Characterization of the Endophytic Mycobiome in Cowpea (<i>Vigna unguiculata</i>) from a Single Location Using Illumina Sequencing
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...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-02-01
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| Series: | Agriculture |
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| Online Access: | https://www.mdpi.com/2077-0472/12/3/333 |
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| author | Tonjock Rosemary Kinge Soumya Ghosh Errol D. Cason Marieka Gryzenhout |
| author_facet | Tonjock Rosemary Kinge Soumya Ghosh Errol D. Cason Marieka Gryzenhout |
| author_sort | Tonjock Rosemary Kinge |
| collection | DOAJ |
| description | 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 <i>Macrophomina</i>, <i>Cladosporium</i>, <i>Phoma</i>, <i>Fusarium</i> and <i>Cryptococcus</i>, 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. |
| first_indexed | 2024-03-09T13:54:46Z |
| format | Article |
| id | doaj.art-241ba92cf9594f4d9883bd2f006f1547 |
| institution | Directory Open Access Journal |
| issn | 2077-0472 |
| language | English |
| last_indexed | 2024-03-09T13:54:46Z |
| publishDate | 2022-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Agriculture |
| spelling | doaj.art-241ba92cf9594f4d9883bd2f006f15472023-11-30T20:43:06ZengMDPI AGAgriculture2077-04722022-02-0112333310.3390/agriculture12030333Characterization of the Endophytic Mycobiome in Cowpea (<i>Vigna unguiculata</i>) from a Single Location Using Illumina SequencingTonjock Rosemary Kinge0Soumya Ghosh1Errol D. Cason2Marieka Gryzenhout3Department of Genetics, University of the Free State, Bloemfontein 9310, South AfricaDepartment of Genetics, University of the Free State, Bloemfontein 9310, South AfricaDepartment of Animal Sciences, University of the Free State, Bloemfontein 9301, South AfricaDepartment of Genetics, University of the Free State, Bloemfontein 9310, South AfricaCowpea 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 <i>Macrophomina</i>, <i>Cladosporium</i>, <i>Phoma</i>, <i>Fusarium</i> and <i>Cryptococcus</i>, 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.https://www.mdpi.com/2077-0472/12/3/333cowpeaendophytefungal diversityenvironmental sequencingphytobiome |
| spellingShingle | Tonjock Rosemary Kinge Soumya Ghosh Errol D. Cason Marieka Gryzenhout Characterization of the Endophytic Mycobiome in Cowpea (<i>Vigna unguiculata</i>) from a Single Location Using Illumina Sequencing Agriculture cowpea endophyte fungal diversity environmental sequencing phytobiome |
| title | Characterization of the Endophytic Mycobiome in Cowpea (<i>Vigna unguiculata</i>) from a Single Location Using Illumina Sequencing |
| title_full | Characterization of the Endophytic Mycobiome in Cowpea (<i>Vigna unguiculata</i>) from a Single Location Using Illumina Sequencing |
| title_fullStr | Characterization of the Endophytic Mycobiome in Cowpea (<i>Vigna unguiculata</i>) from a Single Location Using Illumina Sequencing |
| title_full_unstemmed | Characterization of the Endophytic Mycobiome in Cowpea (<i>Vigna unguiculata</i>) from a Single Location Using Illumina Sequencing |
| title_short | Characterization of the Endophytic Mycobiome in Cowpea (<i>Vigna unguiculata</i>) from a Single Location Using Illumina Sequencing |
| title_sort | characterization of the endophytic mycobiome in cowpea i vigna unguiculata i from a single location using illumina sequencing |
| topic | cowpea endophyte fungal diversity environmental sequencing phytobiome |
| url | https://www.mdpi.com/2077-0472/12/3/333 |
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