Biology subjects

Rahnama, M.

Publications and source records attributed to Rahnama, M..

9 recordsLinked to original sources

bioRxiv2026

Phylogenomic Characterization of Two Alternaria Lineages Associated with Cotton Leaf Spot in Tennessee

Alternaria leaf spot is an important foliar disease of cotton (Gossypium hirsutum L.) and has historically been associated primarily with Alternaria macrospora in the United States. In November 2025, symptomatic Upland cotton leaves from a research greenhouse at Tennessee Technological University's Oakley Farm in Livingston, Tennessee, yielded two Alternaria isolates, 2-2 and 9-1. Quantitative conidial characterization showed substantial overlap in dimensions, septation, and shape. Concatenated ITS-RPB2 phylogenetic analysis supported different broad affinities, placing isolate 2-2 within an A. alternata- dominated group and isolate 9-1 within a group associated with the A. arborescens species complex (AASC), although their immediate relationships were weakly resolved. Phylogenomic analysis of 1,501 single-copy BUSCO orthologs from 63 genomes placed isolate 2-2 within the A. alternata lineage, sister to BMP2343, and isolate 9-1 within the AASC, sister to MOD1-FUNGI6. In controlled pathogenicity assays, isolate 9-1 reproduced foliar lesions on cotton, whereas mock-inoculated plants remained symptomless, and molecularly confirmed re-isolation fulfilled Koch's postulates. Isolate 2-2 produced insufficient conidia under the culture conditions used to prepare a standardized inoculum, and its pathogenicity was therefore not determined. These results reveal phylogenetically distinct Alternaria lineages associated with symptomatic cotton and establish an AASC isolate as a causal agent of cotton leaf spot in Tennessee.

pathology↗

bioRxiv2026

CentroFinder: accurate de novo identification of centromeres in fungal genomes

MotivationCentromeres are essential chromosomal loci, yet their computational identification remains challenging due to rapid sequence evolution, high repeat content, and the absence of conserved defining motifs. This challenge is particularly pronounced in fungi, where centromere architectures vary widely in size, sequence composition, and chromatin organization, limiting the effectiveness of single-feature or motif-based prediction approaches. ResultsWe present CentroFinder, a fungal-specific computational framework for de novo centromere prediction from long-read sequencing-based genome assemblies. CentroFinder integrates multiple genomic and long-read-derived features into a weighted scoring model to identify loci where centromere-associated signals converge. Benchmarking against experimentally mapped centromeres in Cryptococcus deuterogattii, Magnaporthe oryzae, and Neurospora crassa demonstrates that CentroFinder consistently predicts a single centromeric region per chromosome, fully nested within CENP-A-defined domains despite substantial diversity in centromere size, sequence composition, and chromatin context. Availability and ImplementationCentroFinder is freely available as open-source software at https://github.com/RahnamaLab/CentroFinder. The pipeline is designed for high-performance computing environments and leverages features derived from long-read sequencing data.

bioinformatics↗

bioRxiv2025

Conditional Gene Expression in Magnaporthe oryzae via Fungal Nitrate Reductase Promoter Replacement

Functional genomic studies rely on controlled gene expression, which is challenging for essential genes or those active only under specific conditions. We provide a detailed protocol for generating Magnaporthe oryzae (synonym of Pyricularia oryzae) with conditional BUF1 gene expression. This method uses targeted promoter replacement to substitute the native BUF1 promoter with the nitrogen-responsive promoter. This approach enables nitrogen source-dependent control of expression in M. oryzae, leading to observable pigmentation changes that facilitate easy phenotypic screening.

genomics↗

bioRxiv2024

Characterization and Organization of Telomeric-Linked Helicase (TLH) Gene Families in Fusarium oxysporum

Telomere-linked RecQ helicase (TLH) genes have been reported in several fungi and a choanoflagellate in the regions adjacent to the terminal telomere repeats. In this study, we explore the Telomere-linked RecQ helicase (TLH) genes in four strains of Fusarium oxysporum, offering new insights into their genomic structure, functional motifs, and impact on chromosomal ends. We conducted a comprehensive analysis, comparing the TLH genes of F. oxysporum with those previously identified in other organisms and uncovering significant similarities. Through comparative genomics, we identified conserved protein motifs across these genes, including a TLH domain, C2H2, and RecQ helicase motifs. Our phylogenetic analysis positions the F. oxysporum TLH genes in a cluster with other known TLHs, suggesting a shared evolutionary origin. Mutation analysis revealed a relatively low level of deleterious mutations in TLH gene paralogs, with a notable proportion of full-size structures maintained across strains. Analysis of subtelomeric sequences indicates that a region with almost identical sequences flanks the majority of chromosome ends, termed TLH-containing region (TLHcr), across these strains. The presence of TLHcrs at chromosome ends, either as single entities or in arrays, underscores their potential role in telomere function and genome stability. Our findings provide a detailed examination of TLH genes in four strains of F. oxysporum, laying the groundwork for future studies on their biological significance and evolutionary history in fungal genomes.

bioinformatics↗

bioRxiv2023

Pyricularia Populations are Mostly Host-Specialized with Limited Reciprocal Cross-Infection Between Wheat and Endemic Grasses in Minas Gerais, Brazil

Wheat blast, caused by Pyricularia oryzae Triticum (PoT), is an emergent threat to wheat production. Current understanding of the evolution and population biology of the pathogen and epidemiology of the disease has been based on phylogenomic studies that compared the wheat blast pathogen with isolates collected from grasses that were invasive to Brazilian wheat fields. Genetic similarity between isolates from wheat and grasses lead to the conclusion that significant cross-infection occurs, especially on signalgrass (Urochloa spp.); and this in turn prompted speculation that its widespread use as forage is a key driver of the diseases epidemiology. We reanalyzed data from those studies and found that all but one of the isolates from non-wheat hosts were members of PoT and the related Lolium-adapted lineage (PoL1), which meant that the Pyricularia populations typically found on endemic grasses had not yet been sampled. To address this shortcoming, we performed a comprehensive sampling of blast lesions in wheat crops and endemic grasses found in and away from wheat fields in Minas Gerais. A total 1,368 diseased samples were collected (976 leaves of wheat and grasses and 392 wheat heads) which yielded a working collection of 564 Pyricularia isolates. We show that, contrary to earlier implications, PoT was rarely found on endemic grasses and, conversely, members of grass-adapted populations were rarely found on wheat. Instead, most populations were host-specialized with constituent isolates usually grouping according to their host-of-origin. With regard to the dominant role proposed for signalgrass in wheat blast epidemiology, we found only one PoT member in 67 isolates collected from signalgrass grown away from wheat fields, and only three members of Urochloa-adapted populations among hundreds of isolates from wheat. Cross-inoculation assays on wheat and a signalgrass used in pastures (U. brizantha) suggested that the limited cross-infection observed in the field may be due to innate compatibility differences. Whether or not the observed level of cross-infection would be sufficient to provide an inoculum reservoir, or serve as a bridge between wheat growing regions, is questionable and, therefore, deserves further investigation.

microbiology↗

bioRxiv2022

A Re-evaluation of phylogenomic data reveals that current understanding in wheat blast population biology and epidemiology is obfuscated by oversights in population sampling

Wheat blast, caused by the Triticum lineage of Pyricularia oryzae (PoT), is a serious disease that first emerged in Brazil and quickly spread to neighboring countries. The recent appearance of this disease in Bangladesh and Zambia highlights a need to understand the population biology and epidemiology of the disease so as to mitigate pandemic outbreaks. Current knowledge in these areas is largely based on analyses of wheat blast isolates collected in Brazil, and their comparison with isolates from non-wheat, endemic grasses. Those studies concluded that wheat blast is caused by a highly diverse P. oryzae population that lacks host specificity and, as a result, undergoes extensive gene flow with populations infecting non-wheat hosts. Additionally, based on genetic similarity between wheat blast and isolates infecting Urochloa species, it was proposed that the disease originally emerged via a host jump from this grass, and the widespread use of Urochloa as a pasture grass likely plays a central role in wheat blast epidemiology. Inconsistencies with earlier phylogenetic studies prompted us to re-analyze the Brazilian data in the context of a comprehensive, global, phylogenomic dataset. We now show that the seminal studies failed to sample the P. oryzae populations normally found on endemic grasses and, instead, repeatedly sampled PoT and P. oryzae Lolium (PoL) members that happened to be present in these hosts. The resulting lack of accurate and representative information about the grass-infecting populations in Brazil means that current conclusions about wheat blasts evolution, population biology and epidemiology are unsubstantiated and could be equivocal.

microbiology↗

bioRxiv2021

Recombination of standing variation in a multi-hybrid swarm drove adaptive radiation in a fungal pathogen and gave rise to two pandemic plant diseases

Adaptive radiations fuel speciation and are characterized by rapid genetic diversification and expansion into new ecological niches. Historically, these processes were believed to be driven by selection on novel mutations but genomic analyses now indicate that standing variation and gene flow often have prominent roles. How "old" variation is combined, however, and its resulting genetic architecture within newly-adapted populations is not well understood. We reconstructed a recent radiation in the fungus, Pyricularia oryzae, that spawned a population pathogenic to eleven grass genera, and caused two new plant diseases: wheat blast - already a serious threat to global agriculture - and gray leaf spot of ryegrasses. We show that the new population evolved in a multi-hybrid swarm using only the standing variation that was present in seven individuals from five distinct, host-specialized lineages. Sexual and parasexual recombination within the swarm reassorted key host-specificity factors and generated more diversity in possibly just a few weeks than existing lineages had accumulated over hundreds to thousands of years. We suggest that the process was initiated by sexual opportunity arising when a fertile fungal strain was imported into Brazil on Urochloa introduced as forage for beef production; and we further contend that the host range expansion was largely fortuitous, with host selection playing little, if any, role in driving the process. Finally, we believe that our findings point to an overlooked role for happenstance in creating situations that allow organisms to skirt rules that would normally hold evolution in check. Commercial Endorsement DisclaimerMention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. Equal Opportunity/Non-Discrimination StatementUSDA is an equal opportunity provider and employer.

evolutionary biology↗

bioRxiv2019

Transposon-mediated telomere destabilization: a driver of genome evolution in the blast fungus

Magnaporthe oryzae is a filamentous ascomycete fungus that causes devastating diseases of crops that include rice and wheat, and a variety of turf, forage and wild grasses. Strains from ryegrasses possess highly stable chromosome ends that undergo frequent rearrangements during vegetative growth in culture and in planta. Instability is associated with the presence of two related retrotransposons (Magnaporthe oryzae Telomeric Retrotransposons - MoTeRs) inserted within the telomere repeat tracts. The objective of the present study was to determine the mechanisms by which MoTeRs promote telomere instability. Targeted cloning, restriction mapping, and sequencing of both parental and novel telomeric restriction fragments, along with MinION sequencing of DNA from three single-spore cultures, allowed us to document the molecular alterations for 109 newly-formed telomeres. Rearrangement events included truncations of subterminal rDNA sequences; acquisition of MoTeR insertions by "plain" telomeres; insertion of the MAGGY retrotransposons into MoTeR arrays; expansion and contraction of subtelomeric tandem repeats; MoTeR truncations; duplication and terminalization of internal sequences; and breakage at long, interstitial telomeres generated during MoTeR insertion. Together, our data show that when MoTeRs invade the telomeres, they can dramatically perturb the integrity of chromosome ends, leading to the generation of unprotected DNA termini whose repair has the potential to generate chromosome alterations that extend well into the genome interior.

genomics↗

bioRxiv2019

VelA and LaeA are key regulators of the Epichloë festucae transcriptomic response during symbiosis with perennial ryegrass

VelA (or VeA) is a key global regulator in fungal secondary metabolism and development which we previously showed is required during the symbiotic interaction of Epichloe festucae with perennial ryegrass. In this study, comparative transcriptomics analyses of {Delta}velA mutant compared to wild type E. festucae, under three different conditions (in culture, infected seedlings and infected mature plants) were performed to investigate the impact VelA on the E. festucae transcriptome. These comparative transcriptomics studies showed that VelA regulates the expression of genes encoding proteins involved in membrane transport, fungal cell wall biosynthesis, host cell wall degradation and secondary metabolism, along with a number of small secreted proteins and a large number of proteins with no predictable functions. In addition, these results were compared with previous transcriptomics experiments studying the impact of LaeA, another key global regulator of secondary metabolism and development that we have shown is important for the E. festucae- perennial ryegrass interaction. The results showed that although VelA and LaeA regulate a sub-set of E. festucae genes in a similar manner, they also regulated many other genes independently of each other suggesting specialised roles.

molecular biology↗