Revisiting the amalgaviral landscapes in plant transcriptomes expands the host range of plant amalgaviruses

Sidharthan, V. Kavi; Rajeswari, V.; Vanamala, Gayatri

doi:10.1016/j.virol.2022.10.006

Cited by 14 publications

(8 citation statements)

References 75 publications

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“…These results further reiterate the host and waika/waika-like virus co-evolution pattern (Sidharthan et al, 2023a). Interestingly, the size of ORFX-encoded proteins of the two tree waikaviruses identi ed in this study was larger than that of non-tree plant waikaviruses, and this nding is in agreement with our previous study (Sidharthan et al, 2023a). Consistent with our previous ndings (Sidharthan et al, 2023a), coiled-coils were observed near the Nterminal region in the polyprotein of identi ed waikaviruses.…”

Section: Discussionsupporting

confidence: 93%

“…Data-driven virus discovery (DDVD) studies on targeted plant virus groups like amalgavirus (Nibert et al, 2016;Sidharthan et al, 2022a), ophiovirus (Debat et al, 2023), rhabdovirus (Bejerman et al, 2021), solemovirus (Sidharthan et al, 2022b), tymovirus and varicosavirus have unveiled the hidden genetic diversity and expanded the host range of each target virus group using the public domain metatranscriptome data. Our earlier transcriptome shotgun assembly (TSA)-based DDVD study on secoviruses (Sidharthan et al, 2022c) identi ed nine novel secoviral sequences in eight plant species.…”

Section: Introductionmentioning

confidence: 99%

“…Our earlier transcriptome shotgun assembly (TSA)-based DDVD study on secoviruses (Sidharthan et al, 2022c) identi ed nine novel secoviral sequences in eight plant species. In a subsequent sequence read archive (SRA)-based DDVD study on waikaviruses (Sidharthan et al, 2023a), we identi ed twenty-two novel waikaviral sequences and a highly divergent secoviral sequence in transcriptomes of various plant species. On the other hand, exploration of novel plant viral sequences in targeted plant species identi ed novel secoviral sequences in various plant transcriptomes (Park and Hahn, 2019;Sidharthan et al, 2021;Mifsud et al, 2022;Sidharthan et al, 2023b).…”

Section: Introductionmentioning

confidence: 99%

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Probing of plant transcriptomes unveils the hitherto hidden genetic diversity of the family Secoviridae

Sidharthan,

Reddy,

Kiran

et al. 2023

Preprint

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Secoviridae family contains single stranded RNA genome-containing viruses that infect plants. In the present study, we mined publicly available plant transcriptomes and identified sixty-one putative novel secoviral sequences in various plant species ranging from bryophytes to trees, which increased the known secoviral diversity by approximately 0.5-fold. Of the identified viral sequences, 13 were monopartite and 48 were bipartite, and sequences of 52 secoviruses were coding-complete and nine were partial. Except for small open reading frames (ORFs) determined in waikaviral genomes and RNA2 of torradoviruses, all the recovered genomes/genome segments contained a large ORF encoding a polyprotein. Based on genome organization, sequence similarity to known members, phylogeny and secovirus species demarcation criteria, all but three identified novel secoviruses were assigned to different secoviral genera- Cheravirus (3), Comovirus (2), Fabavirus (5), Nepovirus (29), Sadwavirus (3), Sequivirus (1), Stralarivirus (1), Torradovirus (4) and Waikavirus (10). Genome organization of two of the identified waika-like viruses resembled that of the recently identified waika-like virus- Triticum aestivum secovirus. Phylogenetic analysis revealed the host-waikavirus co-evolution pattern in a few waika- and waika-like viruses, the increased phylogenetic diversity of nepoviruses and the phylogenetic clustering of waika-like viruses. The study paves way for further studies on understanding the biological properties of identified novel secoviruses.

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Section: Discussionsupporting

confidence: 93%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Probing of plant transcriptomes unveils the hitherto hidden genetic diversity of the family Secoviridae

Sidharthan,

Reddy,

Kiran

et al. 2023

Preprint

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“…On the other hand, viral taxonomy is witnessing a shift from the traditional taxonomy to the sequence-based taxonomy, which advocates the inclusion of viral sequences known only from metagenomic data in the International Committee on Taxonomy of Viruses (ICTV) taxonomy scheme for comprehensively characterizing global virome [5]. The acceptance of sequence-based viral taxonomy paved way for data-driven virus discovery studies that identi ed several putative novel plant viruses in various plant transcriptomes [6,7,8,9,10,11,12]. Thus, in the present study, we explored the transcriptome datasets of G. sylvestre available in public domain for novel plant viral sequences and identi ed a putative novel cholivirus.…”

Section: Introductionmentioning

confidence: 99%

“…Putative cleavage sites were predicted in viral polyproteins by comparing the known polyprotein sequences of related viruses. Trimmed reads of virus-positive libraries were mapped onto the recovered viral genomes and mean coverage values were obtained as described in [12]. Neighbourhood-joining (NJ) trees were generated using Poisson model with 1000 bootstrap replicates after MUSCLE alignment of protein sequences in MEGA7 v 7.0.26 [19] and the sequence identity matrices were generated using the Sequence Demarcation Tool v 1.2 [20].…”

Section: Introductionmentioning

confidence: 99%

Identification of a putative novel cholivirus in the transcriptome of Gymnema sylvestre R. Br

Sidharthan

Vanamala

Rajeswari³

et al. 2023

Arch Microbiol

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Gymnema sylvestre is a tropical climber species that is widely used in traditional medicine since ages. In the present study, the transcriptome datasets of G. sylvestre available in public domain were screened for the presence of novel plant viral sequences and a putative novel virus tentatively named as Gymnema sylvestre virus 1 (GysV1) was identi ed. Coding-complete genome segments of GysV1 that are 6.35 kb (RNA1) and 3.98 kb (RNA2) long possessed a single large open reading frame coding for a polyprotein. BLASTp, sequence identity and phylogenetic analyses revealed the relatedness of GysV1 to the members of the subgenus Cholivirus (genus Sadwavirus; family Secoviridae; order Picornavirales). Based on the species demarcation criteria of the family Secoviridae, GysV1 can be regarded as a new cholivirus member.

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Identification of two putative novel deltapartitiviruses and an enamovirus in coriander transcriptomes

Kavi Sidharthan,

Diksha,

Singh

et al. 2023

Arch Microbiol

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Coriander is a herbaceous spice and condiment crop also known for its medicinal properties. The present study identi ed two putative novel deltapartitiviruses and an enamovirus tentatively named as Coriandrum sativum deltapartitivirus 1, 2 (CsDPV1, 2) and Coriandrum sativum enamovirus (CsEV) in the publicly available transcriptome-assembled contigs derived from coriander grown in India. CsDPV1 and 2 contained tripartite and bipartite genomes, respectively with each genome segment encoding for a single ORF. CsEV contained ve ORFs encoding for proteins P0, P1, P1-2, P3 and P3-5. Phylogenetic analysis revealed three distinct subgroups of deltapartitiviruses wherein CsDPV1 and 2 grouped in subgroup 3 and 1, respectively while CsEV formed a distinct sub-clade within enamoviruses. Further, presence of CsDPV2 in fruit samples of one of the cultivars from where the virus was identi ed was validated through RT-PCR assay and Sanger sequencing. The study highlights the need for further studies on understanding the importance and biological properties of identi ed novel viruses. Full TextCoriandrum sativum L., commonly known as coriander, is an economically important herbaceous spice crop belonging to the family Apiaceae. Though native to the Mediterranean and Middle East, the crop is widely cultivated in different regions of the world.

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Revisiting the amalgaviral landscapes in plant transcriptomes expands the host range of plant amalgaviruses

Cited by 14 publications

References 75 publications

Probing of plant transcriptomes unveils the hitherto hidden genetic diversity of the family Secoviridae

Probing of plant transcriptomes unveils the hitherto hidden genetic diversity of the family Secoviridae

Identification of a putative novel cholivirus in the transcriptome of Gymnema sylvestre R. Br

Identification of two putative novel deltapartitiviruses and an enamovirus in coriander transcriptomes

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