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The maize stalk borer, Busseola fusca , is an important Lepidopteran pest of cereal crops in Central, East, and Southern Africa. Crop losses due to B. fusca feeding activity vary by region, but can result in total crop loss in areas with high levels of infestation. Genomic resources provide critical insight into the biology of pest species and can allow for the development of effective management tools and strategies to mitigate their impact on agriculture. To this end, we sequenced, assembled, and annotated the genome of B. fusca. The total assembled genome size was 492.9 Mb with 19,417 annotated protein-coding genes. Using a comparative approach, we identified a putative expansion in the Chorion gene family, which is involved in the formation of the egg shell structure. Our analysis revealed high repeat content within the B. fusca genome, with LTR sequences comprising the majority of the repetitive sequence. We hope genomic resources will provide a foundation for future work aimed at developing an integrated pest management strategy to reduce B. fusca's impact on food security. [ABSTRACT FROM AUTHOR]

Sustainable control of plant diseases requires a good understanding of the epidemiological aspects such as the biology of the causal pathogens. In the current study, we used RT-PCR and Next Generation Sequencing (NGS) to contribute to the characterization of maize lethal necrotic (MLN) viruses and to identify other possible viruses that could represent a future threat in maize production in Tanzania. RT-PCR screening for Maize Chlorotic Mottle Virus (MCMV) detected the virus in the majority (97%) of the samples (n = 223). Analysis of a subset (n = 48) of the samples using NGS-Illumina Miseq detected MCMV and Sugarcane Mosaic Virus (SCMV) at a co-infection of 62%. The analysis further detected Maize streak virus with an 8% incidence in samples where MCMV and SCMV were also detected. In addition, signatures of Maize dwarf mosaic virus, Sorghum mosaic virus, Maize yellow dwarf virus-RMV and Barley yellow dwarf virus were detected with low coverage. Phylogenetic analysis of the viral coat protein showed that isolates of MCMV and SCMV were similar to those previously reported in East Africa and Hebei, China. Besides characterization, we used farmers' interviews and direct field observations to give insights into MLN status in different agro-ecological zones (AEZs) in Kilimanjaro, Mayara, and Arusha. Through the survey, we showed that the prevalence of MLN differed across regions (P = 0.0012) and villages (P < 0.0001) but not across AEZs (P > 0.05). The study shows changing MLN dynamics in Tanzania and emphasizes the need for regional scientists to utilize farmers' awareness in managing the disease. [ABSTRACT FROM AUTHOR]

• Sugarcane mosaic virus (SCMV) and Maize chlorotic mottle virus (MCMV) were the only MLN causing viruses detected. • MCMV and SCMV are widely distributed in all maize growing regions in Kenya. • SCMV was more diverse and MCMV was largely conserved with little genetic diversity. • MCMV alone can lead to severe MLN development. • Genetic viral recombination signals detected only in SCMV viral genome samples. Maize is the most important food crop in Kenya accounting for more than 51 % of all staples grown in the country. Out of Kenya's 5.3 million ha total crops area, more than 2.1 million ha is occupied by maize which translates to 40 % of all crops area. However, with the emergence of maize lethal necrosis (MLN) disease in 2011, the average yields plummeted to all-time lows with severely affected counties recording 90–100% yield loss in 2013 and 2014. The disease is mainly caused by Maize chlorotic mottle virus (MCMV) in combination with Sugarcane mosaic virus (SCMV) or other potyviruses. In this study, a country-wide survey was carried out to assess the MLN causing viruses in Kenya, their distribution, genetic diversity, and recombination. The causative viruses of MLN were determined by RT-PCR using virus-specific primers and DAS-ELISA. Next-generation sequencing (NGS) data was generated, viral sequences identified, genetic diversity of MLN viruses was determined, and recombination was evaluated. MCMV and SCMV were detected in all the maize growing regions at varying levels of incidence, and severity while MaYMV, a polerovirus was detected in some samples through NGS. However, there were some samples in this study where only MCMV was detected with severe MLN symptoms. SCMV Sequences were highly diverse while MCMV sequences exhibited low variability. Potential recombination events were detected only in SCMV explaining the elevated level of diversity and associated risk of this virus in Kenya and the eastern Africa region. [ABSTRACT FROM AUTHOR]