viral metagenome Genome sequencing and assembly

The diversity of RNA viruses in Earths oceans remains largely unexplored. Analysis of the RNA metavirome from 10 liters of seawater from Yangshan harbor near Shanghai identified over 4,500 distinct RNA viruses, nearly doubling the RNA virus diversity previously characterized from all sources. Phylogenomic analysis of these sequences supports the previously establishes five-branch gross structure of the RNA virus evolutionary tree but also resulted in the discovery of several major clades, roughly, at the taxonomic ranks of class, order and family. The largest and most remarkable of these new groups is the 719 member-strong Yangshan virus assemblage that consists of viruses with a simple genome structure, typically encoding only RNA-dependent RNA polymerase (RdRP), capping enzyme, and capsid protein, and is the sister group of the expansive Alphavirus supergroup. A distinct feature of the Yangshan virus assemblage is domain permutation in the RdRP that independently occurred in several clades within this group. Another previously unknown clade appears to share ancestry with the potyviruses, the largest known family of plant viruses. In addition, the Aquatic picorna-like viruses-Marnaviridae clade was greatly expanded, with over 800 new viruses identified. The metavirome contains several RdRP-linked protein domains that have not been previously detected in any RNA viruses, such as the SUMO ubiquitin-like protein, phospholipase A2 and PrsW family protease. Multiple viruses utilize alternative genetic codes implying protist (especially ciliate) hosts. The results of this work indicate that the global RNA virome is vast and enormously diverse. However, phylogenetic analysis of the RdRPs shows that the majority of the discovered viruses fall into previously identified major branches suggesting that the megataxa of RNA viruses are already known. PRJNA610033 is the DNA data from Yangshan metavirome; PRJNA605028 is the RNA data.