Complete genome sequence of a novel virga-like virus infecting Hevea brasiliensis

Genomic diversity of Capillovirus uniheveae (Betaflexiviridae) infecting Hevea brasiliensis Muell. Arg. in Hainan, China

BACKGROUND

Rubber tree (Hevea brasiliensis Muell. Arg.) is a significant commercial crop in tropical areas worldwide, with rubber production threatened by Tapping Panel Dryness (TPD). Rubber tree virus 1 (Capillovirus uniheveae; RTV1) was identified in rubber tree samples with TPD symptoms through RNA-seq. However, its genetic diversity may have hindered the detection of RTV1 via RT-PCR, complicating the further identification of RTV1 as the causative agent of TPD. To assess RTV1 prevalence and genomic diversity, rubber tree bark samples with TPD syndrome were collected from various sites in Hainan, China, for RNA-seq and RTV1 genome determination.

RESULTS

Twenty complete RTV1 genomes were determined from 22 samples with TPD syndrome via RNA-seq and RT-PCR. Using degenerate primers based on conserved sequences in the 3'- and 5'-UTR, 20 complete RTV1 genomes were identified directly from 48 trees affected by TPD via RT-PCR. The 40 RTV1 genome sequences showed significant variations, particularly in the RdRp domain. Phylogenetic analysis of full-genome nucleotide sequences divided RTV1 isolates into three phylogroups (A, B, and C), with phylogroup A being the most prevalent (67.5%). Similar results were observed based on RdRp and CP phylogenetic analysis. Additionally, mixed infections with different genotypes were identified in the same tree. Notably, no genetic recombination was observed among different phylogroups, while ten recombination events were identified within phylogroup A.

CONCLUSIONS

RTV1 was identified in approximately 50% of samples with TPD syndrome collected in Hainan, China, with phylogroup A being the most prevalent. Considerable variations were observed in RTV1 nucleotide sequences among different phylogroups. These findings lay a foundation for accurate diagnostics, etiological characterization, and elucidation of the evolutionary relationships of RTV1 populations, providing a strong guarantee for obtaining virus-free rubber tree seedlings, and promoting the healthy and sustainable development of rubber tree plantations.

Deciphering the virome of Chunkung (Cnidium officinale) showing dwarfism-like symptoms via a high-throughput sequencing analysis

BACKGROUND

Viruses have notable effects on agroecosystems, wherein they can adversely affect plant health and cause problems (e.g., increased biosecurity risks and economic losses). However, our knowledge of their diversity and interactions with specific host plants in ecosystems remains limited. To enhance our understanding of the roles that viruses play in agroecosystems, comprehensive analyses of the viromes of a wide range of plants are essential. High-throughput sequencing (HTS) techniques are useful for conducting impartial and unbiased investigations of plant viromes, ultimately forming a basis for generating further biological and ecological insights. This study was conducted to thoroughly characterize the viral community dynamics in individual plants.

RESULTS

An HTS-based virome analysis in conjunction with proximity sampling and a tripartite network analysis were performed to investigate the viral diversity in chunkung (Cnidium officinale) plants. We identified 61 distinct chunkung plant-associated viruses (27 DNA and 34 RNA viruses) from 21 known genera and 6 unclassified genera in 14 known viral families. Notably, 12 persistent viruses (7 DNA and 5 RNA viruses) were exclusive to dwarfed chunkung plants. The detection of viruses from the families Partitiviridae, Picobirnaviridae, and Spinareoviridae only in the dwarfed plants suggested that they may contribute to the observed dwarfism. The co-infection of chunkung by multiple viruses is indicative of a dynamic and interactive viral ecosystem with significant sequence variability and evidence of recombination.

CONCLUSIONS

We revealed the viral community involved in chunkung. Our findings suggest that chunkung serves as a significant reservoir for a variety of plant viruses. Moreover, the co-infection rate of individual plants was unexpectedly high. Future research will need to elucidate the mechanisms enabling several dozen viruses to co-exist in chunkung. Nevertheless, the important insights into the chunkung virome generated in this study may be relevant to developing effective plant viral disease management and control strategies.

Identification and characterization of two closely related virga-like viruses latently infecting rubber trees (Hevea brasiliensis)

A novel virga-like virus, provisionally named Rubber tree latent virus 2 (RTLV2), was identified from rubber tree (Hevea brasiliensis). It is a close relative of the previously reported Rubber tree latent virus 1 (RTLV1). The complete genomes of RTLV1 and RTLV2 were sequenced and comparatively analyzed in terms of genome organization, putative gene products and phylogenetic relationship. Both RTLV1 and RTLV2 have positive-sense single-stranded RNA genomes that encode seven open reading frames (ORFs), forming a similar genomic layout. In phylogenetic analyses based on replicase and coat protein amino acid sequences, RTLV1 and RTLV2 were clustered with unclassified virga-like viruses. They are distinct from currently recognized plant virus families. RTLV1 and RTLV2 can be distinguished from members of Virgaviridae by the presence of a putative coat protein duplex and a poly(A) tail at the 3'-terminus. The authenticity of RTLV1 and RTLV2 as infectious viruses was confirmed through field investigations and transmissibility assays. In conclusion, RTLV1 and RTLV2 represent a novel plant virus group that does not readily fit into current virus families.