Computational protocol: Analysis of DNAs associated with coconut foliar decay disease implicates a unique single-stranded DNA virus representing a new taxon

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[…] Sequences of cloned CFD DNAs were analysed with DNASTAR Lasergene, (v 12.1) (DNASTAR, Inc., Madison, WI). Consensus sequences of a given CFD DNA component were derived from at least three sequences of cloned DNA. Primary contigs (nodes) assembled by SPAdes from the Illumina reads were further assembled using SeqMan Pro of DNASTAR or Geneious (v 8). Guided assemblies were done with SeqMan Pro, Geneious and CLC Genomics Workbench software (v 8.0). Since SPAdes had produced too many obviously misassembled contigs (only DNA-gamma and DNA-S.1 could be de-novo assembled from the SPAdes produced contigs), the single reads (17,427,262 from the CFD_1988/89 sample and 23,513,930 from the CFD_2013 sample) were directly assembled into contigs using Geneious v10.2.3. In the same way all single reads were mapped against the sequences of the cloned RCA products using Geneious v10.2.3.Unmapped reads (Geneious or CLC) were reassembled, and the resulting contigs were checked by BLAST for known virus sequences and obvious contamination by plant, microbe or human sequences.Phylogenetic analyses were conducted in MEGA7 and SDT v. 1.2. Multialignments were done using Muscle as implemented in Geneious or MEGA7. A maximum likelihood tree (100 bootstrap repetitions) was constructed by PhyML with the GTR + G + I substitution model, chosen after model test in Mega7. BBTV DNA-R (GenBank acc. no. S56276) served to root the tree, and nodes with less than 70% bootstrap support were collapsed using Dendroscope, v3.5.8. The final graphics were done in FigTree v1.4.3. (http://tree.bio.ed.ac.uk/software/figtree/). A recombination analysis was carried out using the recombination detection package RDP4. […]

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