Metagenomics Analysis of the Wheat Virome Identifies Novel Plant and Fungal-Associated Viral Sequences

Abstract

Wheat viruses including wheat streak mosaic virus, Triticum mosaic virus, and barley yellow dwarf virus cost substantial losses in crop yields every year. Although there have been extensive studies conducted on these known wheat viruses, currently, there is limited knowledge about all components of the wheat (Triticum aestivum L.) virome. Here, we determined the composition of the wheat virome through total RNA deep sequencing of field-collected leaf samples. Sequences were de novo assembled after removing the host reads, and BLASTx searches were conducted. In addition to the documented wheat viruses, novel plant and fungal-associated viral sequences were identified. We obtained the full genome sequence of the first umbra-like associated RNA virus tentatively named wheat umbra-like virus in cereals. Moreover, a novel bi-segmented putative virus tentatively named wheat-associated vipovirus sharing low but significant similarity with both plant and fungal-associated viruses was identified. Additionally, a new putative fungal-associated tobamo-like virus and novel putative Mitovirus were discovered in wheat samples. The discovery and characterization of novel viral sequences associated with wheat is important to determine if these putative viruses may pose a threat to the wheat industry or have the potential to be used as new biological control agents for wheat pathogens either as wild-type or recombinant viruses.

Bacteriophages Roam the Wheat Phyllosphere

“…This study demonstrates that the bacteriophage community can alter the relative abundance of the dominant bacterial taxa. Although previous studies have surveyed phyllosphere viral communities [14][15][16][17][18][19], their methodologies and analyses have focused on eukaryotic viruses, thus overlooking bacteriophages. Therefore, knowledge about the bacteriophage community regarding species diversity and genomic potential does not exist in the literature.…”

Two new umbravirus-like associated RNAs (ulaRNAs) discovered in maize and johnsongrass from Ecuador

“…The hypothetical product of ORF4 is a protein of 212 aa (23.6 kDa) and 207 aa (23 kDa), for MULV and JgULV, respectively, sharing 48% aa identity, and 44-48% identity with the single ORF orthologs of 21-22 kDa from FULV, SULV, OULV and EMaV. The recently reported wheat umbra-like virus (WULV), a new ulaRNA of 3.5 kb [15], has one ORF overlapping at the end of ORF2, and is suggested to have an additional ORF starting 48-nt apart from the termination codon of the previous ORF. However, this second ORF is in frame with no intervening termination codons and thus its identity as a separate ORF requires further examination.…”

Pest categorisation of High Plains wheat mosaic virus

“…Infected wheat plants show symptoms ranging from mild to severe mosaic, chlorosis and necrosis, whereas red striping and chlorotic streaks are typically displayed by infected maize plants (Jensen et al, 1996 ). In the USA, HPWMoV is frequently found in fields also infected by the potyvirids wheat streak mosaic virus (WSMV) and/or Triticum mosaic virus (TriMV) (Mahmood et al, 1998 ; Seifers et al, 2002 , 2008 ; Hein et al, 2012 ; Redila et al, 2021 ). Typical symptoms caused by single infections of these viruses are difficult to distinguish from each other and co‐infected plants may show exacerbated symptoms (Burrows et al, 2009 ).…”