Neoparamoeba perurans, the aetiological agent of amoebic gill disease (AGD), remains a persistent threat to Atlantic salmon mariculture operations worldwide. The development of improved methods of AGD control has been hindered by the limited understanding of the biology of N. perurans and the mechanisms by which amoebic gill disease pathogenesis is facilitated. An RNAseq approach was employed using an illumina sequencing platform to compare wild type (virulent) and clonal (avirulent) N. perurans isolates to investigate potential virulence factors associated with AGD pathogenesis.</p><p>Experimental design: transcriptome data were generated from pooled isolates of gill derived wild type N. perurans (n =3) and in vitro cultured N. perurans (n =3).