A novel RNA virus, Thesium chinense closterovirus 1, identified by high-throughput RNA-sequencing of the parasitic plant Thesium chinense

Abstract

The genome sequence of a closterovirus (genus Closterovirus, family Closteroviridae), tentatively named Thesium chinense closterovirus 1 (TcCV1), was identified by performing high-throughput RNA-sequencing of the haustoria and root tissues of Thesium chinense, a parasitic plant. The TcCV1 genome was predicted to encode nine proteins, eight of which have orthologs in previously identified closteroviruses. The TcCV1 RNA-dependent RNA polymerase (RdRp) and heat shock protein 70 homolog (Hsp70h) showed 27.8-68.2% and 23.8-55.1% amino acid identity, respectively, to orthologous proteins of known closteroviruses. The putative +1 ribosomal frameshifting site required for producing RdRp was identified as GUUUAGC with UAG stop codon and the skipped nucleotide U. Phylogenetic trees based on RdRp and Hsp70h show that TcCV1 is a novel member of the genus Closterovirus, forming a subclade with a group of known closteroviruses, including mint virus 1 and carnation necrotic fleck virus. The genome sequence of TcCV1 may be useful for studying the genome evolution of closteroviruses.

Discovery and Genome Characterization of a Closterovirus from Wheat Plants with Yellowing Leaf Symptoms in Japan

“…WhCV1-WL19a ORF1b encoded the RdRP domain (420 aa, viral RNA-directed RNA polymerase, pfam00978) presumably expressed via a +1 ribosomal frameshift from ORF1a, which is a common feature of closterovirids [ 28 , 29 ] ( Figure 2 A,B). In WhCV1 and other closterovirids, the sequence of the putative +1 slippery site of the first ORF (ORF1a) has the conserved motif “GUU_stop_C”, with some exceptions [ 14 , 30 ] ( Figure 2 C). The sequence of the putative +1 slippery site (… 7408 GUU UAG C; ORF1a stop codon is underlined) is presented in Figure 2 C. The frameshifting translation from the first gene unit (ORF1a/1b) in the WhCV1-WL19a genome would likely be able to produce a large fusion protein of 3197 kDa (2898 aa), forming the common module “Met-Hel-RdRP” of the alphavirus-like superfamily [ 31 ].…”

“…Most of the members of the family Closteroviridae are pathogens of or associated with dicotyledonous crops, including vegetables and fruit trees. In recent studies, the de novo RNA-sequencing (RNA-seq) approach has enabled researchers to uncover many thus-far-unknown viral genome sequences in the family, including the members or candidates of the genus Closterovirus [ 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 ].…”

Discovery of two novel potyvirus genome sequences by high-throughput RNA sequencing in Aconitum carmichaelii tissue samples

“…The advent of high-throughput RNA sequencing (RNA-seq) has provided a tool for characterizing these viruses (Nibert et al, 2016;Bejerman and Debat, 2022). Numerous novel RNA virus genome sequences have been identified within assembled transcriptome contigs from diverse plant RNA-seq datasets Park et al, 2021;Shin et al, 2022a;Shin et al, 2022b;Choi et al, 2022;Choi et al, 2023). In this study, we report discovery of two novel potyvirus genome sequences by high-throughput RNA-seq of Aconitum carmichaelii tissue samples.…”

Exploring Information Exchange between Thesium chinense and Its Host Prunella vulgaris through Joint Transcriptomic and Metabolomic Analysis

“…Parasitic planta may actively manipulate host physiology by transferring phytohormones [ 23 ]. Recent research efforts on T. chinense have primarily concentrated on exploring its vitro anti-inflammatory and antimicrobial activity using extracts [ 7 , 29 , 30 ], host range and selectivity [ 18 ] and understanding the developmental reprogramming involved in haustoria formation [ 31 ]. Nevertheless, there remains a scarcity of studies examining the intricate information exchange between T. chinense and its host plants.…”