The Sisal Virome: Uncovering the Viral Diversity of Agave Varieties Reveals New and Organ-Specific Viruses

Abstract

Sisal is a common name for different plant varieties in the genus Agave (especially Agave sisalana) used for high-quality natural leaf fiber extraction. Despite the economic value of these plants, we still lack information about the diversity of viruses (virome) in non-tequilana species from the genus Agave. In this work, by associating RNA and DNA deep sequencing we were able to identify 25 putative viral species infecting A. sisalana, A. fourcroydes, and Agave hybrid 11648, including one strain of Cowpea Mild Mottle Virus (CPMMV) and 24 elements likely representing new viruses. Phylogenetic analysis indicated they belong to at least six viral families: Alphaflexiviridae, Betaflexiviridae, Botourmiaviridae, Closteroviridae, Partitiviridae, Virgaviridae, and three distinct unclassified groups. We observed higher viral taxa richness in roots when compared to leaves and stems. Furthermore, leaves and stems are very similar diversity-wise, with a lower number of taxa and dominance of a single viral species. Finally, approximately 50% of the identified viruses were found in all Agave organs investigated, which suggests that they likely produce a systemic infection. This is the first metatranscriptomics study focused on viral identification in species from the genus Agave. Despite having analyzed symptomless individuals, we identified several viruses supposedly infecting Agave species, including organ-specific and systemic species. Surprisingly, some of these putative viruses are probably infecting microorganisms composing the plant microbiota. Altogether, our results reinforce the importance of unbiased strategies for the identification and monitoring of viruses in plant species, including those with asymptomatic phenotypes.

Molecular Characterization of a Novel Virga-like Virus Detected From Wheat

“…However, we also detected three contigs related to Barley stripe mosaic virus (BSMV) and it will not be discussed in this study. A BLASTx search revealed that one contig (3479 nt) shared 52.62% amino acid pairwise identity with Sisal-associated virgavirus A (a virus found in Agave sisalana that belongs to unclassi ed Virgaviridae)[6], while the other contig (3436 nt) shared 48.63% amino acid pairwise identity with Sisal-associated virgavirus C [11]. Moreover, we found that the contigs displayed no signi cant similarity using BLASTn.…”

“…According to the 2020 International Committee on Taxonomy of Viruses (ICTV) taxonomy (https://talk.ictvonline.org/ictv-reports/ictv_online_report/positive-sense-rnaviruses/w/virgaviridae), the family includes the genera Furovirus, Hordeivirus, Goravirus, Pecluvirus, Pomovirus, Tobamovirus, and Tobravirus. In recent years, many viruses belonging to the Virgaviridae family but different from any of the known genera in this family have been characterized in different hosts [10][11][12]. Therefore, those viruses were temporarily assigned to unclassi ed Virgaviridae.…”

Molecular Characterization of a Novel Virga-like Virus Isolated From Wheat

“…By comparing NT and NR databases, as well as Pfam and Swissprot databases, two assembled contigs were found to be homologous to viral RNA-directed RNA-polymerase. A BLASTx search against the two selected contigs revealed that one contig (3479 nt) shared 52.62% amino acid pairwise identity with Sisal-associated virgavirus A (a virus found in Agave sisalana that belongs to unclassi ed Virgaviridae)[6], while the other contig (3436 nt) shared 48.63% amino acid pairwise identity with Sisal-associated virgavirus C [11]. Moreover, we found that the contigs displayed no signi cant similarity using BLASTn.…”

“…According to the 2020 International Committee on Taxonomy of Viruses (ICTV) taxonomy (http:// ictv.global/report), the family includes the genera Furovirus, Hordeivirus, Goravirus, Pecluvirus, Pomovirus, Tobamovirus, and Tobravirus. In recent years, many viruses belonging to the Virgaviridae family but different from any of the known genera in this family have been characterized in different hosts [10][11][12]. Therefore, those viruses were temporarily assigned to unclassi ed Virgaviridae.…”

Molecular characterization of a novel virga-like virus associated with wheat

“…According to the 2020 International Committee on Taxonomy of Viruses (ICTV) taxonomy (https://talk.ictvonline.org/ictv-reports/ictv_online_report/positive-sense-rnaviruses/w/virgaviridae), this virus family contains seven genera such as Furovirus, Hordeivirus, Goravirus, Pecluvirus, Pomovirus, Tobamovirus, and Tobravirus. However, in recent years many new viruses which couldn't be recognized belonging to any above known genera in the Virgaviridae family have been discovered in many different plant hosts [10][11][12] and these new viruses were therefore assigned as unclassi ed Virgaviridae.…”