Metagenomic-based screening and molecular characterization of cowpea-infecting viruses in Burkina Faso

Cowpea, ( Vigna unguiculata L. (Walp)) is an annual tropical grain legume. Often referred to as "poor man's meat", cowpea is one of the most important subsistence legumes cultivated in West Africa due to the high protein content of its seeds. However, African cowpea production can be seriously constrained by viral diseases that reduce yields. While twelve cowpea-infecting viruses have been reported from Africa, only three of these have so-far been reported from Burkina Faso. Here we use a virion-associated nucleic acids (VANA)-based metagenomics method to screen for the presence of cowpea viruses from plants collected from the three agro-climatic zones of Burkina Faso. Besides the three cowpea-infecting virus species which have previously been reported from Burkina Faso (Cowpea aphid borne mosaic virus [Family Potyviridae ], the Blackeye cowpea mosaic virus--a strain of Bean common mosaic virus--[Family Potyviridae ] and Cowpea mottle virus [Family Tombusviridae ]) five additional viruses were identified: Southern cowpea mosaic virus (Sobemovirus genus), two previously uncharacterised polerovirus-like species (Family Luteoviridae ), a previously uncharacterised tombusvirus-like species (Family Tombusviridae ) and a previously uncharacterised mycotymovirus-like species (Family Tymoviridae ). Overall, potyviruses were the most prevalent cowpea viruses (detected in 65.5% of samples) and the Southern Sudan zone of Burkina Faso was found to harbour the greatest degrees of viral diversity and viral prevalence. Partial genome sequences of the two novel polerovirus-like and tombusvirus-like species were determined and RT-PCR primers were designed for use in Burkina Faso to routinely detect all of these cowpea-associated viruses

Molecular characterization of the main fungi associated to Bambara groundnut foliar diseases in Burkina Faso

Objective: This study aims to update the database of fungi associated to Bambara groundnut foliar diseases in Burkina Faso using both molecular and morphological identification approaches.Methodology and Results: In this study, molecular approach based on the sequencing of ITS (Internal Transcripted Spacer) region of fungi and  morphological approach were used to identify the main fungi associated to Bambara groundnut foliar diseases. The study was performed with universal polymerase chain reaction (PCR) primer ITS1/ITS4. BlastN comparisons between 19 fungal isolates contigs of the 16 major fungi were produced by their DNA sequences assembly and GenBank sequences yielded identity scores of 99 to 100 % with all of them. The degrees of similarity between these contigs and the loci sequences of classified fungi in GenBank indicate that our fungal isolates are the same species with those in Genbank, particularly the first of the list show after the blastN. It is the first report of molecular characterization of the main fungi infecting Bambara groundnut in Burkina Faso.Conclusion and Application of results: Nineteen fungi associated to  Bambara groundnut foliar diseases were identified and can be taken as targets in varietal improvement of Bambara groundnut for resistance to fungal diseases in Burkina Faso.Key words: Bambara groundnut, fungi, molecular characterization, PCR primer ITS1/ITS4, Burkina Faso

Complete genome sequence of a novel marafivirus infecting pearl millet in Burkina Faso

International audiencePearl millet (Pennisetum glaucum (L.) R. Br.) is a staple food that is widely cultivated in sub-Saharan Africa. In August 2018, a survey was conducted in the main producing regions of Burkina Faso, and leaf samples were analyzed using virion-associated nucleic acid (VANA)-based metagenomic approach and Illumina sequencing. A new virus, tentatively named "Pennisetum glaucum marafivirus" (PGMV), was detected, and its complete nucleotide sequence of 6364 nucleotides was determined. The sequence contains a large open reading frame (ORF) encoding a polyprotein of 224.2 kDa with five domains (methyltransferase, papain-like protease, helicase, RNA-dependent RNA polymerase, and coat proteins), typical of marafiviruses. Additionally, a characteristic conserved marafibox domain was detected in the genome. The nucleotide sequence of the complete PGMV genome shares 68.5% identity with that of sorghum bicolor marafivirus, and its coat protein shares 58.5% identity with that of oat blue dwarf virus. Phylogenetic analysis confirmed that the pearl millet virus is unambiguously grouped with members of the genus Marafivirus in the family Tymoviridae. This is the first report on the occurrence of a marafivirus in pearl millet

Selection of plant virus VANA-contigs and VANA-reads recovered from cowpea plants collected in Burkina Faso.

<p>Selection of plant virus VANA-contigs and VANA-reads recovered from cowpea plants collected in Burkina Faso.</p

List of cowpea-infecting viruses present in Africa.

<p>List of cowpea-infecting viruses present in Africa.</p

List of detection primers designed in this study.

<p>List of detection primers designed in this study.</p

Virus prevalence and mixed infection prevalence of 52 cowpea plants based on VANA-based and RT-PCR-based detection results.

<p>Virus prevalence and mixed infection prevalence of 52 cowpea plants based on VANA-based and RT-PCR-based detection results.</p

Geographical distribution and prevalence of Cowpea viruses in Burkina Faso.

<p>Geographical distribution and prevalence of Cowpea viruses in Burkina Faso.</p