Conserved Untranslated Regions of Multipartite Viruses: Natural Markers of Novel Viral Genomic Components and Tags of Viral Evolution

Abstract

Viruses with split genomes are categorized as being either segmented or multipartite according to whether their genomic segments occur in single or different virions. Some complexity will exist, in that inherited “core” vital segments viruses may renew the others once host and environmental alterations keep driving viral evolution. Despite this uncertainty, empirical observations have been made across the split genomes in the untranslated regions (UTRs) on the short or long stretches of conserved or identical sequences. In this study, we describe a methodology that combines RNA and small RNA sequencing, conventional BLASTx, and iterative BLASTn of UTRs to detect viral genomic components even if they encode orphan genes (ORFans). Within the phylum Kitrinoviricota, novel putative multipartite viruses and viral genomic components were annotated using data obtained from our sampling or publicly available sources. The novel viruses, as extensions or intermediate nodes, enriched the information of the evolutionary networks. Furthermore, the diversity of novel genomic components emphasized the evolutionary roles of reassortment and recombination, as well as genetic deletion, strongly supporting the genomic complexity. These data also suggest insufficient knowledge of these genomic components for categorizing some extant viral taxa. The relative conservation of UTRs at the genome level may explain the relationships between monopartite and multipartite viruses and how the multipartite viruses can have a life strategy involving multiple host cells.

A Novel Lineage of Cile-Like Viruses Discloses the Phylogenetic Continuum Across the Family Kitaviridae

“…When the 3′-termini of the cileviruses CiLV-C, CiLV-C2, and PfGSV were included in the alignment, the presence of highly conserved nucleotide sequences in all these viruses became evident, likely denoting the putative functional role of these sequences as described in other viruses ( Dreher, 1999 ; Liu et al, 2020 ; Rasekhian et al, 2021 ). The implementation of the UTR-backed iterative BLASTN approach ( Zhang et al, 2022 ) using the 3′-terminus conserved nucleotide sequences of SvRSV, LigCSV, and LigLV, resulted in the recovery of contigs corresponding to the RNA1 and RNA2 segments already known, and new putative genomic segments were not identified.…”

“…Viral segments of SvRSV, LigCSV, LigLV, and those of typical cileviruses were aligned using MAFTT ( Katoh and Standley, 2013 ) and visualized using the Jalview program ( Procter et al, 2021 ). Sequences comprising 90–120 nts of the highly conserved 3′ untranslated regions (UTR) of SvRSV, LigCSV, and LigLV were used to search for the presence of putative non-detected viral segments in the HTS-contigs libraries using the UTR-backed iterative BLASTN approach ( Zhang et al, 2022 ). Previously, BLASTN databases were built from the HTS-contig libraries of each sample using Geneious software package v 11.1.4 ( Kearse et al, 2012 ).…”

Identification of Seven Additional Genome Segments of Grapevine-Associated Jivivirus 1

“…The four grapevine samples analyzed in this fashion showed evidence of GaJV-1 infection, with two of them, i31 and i33, showing the most reads for GaJV-1 genomic RNAs (respectively, 1.6 and 1.5% of total reads). Further analysis was therefore focused on the contigs assembled for the i31 sample, allowing the identification, as reported independently [ 17 , 18 ], of homologies in the 5′ and 3′ non-coding regions (NCRs) of the contigs for the three GaJV-1 genomic RNAs. These conserved 5′ and 3′ NCRs were then used in BLASTN searches of all the contigs assembled from these two samples.…”

“…The notion that the genomes of jiviviruses may contain additional genome segments of the three previously identified was recently proposed on the basis of a datamining study investigating conserved genome ends [ 18 ]. However, this study only identified one additional segment for GaJV-1 and two additional segments in two viruses identified from pecan datasets and that are presumably identical to the CaJV-1 and CaJV-2 viruses reported here.…”

“…This rationale was reinforced by the identification in the same datasets of a second virus with similar genomic organization, which was consequently named grapevine-associated jivivirus 2 (GaJV-2). More recently, the interest of using the conservation of terminal non-coding sequences to identify genome segments of poorly known viruses with divided genomes led to the identification of several potential other jiviviruses from public transcriptome shotgun assembly data (TSA) from several plant species including pecan ( Carya illinoinensis ), Sarcandra glabra , Pinus flexilis and Picea glauca [ 18 ]. This study also potentially identified two additional genome segments of GaJV-1 and GaJV-2 and up to three or four additional segments for the Carya jiviviruses and the citrus jivivirus, respectively [ 18 ].…”