ORF finder, and annotated based on their similarity to previous published virus genomes. <br><br>