Biology subjects

Alemu, T.

Publications and source records attributed to Alemu, T..

4 recordsLinked to original sources

bioRxiv2025

Pan-genome analyses of 226 finger millet-infecting Magnaporthe oryzae strains from eastern Africa reveal two lineages that differ in their genetic make-up, virulence and effector gene content with gene loss driven by homologous recombination between Pot2 elements

Blast disease, caused by the filamentous ascomycete Magnaporthe oryzae, is the main biotic constraint to finger millet production in eastern Africa. M. oryzae is a pathogen on many grass species, but the high host-specificity of blast isolates underscores the need to study pathogen diversity and virulence at the host level. Here, we fill a void on knowledge on finger millet-infecting strains of M. oryzae by sequencing 226 isolates pure-cultured from infected tissues, mainly peduncles and panicles, sampled from field-grown finger millet accessions across Ethiopia, Kenya, Tanzania and Uganda. Phylogenetic analysis showed that eastern African isolates are genetically distinct from Asian isolates, and differentiated into two groups potentially driven by climate variables. One group was dominated by isolates from Kenya and Uganda (KU group), and the other by isolates from Ethiopia and Tanzania (ET group). Analysis of the portfolio of 887 predicted effector genes showed that the KU group had significantly fewer effectors, concomitant with higher virulence levels on the two finger millet accessions tested. We demonstrate that homologous recombination between transposable elements, leading to genomic deletions, plays a key role in gene removal. Transcript profiling of fungal genes in compatible and incompatible interactions revealed upregulation in the incompatible interaction as a characteristic of an estimated 30% of effector genes, including seven of the eight homologs of known avirulence genes from rice-infecting M. oryzae identified in our study. Prioritization of these effectors for functional validation will pave the way for identifying cognate resistance genes and improving finger millet for resistance to blast disease.

plant biology↗

bioRxiv2024

Genetic Diversity of Zymoseptoria tritici Populations in Central and South-eastern Ethiopia

Septoria tritici blotch (STB), caused by the hemibiotrophic fungus Zymoseptoria tritici, is a serious threat to global wheat production, and a major bottleneck to wheat production in Ethiopia. Accurate identification and analysis of the pathogens genetic structure helps inform robust STB management. This study analyzed the molecular identity and genetic structure of 200 Z. tritici isolates retrieved from diseased crops in central and south-eastern regions of Ethiopia. Allelic diversity at 12 simple sequence repeat (SSR) loci was examined for all 200 isolates, and 165 isolates were identified by Sanger sequencing of the internal transcribed spacer (ITS) region of nuclear DNA (rDNA) region. The microsatellites were highly polymorphic, with mean number of alleles (Na) = 6.23, effective alleles (Ne) =2.90, Neis gene diversity (H) =0.57, and polymorphic information content (PIC) =0.59, and an analysis of molecular variance confirmed the presence of low population differentiation (Fixation Index (FST) = 0.02, Gene Flow (Nm) = 14.7), with 95% of the total genetic variation residing within populations, and only 5% residing between populations. The highest genetic diversity (Number of allele (Na) = 9.33, Effective number of allele (Ne) = 3.41 and Neis gene diversity (H) = 0.68) was observed in the Oromia special zone surrounding Finfinnee (OSZ) Z. tritici populations, followed by Arsi and North Shewa populations, indicating that these areas are ideal for multi-location germplasm resistance screening, and also pathogen genetic and genomic analyses. Cluster analyses did not clearly divide the populations into genetically separate clusters according to their geographic sampling areas, probably because of high gene flow. All individual samples showed genetic admixture, and shared genomic backgrounds from two subgroups (K=2). Overall, the SSR markers proved to be highly informative and effective genetic tools for unlocking the pathogens genetic structure. The Z. tritici populations of central and southeast Ethiopia exhibit high genetic diversity, indicating the need to deploy durable and diverse disease management strategies. North Shewa, OSZ, Arsi and West Arsi administrative zones represent hotspots for genetic and genomic analyses of Z. tritici. Moreover, these areas would be excellent locations for host-pathogen interaction studies, and wheat germplasm screening for STB resistance.

plant biology↗

bioRxiv2022

Bioassay evaluation, GC-MS Analysis and Acute Toxicity Assessment of Methanolic Extracts of Trichoderma species in an Animal Model

Fungi of the genus Trichoderma have been marketed for the control of crop pests, weeds, and diseases. However, some Trichoderma species may produce toxic secondary metabolites; the existence of these compounds in bioformulated products, along with their relative risk, should receive due attention to ensure human safety. In this study, we investigated the in vitro antagonistic potential of T. asperellum AU131 and T. longibrachiatum AU158 as a biocontrol agent against F. xylarioides and the associated antagonistic mechanism with bioactive substances. Swiss albino mice were used to evaluate the in vivo toxicity and pathogenicity of T. asperellum AU131 and T. longibrachiatum AU158 methanolic crude extracts and spore suspensions, respectively, in a preliminary safety assessment for use as biofungicides. Metabolite profiling of the crude extracts were performed by Gas Chromatography-Mass Spectrometry (GC-MS). The agar diffusion assay of the crude extracts from both T. asperellum AU131 and T. longibrachiatum AU158 were the most effective at a concentration of 200g/mL, causing 62.5%, and 74.3% inhibition, respectively. A GC-MS analysis of crude extracts from both bioagents identified 23 volatile secondary metabolites classified as alcohols, acids, sesquiterpenes, ketones and aromatic compounds. The oral administration of crude extracts (doses of 600, 1200, 2000 and 5000 mg/kg body weight) and spore suspensions (doses of 1 x 106, 1 x 107, 1 x 108 and 1 x 109 spores/mL) to female Swiss albino mice over 14 days did not show any significant signs of toxicity, mortality or changes to body weight. The highest dose, 5000 mg/kg, can be used to determine the no observed effect level of crude extracts and spore suspensions of T. asperellum AU131 and T. longibrachiatum AU158 when calculating safety margins. It can be concluded that these two Trichoderma species can serve as a biocontrol agents against F. xylarioides and the mechanism for this function was due to the secondary metabolites with effective bioactive substance. Moreover, the tested spore suspensions and crude extracts were not pathogenic or toxic, respectively, when administered to Swiss albino mice at various doses.

microbiology↗

bioRxiv2022

Biodiversity of the Genus Trichoderma in the Rhizosphere of Coffee (Coffea arabica) Plants in Ethiopia and their Potential Use in Biocontrol of Coffee Wilt Disease

The present study investigated the distribution status and biodiversity of Trichoderma species surveyed from coffee rhizosphere soil samples from Ethiopia and their potential for biocontrol of coffee wilt disease (CWD) caused by Fusarium xylarioides. Trichoderma isolates were identified based on molecular approaches and morphological characteristics followed by biodiversity analysis using different biodiversity indices. The antagonistic potential of Trichoderma isolates was evaluated against F. xylarioides using the dual confrontation technique and agar diffusion bioassays. A relatively high diversity of species was observed including 16 taxa and 11 undescribed isolates. Trichoderma asperellum, T. asperelloides and T. longibrachiatum were classified as abundant species, with dominance (Y) values of 0.062, 0.056 and 0.034, respectively. Trichoderma asperellum was the most abundant species (comprising 39.6% of all isolates) in all investigated coffee ecosystems. Shannons biodiversity index (H), the evenness (E), Simpsons biodiversity index (D), and the abundance index (J) were calculated for each coffee ecosystem, revealing that species diversity and evenness were highest in the Jimma zone (H =1.97, E = 0.76, D = 0.91, J = 2.73). The average diversity values for Trichoderma species originating from the coffee ecosystem were H = 1.77, D = 0.7, E = 0.75 and J = 2.4. In vitro confrontation experiments revealed that T. asperellum AU131 and T. longibrachiatum AU158 reduced the mycelial growth of F. xylarioides by over 80%. The potential use of these Trichoderma species for disease management of F. xylarioides and to reduce its impact on coffee cultivation is discussed in relation to Ethiopias ongoing coffee wilt disease crisis.

microbiology↗