Biology subjects

Prado, K.

Publications and source records attributed to Prado, K..

3 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

UnigeneFinder: An automated pipeline for gene calling from transcriptome assemblies without a reference genome

For most species in nature, transcriptome data is much more readily available than genome data. Without a reference genome, however, gene calling is cumbersome and inaccurate due to the high degree of redundancy in de novo transcriptome assemblies. To simplify and increase the accuracy of de novo transcriptome assembly in the absence of a reference genome, we developed UnigeneFinder. Combining several clustering methods, UnigeneFinder substantially reduces the redundancy typical of raw transcriptome assemblies. This pipeline offers an effective solution to the problem of inflated transcript numbers, achieving a closer representation of the actual underlying genome. UnigeneFinder performs comparably or better, compared to existing tools, on plant species with varying genome complexities. UnigeneFinder is the only available transcriptome redundancy solution that fully automates the generation of primary transcript, coding region, and protein sequences, analogous to those available for high quality reference genomes. These features, coupled with the pipelines cross-platform implementation and focus on automation and an accessible user interface, make UnigeneFinder a useful tool for many downstream sequence-based analyses in non-model organisms lacking a reference genome, including differential gene expression analysis, accurate ortholog identification, functional enrichments, and evolutionary analyses. UnigeneFinder also runs efficiently both on high-performance computing (HPC) systems and personal computers, further reducing barriers to use.

bioinformatics↗

bioRxiv2023

Photosynthetic acclimation mediates exponential growth of a desert plant in Death Valley summer

Heat waves, now more frequent and longer due to climate change, devastate plant productivity. Although rare, thermophilic plants could hold keys to engineering heat resilience in crop plants. Tidestromia oblongifolia is a thermophilic flowering plant that thrives at temperatures above 45{degrees}C. When exposed to Death Valley summer conditions, T. oblongifolia increased its thermal optimum of photosynthesis within a day and accelerated growth within 10 days. The physiological changes were accompanied by morphological, anatomical, and gene expression changes revealed by a newly sequenced genome. In bundle sheath cells where Rubisco fixes CO2, mitochondria relocated to chloroplasts and novel, cup-shaped chloroplasts appeared. Understanding how this plant acclimates under heat may afford new ways of engineering heat tolerance in crop plants. One-Sentence SummaryTidestromia oblongifolias acclimation to Death Valley is accompanied by changes in gene expression, organellar dynamics, and photosynthesis.

plant biology↗