Novel RNA viruses in oysters revealed by virome

Abstract

Eighteen novel RNA viruses were found in Crassostrea hongkongensis. Phylogenic analysis shows evidence of recombination between major genes of viruses. Picobirnaviruses are ubiquitous and abundant in oysters.

Figure 1

The variety of novel RNA viruses found in oysters. (A) Clustering network of 147 RdRp protein sequences. (B) Clustering network of 99 capsid protein sequences. The networks were visualized using the Fruchterman‐Reingold algorithm in Gephi (version 0.9.2). Dots represent different sequences. Edges indicate that the DIAMOND BLASTP scores between the connected dots were ≥57 (A) and ≥43.5 (B).

Figure 2

Phylogenic analysis shows evidence of recombination between major viral proteins. Phylogenetic trees of RdRp (A) and capsid proteins (B) of oyster‐associated Sobelivirales. The maximum likelihood phylogenetic tree was constructed using IQtree (version 2.1.4) with the sequences. ModelFinder was set as MFP and 1000 ultrafast bootstrap replicates were used. Bootstrap values >70 are shown. The domains in the genome structure were annotated using the NCBI Conserved Domain Database.

Figure 3

Comparison of the topological structure between the RdRp and capsid phylogenic trees of picornaviruses found in oysters. The trees were constructed using Iqtree (version 2.1.4) based on the RdRp (A) and capsid protein (B) sequences. ModelFinder was set to MFP and 1000 ultrafast bootstrap replicates were used. Bootstrap values >70 are shown.