Computational protocol: Expanding our Understanding of the Seaweed Holobiont: RNA Viruses of the Red Alga Delisea pulchra

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[…] Sequence reads were trimmed and adaptors removed using Trimmomatic V0.32 () and assembled using SPAdes 3.1.1 (). Contigs were compared to the nucleotide sequence database (nt) of the National Centre for Biotechnology Information (NCBI) using blastn to identify contaminating ribosomal sequences. Contigs with an alignment length >75% of the query length and an e-value <10-4 were classified as contaminations and removed by Deconseq 0.4.3 () from the sequence data. Contigs were finally classified into families using blastx and tblastx against the nr and refseq viral database () with an e-value cut-off smaller 10-5. The coverage of each contig was used to get a relative quantitative measure of the viral abundance (Figure ). All partial or complete viral sequences have been submitted to the GenBank database under the accession no. LIKW00000000 (individual a) and LIKX000000000 (individual b). [...] Reference sequences of the RNA-dependent RNA polymerase (RdRp) from different viruses were obtained from NCBI. Multiple alignment of amino acid sequences of the RdRp were constructed using ClustalW implemented in BioEdit 7.2.5 (; ). Phylogenetic trees were calculated based on the conserved regions of the RdRp using Mega 6.0 (). Phylogenetic trees were calculated using the maximum likelihood method with partial position deletion, a Poisson model and 1000 bootstrap replications. RdRp sequences analyzed in the phylogenetic tree have been submitted to GenBank database and can be found under the accession numbers Totivirus: KT455444-KT455461 and Picornaviridae KT455462-KT455464. […]

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