Molecular characterization of a novel cytorhabdovirus with a unique genomic organization infecting yerba mate (<i>Ilex paraguariensis</i>) in Argentina

Bejerman, Nicolás; Acevedo, Raúl M.; Breuil, Soledad de; Ruíz, Oscar Adolfo; Sansberro, Pedro Alfonso; Dietzgen, Ralf G.; Nome, Claudia; Debat, Humberto Julio

doi:10.1101/2020.01.28.923201

Cited by 2 publications

(2 citation statements)

References 18 publications

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“…In the last few years several novel plant rhabdoviruses, which may be asymptomatic, have been reported in HTS studies (Baek et al, 2019; Bejerman et al, 2020c; Bulos et al, 2021; Ding et al, 2019; Koloniuk et al, 2018; Orfanidou et al, 2020; Read et al, 2019; Wu et al, 2018). Thus, it is tempting to speculate that some plant rhabdovirus-like sequences may be hidden in published plant transcriptome databases, generated with diverse objectives beyond virus research, where viral RNA was inadvertently co-purified with endogenous plant RNA and sequenced.…”

Section: Discussionmentioning

confidence: 99%

Illuminating the plant rhabdovirus landscape through metatranscriptomics data

Bejerman

Dietzgen

Debat

2021

Preprint

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Rhabdoviruses infect a large number of plant species and cause significant crop diseases. They have a negative-sense, single-stranded unsegmented or bisegmented RNA genome. The number of plant-associated rhabdovirid sequences has grown in the last few years in concert with the extensive use of high-throughput sequencing platforms. Here we report the discovery of 26 novel rhabdovirus genomes associated with 24 different host plant species and one insect, which were hidden in public databases. These viral sequences were identified through homology searches in more than 3,000 plant and insect transcriptomes from the NCBI Sequence Read Archive (SRA) using known plant rhabdovirus sequences as query. Identification, assembly and curation of raw SRA reads resulted in sixteen viral genome sequences with full-length coding regions and ten partial genomes. Highlights of the obtained sequences include viruses with unique and novel genome organizations among known plant rhabdoviruses. Phylogenetic analysis showed that thirteen of the novel viruses were related to cytorhabdoviruses, one to alphanucleorhabdoviruses, five to betanucleorhabdoviruses, one to dichorhaviruses, and six to varicosaviruses. These findings resulted in the most complete phylogeny of plant rhabdoviruses to date and shed new light on the phylogenetic relationships and evolutionary landscape of this group of plant viruses. Furthermore, this study provides additional evidence for the complexity and diversity of plant rhabdovirus genomes and demonstrates that analyzing SRA public data provides an invaluable tool to accelerate virus discovery, gain evolutionary insights and refine virus taxonomy.

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Section: Discussionmentioning

confidence: 99%

Illuminating the plant rhabdovirus landscape through metatranscriptomics data

Bejerman

Dietzgen

Debat

2021

Preprint

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“…The yerba mate tree is native and adapted to the Atlantic Forest biome environment, however the full-sun monoculture practice of this crop is extensive (Montagnini et al 2011). In this context, yerba mate is negatively affected by diverse insect and acari pests, in addition to fungi and viral pathogens (Sosa et al 2011;Debat et al 2014a;Rybak et al 2014;Bejerman et al 2017Bejerman et al , 2020Bergottini et al 2017). The most important abiotic stress that affects yerba mate in this extensive agricultural system is the direct solar radiation that causes higher evapotranspiration demand and drought stress that ultimately reduces the plantation productivity (Gortari et al 2019.…”

Section: Original Paper the Dnaj Gene Family In Yerba Mate (Ilex Para...mentioning

confidence: 99%

The DNAJ gene family in yerba mate (Ilex paraguariensis): genome-wide identification, structural characterization, orthology based classification and expression analysis

Aguilera

Debat²,

Castrillo

et al. 2023

Rodriguésia

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Dry leaves and twigs of yerba mate are widely infusion-consumed in southern Southamerica. Endemic and adapted to the Atlantic Forest, its extensive full-sun monoculture links to diverse biotic (pest, pathogens) and abiotic stresses (solar radiation, drought), impacting its productivity, ecology and socioeconomic niche. We focused in comprehensively characterize the DNAJ gene family in yerba mate to predict its possible roles on development and diverse stress responses to further assist crop manage. Our results suggest that yerba mate DNAJ proteins account 140 diverse members of six structural types displaying potential variable roles in protein homeostasis control. We were able to classify them into 51 distinct orthology groups, in agreement to Arabidopsis, and performed translational genomics of function, localization, expression and stress responsiveness data. Genome mapping and expression analysis indicated that yerba mate DNAJ genes differ in expression, nucleotide composition, length and exon-intron structure. Intronless or few introns genes -linked to rapid stress response- accounted 85 DNAJs. Promoters of DNAJ genes harbored a 73.2% of cis-acting regulatory elements involved in response to diverse stresses, hormones and light, simultaneously. We hypothesize that yerba mate DNAJs assist to plant survival during multiple stresses linked to current dominant agroecosystem but promote its growth under shade.

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Molecular characterization of a novel cytorhabdovirus with a unique genomic organization infecting yerba mate (Ilex paraguariensis) in Argentina

Cited by 2 publications

References 18 publications

Illuminating the plant rhabdovirus landscape through metatranscriptomics data

Illuminating the plant rhabdovirus landscape through metatranscriptomics data

The DNAJ gene family in yerba mate (Ilex paraguariensis): genome-wide identification, structural characterization, orthology based classification and expression analysis

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