Unravelling the endophytic virome inhabiting maize plant

Endophytes are well-known for their symbiotic interaction with plants and their ability to promote plant growth by producing various metabolites. The most well-studied endophytes are bacteria and fungi. For generations, viruses were misnamed, and their symbiotic associations were ambiguous. Recent advances in omics techniques, particularly next-generation sequencing, have given rise to novel developments in the mutualistic relationships that exist between plants and viruses. Endogenous viruses have received a lot of attention in the animal world, but limited information exists on their functions and importance to plants. Therefore, endophytic viral populations inhabiting the root of a maize plant were assessed in this study for the first time using shotgun metagenomics. Complete DNA was extracted and sequenced using shotgun metagenomics from the maize roots in farming sites where organic fertilization (FZ), inorganic fertilization (CZ), and maize planted with no fertilization (NZ) are being practised in an experimental field. Our results identified 2 orders namely: Caudovirales (67.5%) and Herpesvirales (28.5%) which dominated the FZ site, although they do not show any significant difference (p > 0.05) across the sites. At the class level Microviridae, Phycodnaviridae, Podoviridae, Phycodnaviridae, and Poxviridae dominated the FZ site. Myoviridae and Podoviridae were more abundant in the CZ site, while only Siphoviridae predominated the inorganic fertiliser site (NZ). Diversity analysis revealed that viral populations were more abundant in organic fertilization (FZ). Taken together, this research adds to our understanding of the symbiotic integration of endophytic viruses with maize plants and that their abundance is affected by farming practices. In addition, their potential can be exploited to solve a variety of agronomic issues.