Metaviromic insights into the viral community associated with Dendrobium catenatum

TL;DR

This study explores the diverse viral community in the orchid Dendrobium catenatum, revealing interactions with fungi and evidence of virus evolution across different hosts.

Contribution

The study identifies a diverse virome in Dendrobium catenatum, including mycoviruses and endogenous viral elements, and provides insights into cross-kingdom virus-host interactions.

Findings

Sixteen exogenous viral species from seven families were detected in Dendrobium catenatum.

Seven endogenous viral elements were identified, with Mitoviridae being predominant.

Phylogenetic and compositional analyses suggest horizontal virus transfer and co-evolutionary pressures.

Abstract

Metatranscriptomic analysis of public RNA-seq data from Dendrobium catenatum, an economically and culturally important orchid, revealed a highly diverse virome. Sixteen exogenous viral species were detected, representing seven families of RNA viruses, including positive-sense ssRNA viruses (Botourmiaviridae, Mitoviridae, Narnaviridae, Endornaviridae, and Fusariviridae) and double-stranded RNA viruses (Phlegviridae and Partitiviridae). In addition, seven endogenous viral elements (EVEs) were identified, with a predominance of Mitoviridae, suggesting historical viral integration events. The detected virome reflected complex interactions between plant-associated fungi and the host orchid, and many of detected viral families are commonly associated with fungal hosts, suggesting that several viruses may be of mycoviral origin, though their exact host remains to be confirmed. Phylogenetic analyses and compositional correlations point toward potential horizontal virus transfer events across kingdom boundaries, further complicating the ecological network of virus-host relationships. To explore virus-host adaptation, we also analyzed codon usage and dinucleotide/trinucleotide composition profiles, revealing clustering patterns that suggest co-evolutionary pressures and potential host-specific optimization of viral genomes. These molecular signatures enhance our understanding of how viruses may adapt to diverse hosts and underscore the complex evolutionary dynamics shaping the D. catenatum holobiont. These findings not only broaden our knowledge of orchid-associated viral diversity but also provide critical insights into virus evolution and cross-kingdom virome interactions.

The online version contains supplementary material available at 10.1007/s42770-025-01816-5.

Figures