Complete Genome Sequences of Two Viruses Found in Echinacea Seeds

Jim Crocker
19th July, 2024

Complete Genome Sequences of Two Viruses Found in Echinacea Seeds

Echinacea purpurea

Photographer: Miranda Kohout

Key Findings

  • Researchers in Korea discovered two new viruses in echinacea seeds, named Echinacea-associated tombusviruses 1 and 2 (EaTV1 and EaTV2)
  • These viruses belong to the Tombusviridae family and share features like RNA-dependent RNA polymerases and coat proteins, essential for viral replication
  • EaTV1 and EaTV2 show close evolutionary ties with oat chlorotic stunt virus and other unassigned tombusviruses, suggesting complex evolutionary pathways
Echinacea is a popular herbaceous plant from North America, widely cultivated for its attractive flowers and medicinal properties. Recently, researchers from the Animal and Plant Quarantine Agency in the Republic of Korea have identified two novel viruses associated with echinacea seeds, using high-throughput sequencing technologies[1]. These viruses, tentatively named Echinacea-associated tombusviruses 1 and 2 (EaTV1 and EaTV2), belong to the family Tombusviridae, aligning closely with oat chlorotic stunt virus (OCSV) and other unassigned tombusviruses. The family Tombusviridae encompasses a diverse group of plant viruses, known for their small, icosahedral structures and plus-sense RNA genomes. These viruses are notorious for their ability to hijack the host’s translational machinery to synthesize viral proteins, a process that is crucial for their replication and infection cycle[2]. The discovery of EaTV1 and EaTV2 adds to this family, expanding our understanding of viral diversity and evolution within this group. The study identified key features of EaTV1 and EaTV2 that are characteristic of Tombusviridae. These include the presence of RNA-dependent RNA polymerases (RdRp) and coat proteins, which are essential for viral replication and particle formation. Interestingly, the EaTVs lack poly(A) tails, a common feature among Tombusviridae, and exhibit putative readthrough sites, which are sequences that allow the ribosome to continue translation beyond the typical stop codon. These structural features suggest that EaTVs utilize non-canonical translational mechanisms to maximize their genetic coding potential, a strategy observed in other RNA viruses[2]. Phylogenetic analysis revealed that EaTV1 and EaTV2 form a monophyletic group with OCSV and several unassigned tombusviruses, indicating a close evolutionary relationship. OCSV is currently the only member of the genus Avenavirus, suggesting that EaTVs could either be new members of this genus or closely related sister species. This finding aligns with previous studies that have shown the evolutionary complexity and diversity within the Tombusviridae family[3]. For instance, recombination events and positive selection pressures have been documented in various genera of Tombusviridae, highlighting the dynamic nature of their genomes[3]. The identification of EaTVs also provides insights into the evolutionary processes shaping the Tombusviridae family. The conservation of RdRp and coat proteins among EaTVs and other unassigned tombusviruses, despite their divergent similarities, points to complex evolutionary pathways. This suggests that while certain functional domains are preserved due to their critical roles in the viral life cycle, other regions may undergo significant changes, possibly due to host-virus interactions or environmental pressures[4]. In summary, the discovery of Echinacea-associated tombusviruses 1 and 2 by the Animal and Plant Quarantine Agency in the Republic of Korea adds valuable knowledge to the Tombusviridae family. These viruses exhibit typical features of Tombusviridae, such as the absence of poly(A) tails and the presence of putative readthrough sites, and show close evolutionary ties with OCSV and other unassigned tombusviruses. The study underscores the importance of continuous surveillance and characterization of plant viruses to understand their diversity, evolution, and potential impact on agriculture and horticulture.

GeneticsBiochemPlant Science

References

Main Study

1) Complete genome sequences of two tombusvirus-like viruses identified in Echinacea purpurea seeds.

Published 18th July, 2024

https://doi.org/10.1007/s11262-024-02092-5

Related Studies

2) Non-canonical translation in RNA viruses.

https://doi.org/10.1099/vir.0.042499-0

3) Positive selection, molecular recombination structure and phylogenetic reconstruction of members of the family Tombusviridae: Implication in virus taxonomy.

https://doi.org/10.1590/S1415-47572011005000046

4) Tombusvirus polymerase: Structure and function.

https://doi.org/10.1016/j.virusres.2017.01.012


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