Identification of two novel putative satellite RNAs with hammerhead structures in the virome of French and Spanish carrot samples

Babalola, Bisola Mercy; Schönegger, Deborah; Faure, Chantal; Marais, Armelle; Fraile, Aurora; García‐Arenal, Fernando; Candresse, Thierry

doi:10.1007/s00705-022-05538-z

Cited by 2 publications

(3 citation statements)

References 16 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The GUA trinucleotide was also present at the same positions of the (+) HHRz of FHVd-LR [ 25 ] and in the (−) HHRz of the Vd-LsatRNAs of velvet tobacco mottle virus and lucerne transient streak virus [ 45 , 46 ]. The AUA was previously reported in the (+)-strand RNA of the satellite of barley yellow dwarf virus [ 47 ] and two novel viroid-like RNAs likely associated with carrot red leaf virus [ 48 ]. The sequence variability observed in the HHRzs always preserved the predicted active ribozyme structure because most changes were mapped at the hammerhead loops, preserving the potential tertiary interactions between some nucleotides, or did not modify base pairing of the stems ( Figure 4 ).…”

Section: Resultsmentioning

confidence: 88%

A Novel Self-Cleaving Viroid-Like RNA Identified in RNA Preparations from a Citrus Tree Is Not Directly Associated with the Plant

Navarro

Gisel

et al. 2022

Viruses

View full text Add to dashboard Cite

Viroid and viroid-like satellite RNAs are infectious, circular, non-protein coding RNAs reported in plants only so far. Some viroids (family Avsunviroidae) and viroid-like satellite RNAs share self-cleaving activity mediated by hammerhead ribozymes (HHRzs) endowed in both RNA polarity strands. Using a homology-independent method based on the search for conserved structural motifs of HHRzs in reads and contigs from high-throughput sequenced RNAseq libraries, we identified a novel small (550 nt) viroid-like RNA in a library from a Citrus reticulata tree. Such a viroid-like RNA contains a HHRz in both polarity strands. Northern blot hybridization assays showed that circular forms of both polarity strands of this RNA (tentatively named citrus transiently-associated hammerhead viroid-like RNA1 (CtaHVd-LR1)) exist, supporting its replication through a symmetric pathway of the rolling circle mechanism. CtaHVd-LR1 adopts a rod-like conformation and has the typical features of quasispecies. Its HHRzs were shown to be active during transcription and in the absence of any protein. CtaHVd-LR1 was not graft-transmissible, and after its first identification, it was not found again in the original citrus source when repeatedly searched in the following years, suggesting that it was actually not directly associated with the plant. Therefore, the possibility that this novel self-cleaving viroid-like RNA is actually associated with another organism (e.g., a fungus), in turn, transiently associated with citrus plants, is proposed.

show abstract

Section: Resultsmentioning

confidence: 88%

A Novel Self-Cleaving Viroid-Like RNA Identified in RNA Preparations from a Citrus Tree Is Not Directly Associated with the Plant

Navarro

Gisel

et al. 2022

Viruses

View full text Add to dashboard Cite

show abstract

“…A detailed description of their diversity, distribution and preferential association with either wild or cultivated carrots within this metagenomic study has recently been published [ 38 ]. Moreover, two novel hammerhead ribozyme containing single-stranded circular satellite RNAs, carrot red leaf virus satellite 1 (CtRLV Sat1) and carrot red leaf virus satellite 2 (CtRLV Sat2) have also been identified in Spanish and French carrot populations and reported in detail recently [ 39 ].…”

Section: Resultsmentioning

confidence: 99%

“…The carrot virome was equally rich in subviral agents, with four different tombus-like-associated RNAs identified in French and Spanish carrot populations [ 38 ]. In addition, both linear and small circular, hammerhead-containing satellite RNAs [ 39 ] were detected. Synergistic interaction between poleroviruses and umbraviruses have been reported with destructive effects on different crops [ 50 , 51 ] but there is little information on their precise interactions and even less so on the level of specificity or promiscuousness involved.…”

Section: Discussionmentioning

confidence: 99%

Carrot populations in France and Spain host a complex virome rich in previously uncharacterized viruses

et al. 2023

Self Cite

View full text Add to dashboard Cite

High-throughput sequencing (HTS) has proven a powerful tool to uncover the virome of cultivated and wild plants and offers the opportunity to study virus movements across the agroecological interface. The carrot model consisting of cultivated (Daucus carota ssp. sativus) and wild carrot (Daucus carota ssp. carota) populations, is particularly interesting with respect to comparisons of virus communities due to the low genetic barrier to virus flow since both population types belong to the same plant species. Using a highly purified double-stranded RNA-based HTS approach, we analyzed on a large scale the virome of 45 carrot populations including cultivated, wild and off-type carrots (carrots growing within the field and likely representing hybrids between cultivated and wild carrots) in France and six additional carrot populations from central Spain. Globally, we identified a very rich virome comprising 45 viruses of which 25 are novel or tentatively novel. Most of the identified novel viruses showed preferential associations with wild carrots, either occurring exclusively in wild populations or infecting only a small proportion of cultivated populations, indicating the role of wild carrots as reservoir of viral diversity. The carrot virome proved particularly rich in viruses involved in complex mutual interdependencies for aphid transmission such as poleroviruses, umbraviruses and associated satellites, which can be the basis for further investigations of synergistic or antagonistic virus-vector-host relationships.

show abstract

Identification of two novel putative satellite RNAs with hammerhead structures in the virome of French and Spanish carrot samples

Cited by 2 publications

References 16 publications

A Novel Self-Cleaving Viroid-Like RNA Identified in RNA Preparations from a Citrus Tree Is Not Directly Associated with the Plant

A Novel Self-Cleaving Viroid-Like RNA Identified in RNA Preparations from a Citrus Tree Is Not Directly Associated with the Plant

Carrot populations in France and Spain host a complex virome rich in previously uncharacterized viruses

Contact Info

Product

Resources

About