Libraries were barcoded with Bioo Scientific adaptors so they could be pooled for sequencing.
Samples to be pooled for sequencing were mixed in equal quantities and concentrated using QIAquick PCR purification kit (Qiagen) before sequencing on the GS FLX Titanium sequencer (Agowa GmBH, Berlin, Germany).
To facilitate quantitative sampling of the viral population, cDNA generation from viral RNA and subsequent PCR reactions used high template volume, low cycle numbers, and multiple replicates that were pooled for sequencing (Fig. S5).
Four accessions in each RAD_P library and two in each RAD_B library were pooled for sequencing.
The two fractions were pooled for sequencing paired end 100 bp using Illumina HiSeq2000.
Equivalent concentrations of the RNAs from the tissues of the 17 fish were pooled for sequencing.
Afterwards second strand synthesis was performed, adapters were ligated and the 7 tagged-libraries were pooled for sequencing.
When possible, equal molar amount of barcoded PCR products (100ng) from each sample was pooled for sequencing.
Samples from the same organ of different conspecific individuals were pooled for sequencing (MID1 = leaves, MID2 = stems, MID3 = roots).
After quantification and sizing, libraries were pooled for sequencing on a MiSeq (pooled library input at 10 pM) on a 300/300 paired end run (Illumina, San Diego, CA, United States).
