Identification, characterization and full-length sequence analysis of a novel endornavirus in common sunflower (Helianthus annuus L.)

Liu, Wenwen; Xin, Min; Cao, Mengji; Qin, Meng; Liu, Hui; Zhao, Shou-qi; Wang, Xifeng

doi:10.1016/s2095-3119(18)61963-x

Cited by 7 publications

(5 citation statements)

References 41 publications

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“…The size, polarity and hotspot profiles of HaEV-derived siRNAs in sunflower leaves 17 resemble those of HvEV-derived siRNAs in barley leaves described above. The only difference is that neither 21 nor 22 nt siRNAs derived from HaEV exhibit any strong bias in relative frequencies of 5’-terminal nucleotides 17 , which may reflect differences in AGO family proteins or their expression in sunflower ( Asteraceae ) compared to barley ( Poaceae ). Consistent with our findings for the furovirus JSBWMV, sRNA sequencing analysis of a related furovirus Chinese wheat mosaic virus (CWMV) in wheat ( Poaceae ) leaves 18 has revealed viral siRNA size, polarity and hotspot profiles strikingly similar to those of JSBWMV as well as a strong bias to 5′A and 5′U in both 21 and 22 nt siRNAs, albeit less pronounced than reported herein.…”

Section: Resultssupporting

confidence: 52%

Section: Resultsmentioning

confidence: 99%

“…Previously, sRNA sequencing has been employed to investigate viral siRNA biogenesis for only one Endornaviridae , Helianthus annuus alphaendornavirus (HaEV) 17 . The size, polarity and hotspot profiles of HaEV-derived siRNAs in sunflower leaves 17 resemble those of HvEV-derived siRNAs in barley leaves described above. The only difference is that neither 21 nor 22 nt siRNAs derived from HaEV exhibit any strong bias in relative frequencies of 5’-terminal nucleotides 17 , which may reflect differences in AGO family proteins or their expression in sunflower ( Asteraceae ) compared to barley ( Poaceae ).…”

Section: Resultsmentioning

confidence: 99%

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Plant virome reconstruction and antiviral RNAi characterization by deep sequencing of small RNAs from dried leaves

Golyaev

Candresse

Rabenstein

et al. 2019

Sci Rep

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In plants, RNA interference (RNAi) generates small interfering (si)RNAs from entire genomes of viruses, satellites and viroids. Therefore, deep small (s)RNA sequencing is a universal approach for virome reconstruction and RNAi characterization. We tested this approach on dried barley leaves from field surveys. Illumina sequencing of sRNAs from 2 plant samples identified in both plants Hordeum vulgare endornavirus (HvEV) and barley yellow mosaic bymovirus (BaYMV) and, additionally in one plant, a novel strain of Japanese soil-borne wheat mosaic furovirus (JSBWMV). De novo and reference-based sRNA assembly yielded complete or near-complete genomic RNAs of these viruses. While plant sRNAs showed broad size distribution, viral sRNAs were predominantly 21 and 22 nucleotides long with 5′-terminal uridine or adenine, and were derived from both genomic strands. These bona fide siRNAs are presumably processed from double-stranded RNA precursors by Dicer-like (DCL) 4 and DCL2, respectively, and associated with Argonaute 1 and 2 proteins. For BaYMV (but not HvEV, or JSBWMV), 24-nucleotide sRNAs represented the third most abundant class, suggesting DCL3 contribution to anti-bymovirus defence. Thus, viral siRNAs are well preserved in dried leaf tissues and not contaminated by non-RNAi degradation products, enabling both complete virome reconstruction and inference of RNAi components mediating antiviral defense.

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Section: Resultssupporting

confidence: 52%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Plant virome reconstruction and antiviral RNAi characterization by deep sequencing of small RNAs from dried leaves

Golyaev

Candresse

Rabenstein

et al. 2019

Sci Rep

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“…The genomes of these viruses do not code for a CP, and therefore, it is not surprising that virions have not been reported in endornavirusinfected cells (Valverde et al, 1990;Zabalgogeazcoa and Gildow, 1992;Fukuhara, 1999). Limited studies on the cellular location of the RNA of plant endornaviruses suggest that they are concentrated in the cytoplasm (Lefebvre et al, 1990;Valverde et al, 1990;Okada et al, 2013;Liu et al, 2018). The replicative form of the genomic RNA (dsRNA) of VfEV-infected V. faba has been found to be associated with cytoplasmic vesicles and viral dsRNA isolated from purified vescicles (Lefebvre et al, 1990).…”

Section: Discussionmentioning

confidence: 99%

Ultrastructural Analysis of Cells From Bell Pepper (Capsicum annuum) Infected With Bell Pepper Endornavirus

et al. 2020

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Endornaviruses include viruses that infect fungi, oomycetes, and plants. The genome of plant endornaviruses consists of linear ssRNA ranging in size from approximately 13-18 kb and lacking capsid protein and cell-to-cell movement capability. Although, plant endornaviruses have not been shown to cause detectable changes in the plant phenotype, they have been associated with alterations of the host physiology. Except for the association of cytoplasmic vesicles with infections by Vicia faba endornavirus, effects on the plant cell ultrastructure caused by endornaviruses have not been reported. Bell pepper endornavirus (BPEV) has been identified in several pepper (Capsicum spp.) species. We conducted ultrastructural analyses of cells from two near-isogenic lines of the bell pepper (C. annuum) cv. Marengo, one infected with BPEV and the other BPEV-free, and found cellular alterations associated with BPEV-infections. Some cells of plants infected with BPEV exhibited alterations of organelles and other cell components. Affected cells were located mainly in the mesophyll and phloem tissues. Altered organelles included mitochondrion, chloroplast, and nucleus. The mitochondria from BPEV-infected plants exhibited low number of cristae and electron-lucent regions. Chloroplasts contained plastoglobules and small vesicles in the surrounding cytoplasm. Translucent regions in thylakoids were observed, as well as hypertrophy of the chloroplast structure. Many membranous vesicles were observed in the stroma along the envelope. The nuclei revealed a dilation of the nuclear envelope with vesicles and perinuclear areas. The organelle changes were accompanied by membranous structure rearrangements, such as paramural bodies and multivesicular bodies. These alterations were not observed in cells from plants of the BPEV-free line. Overall, the observed ultrastructural cell alterations associated with BPEV are similar to those caused by plant viruses and viroids and suggest some degree of parasitic interaction between BPEV and the plant host.

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“…While these novel variants of ACMV created by CRISPR/Cas9 mutagenesis might not multiply themselves, they depend on wild-type ACMV to proliferate in N. benthamiana ( Mehta et al, 2019 ). The combination of two gRNAs, particularly at distance from each other, would significantly delay resistance breakdown in comparison to using only one sgRNA ( Liu et al, 2018 ).…”

Section: Crispr-based Technologies For Plant Virus Interferencementioning

confidence: 99%

Integrating CRISPR-Cas and Next Generation Sequencing in Plant Virology

et al. 2021

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Plant pathology has been revolutionized by the emergence and intervention of next-generation sequencing technologies (NGS) which provide a fast, cost-effective, and reliable diagnostic for any class of pathogens. NGS has made tremendous advancements in the area of research and diagnostics of plant infecting viromes and has bridged plant virology with other advanced research fields like genome editing technologies. NGS in a broader perspective holds the potential for plant health improvement by diagnosing and mitigating the new or unusual symptoms caused by novel/unidentified viruses. CRISPR-based genome editing technologies can enable rapid engineering of efficient viral/viroid resistance by directly targeting specific nucleotide sites of plant viruses and viroids. Critical genes such as eIf (iso) 4E or eIF4E have been targeted via the CRISPR platform to produce plants resistant to single-stranded RNA (ssRNA) viruses. CRISPR/Cas-based multi-target DNA or RNA tests can be used for rapid and accurate diagnostic assays for plant viruses and viroids. Integrating NGS with CRISPR-based genome editing technologies may lead to a paradigm shift in combating deadly disease-causing plant viruses/viroids at the genomic level. Furthermore, the newly discovered CRISPR/Cas13 system has unprecedented potential in plant viroid diagnostics and interference. In this review, we have highlighted the application and importance of sequencing technologies on covering the viral genomes for precise modulations. This review also provides a snapshot vision of emerging developments in NGS technologies for the characterization of plant viruses and their potential utilities, advantages, and limitations in plant viral diagnostics. Furthermore, some of the notable advances like novel virus-inducible CRISPR/Cas9 system that confers virus resistance with no off-target effects have been discussed.

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Identification, characterization and full-length sequence analysis of a novel endornavirus in common sunflower (Helianthus annuus L.)

Abstract: Identification, characterization and full-length sequence analysis of a novel endornavirus in common sunflower (Helianthus annuus L.

Cited by 7 publications

References 41 publications

Plant virome reconstruction and antiviral RNAi characterization by deep sequencing of small RNAs from dried leaves

Plant virome reconstruction and antiviral RNAi characterization by deep sequencing of small RNAs from dried leaves

Ultrastructural Analysis of Cells From Bell Pepper (Capsicum annuum) Infected With Bell Pepper Endornavirus

Integrating CRISPR-Cas and Next Generation Sequencing in Plant Virology

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