Characterization of the Endophyte Mycobiome in Cowpea (Vigna Unguiculata) Using Illumina Sequencing

Abstract Cowpea is an important crop for small-scale farmers in poor areas, but is also being developed for commercial agriculture as a possible substitute for commercial legumes. Endophytic fungi are omnipresent and play crucial but diverse roles in plants. This study characterized the endophyte component of the cowpea mycobiome from leaves, main and crown stems, and roots using Illumina MiSeq of the ITS2 region of the ribosomal operon. Ascomycetes exhibited the highest diversity, with Molecular Operational Taxonomic Units (MOTUs) assigned as Macrophomina, Cladosporium, Phoma, Fusarium and Cryptococcus, among the most dominant genera. The highest fungal species richness was found in roots followed by leaves. Certain MOTUS showed preferential colonization patterns for above or below ground tissues. Several MOTU generic groups known to include phytopathogenic species were found, with relative abundances ranging from high to very low. Phylogenetic analyses of reads for some MOTUs showed that a level of identification could be obtained to species level, while the absences of other species, including phytopathogens, could be shown. This is the first study that adopted a holistic metagenomic typing approach to study the fungal endophytes of cowpea, a crop that is so integral for low-income households of the world.