Unraveling the viral footprint: comprehensive genomic exploration of endogenous viral elements in Musa spp. and Ensete sp

Abstract

Endogenous viral elements (EVEs) are virus-derived sequences integrated into host germline genomes, propagating across generations and potentially becoming fixed through natural selection or genetic drift. While extensively studied in animals, EVEs have been less frequently reported in plants. This study performed a comprehensive genome-wide analysis across 15 species, subspecies, and cultivars of Musa and Ensete to identify sequences associated with viral interactions. Our analysis revealed EVEs associated with four plant virus families: Tospoviridae, Caulimoviridae, Solemoviridae, and Mimiviridae. Phylogenetic analysis showed that these EVEs clustered with their corresponding viruses, with viruses from the same family grouping together. We identified 11 distinct Banana Streak Virus species across Musa genomes. Most corresponding EVEs were annotated as hypothetical proteins, while others aligned with functional proteins, including Polyprotein P3, movement protein, capsid protein, protease, reverse transcriptase, and ribonuclease H. These EVEs appear to be stable components of the Musa genome, which may potentially contribute to growth, development, metabolism, and stress responses. This study provides insights into virus-host interactions and evolutionary relationships among Musa and Ensete species, highlighting the prevalence and distribution of EVEs in Musa genomes and offering a foundation for future investigations into their functional roles and evolutionary significance.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04412-4.

Keywords: Endogenous banana streak virus sequences; Endogenous pararetroviruses; Endogenous viral elements; Musa spp; Virome diversity.