A planarian nidovirus expands the limits of RNA genome size

Amir Saberi; Anastasia A. Gulyaeva; John L. Brubacher; Phillip A. Newmark; Alexander E. Gorbalenya

Identification of a large RNA virus from planarians. To examine whether this limit applies beyond the currently recognized ~3000 RNA virus species that infect just hundreds of host species, further sampling of virus diversity is required. To this end, we analyzed de novo transcriptomes of the planarian Schmidtea mediterranea (24) , in which viruses remain virtually unknown, and which exists as two reproductively distinct strains: sexuals that reproduce as simultaneous hermaphrodites and asexuals that reproduce via transverse fission (25) . We determined the complete genome sequence of a putative nidovirus corresponding to one particularly large contig (SI Text, Table S2 , Fig. S1 ). Excluding the polyadenylated tail, the fully assembled genome contains 41,103 nucleotides (nt) and encodes a single 40,671-nt ORF that is flanked by a 128-nt 5'-UTR and a 304-nt 3'-UTR (Fig. 1B,C) . The presence of this RNA in vivo was confirmed by RT-PCR amplification of overlapping regions of 4-7 kb, 5'-RACE, and multiple EST clones (Fig. S1) (26) . These sequences could not be amplified from S. mediterranea genomic DNA, nor could they be found in the genome (27) ; thus, they appear to derive from an exogenous source. Based on several criteria (see below), we assigned this RNA sequence to the genome of a virus we dubbed Planarian Secretory Cell Nidovirus (PSCNV). PSCNV circulates in both sexual and asexual host strains: analysis of RNA-seq data from three laboratories revealed its very low (<0.1%), albeit predominantly non-synonymous variation (SI Text, Tables S3,4). Analysis of Planaria torva transcriptome identified three contigs of the cumulative ~9400 nt size, whose regions displayed from 25% to 48% aa identity with PSCNV, indicative of at least one additional putative nidovirus (SI Text, Fig. S2 ) (28) . author/funder. All rights reserved. No reuse allowed without permission.