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. 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. It also confirmed the absences of other species, including phytopathogens. This is the first study that adopted a holistic metagenomic typing approach to study the fungal endophytes of cowpea from a single location, a crop that is so integral for low-income households of the world.
Highlights
Cowpea (Vigna unguiculata) is one of the most economically important indigenous African legume crops [1] and is cultivated in more than 60 countries of Asia, Oceania, the Middle East, southern Europe, Africa, southern United States of America and Central and South America [2]
The present study aims to characterize the composition of the fungal endophyte communities associated with different above and below ground cowpea tissues with a next generation sequencing (NGS) approach, in this case using an Illumina MiSeq platform
We focused on three main questions: (i) What is the composition of the fungal endophytic communities found in cowpea from a single location in South Africa at a single time? (ii) What is the fungal endophyte composition in the different plant tissues of cowpea at a single time? (iii) Do the plant parts harbour any latent pathogens or potentially beneficial fungi? The study represents the first high throughput
Summary
Cowpea (Vigna unguiculata) is one of the most economically important indigenous African legume crops [1] and is cultivated in more than 60 countries of Asia, Oceania, the Middle East, southern Europe, Africa, southern United States of America and Central and South America [2]. Damping-off and stem rot diseases are caused by many different species of fungi, including Pythium aphanidermatum, Rhizoctonia solani, Phytophthora sp., Fusarium solani and Sclerotium rolfsii [14,15]. Culture-based and environmental sequencing studies of surface sterilized stems and leaves have revealed an astounding diversity of fungal species existing sub-cuticularly or deeper within the tissues of healthy plants [25,26]. Such fungi are designated as endophytes, a term long used to indicate fungal residence within plant tissues rather than on plant surface asymptomatically without causing visible disease symptoms [27].
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