Biology subjects

Abdalrahem, A.

Publications and source records attributed to Abdalrahem, A..

3 recordsLinked to original sources

bioRxiv2026

Haplotype-phased assemblies of the two poplar rust fungi species: Melampsora larici-populina and Melampsora allii-populina

Dikaryotic rust fungi maintain two distinct haploid nuclei for most of their life cycle, making their large, repeat-rich genomes difficult to assemble and phase. Here we present haplotype-phased, near chromosome-scale genome assemblies for the poplar rust pathogens Melampsora larici-populina 98AG31 and Melampsora allii-populina 12AY07, generated using PacBio HiFi sequencing and Hi-C-guided scaffolding. For each species, we resolved 18 chromosomes per haplotype, providing the first near chromosome-level representations of poplar rust fungal species. M. larici-populina diploid assembly spans ~203 Mb, while M. allii-populina reaches ~416 Mb, with high completeness and strong collinearity between haplotypes. Compared with previous fragmented or collapsed references, these assemblies greatly improve contiguity, recover centromeric and telomeric features, and support the transposable element-driven genome size expansion in M. allii-populina. The haplotype-aware annotations of genes and predicted effectors derived from these resources will enable detailed analyses of genome architecture, repeat dynamics, and key loci such as avirulence genes. Together, these assemblies provide a robust genomic resource for investigating host adaptation, virulence evolution, and population diversity in poplar rust fungi.

genomics↗

bioRxiv2025

Behind the shadow play: Shedding light on the population genetics of partially clonal organisms through clone age distributions

Partial clonality is widespread in natural populations; however, the distributions of clone ages under different rates of clonality and their effects on genetic diversity remain unexplored. To fill this gap, we simulated partially clonal populations over 10,000 generations across a range of clonality and mutation rates. Using a forward-in-time individual-based model, we evaluated genetic and genotypic indices alongside measures of clone age distribution to examine how different clonality rates influence clone age distributions, and how these distributions impact population structure and genetic diversity over time. Our results reveal two distinct trajectories: (i) at low to moderate rates of clonality evolution is driven by sharp and predictable patterns of rapid clone turnovers, resulting in predominantly young clones which relative abundances well align with genotypic indices ; (ii) at extreme rates of clonality, demographic stochasticity generates very variable clone age distributions which mirror the high variance of mean and variance of FIS that summarize gene reshuffling between individuals. Interestingly, a portion of the variability of these indices can be explained by differences in clone age distribution that occur by chance. Our results, therefore, complement previous theoretical studies on the population genetics of partial clonality by providing biological insights into how clonal turnover dynamics shape the temporal evolution and variability of highly clonal populations. These results have practical implications for inferring evolutionary trajectories and managing partially clonal species.

evolutionary biology↗

bioRxiv2025

Long-lasting coexistence of multiple asexual lineages alongside their sexual counterparts in a fungal plant pathogen

Sexual-to-asexual transitions within species are crucial for understanding reproductive evolution, yet the coexistence of both modes of fungal species in the same environment is poorly documented. Here, we report this transition in a plant pathogen species that coexists within the same geographical environment. Our biological model is the poplar rust fungus Melampsora larici-populina, which displays a complex life cycle typical of rust fungi (Pucciniales). It alternates between two unrelated hosts to complete an obligate sexual life cycle once a year. We conducted a comprehensive population genetic analysis, using 21 microsatellite markers and data from 2,122 individuals gathered over 30 years from various locations in France. Our results demonstrate the existence of many distinct lineages that reproduce asexually through the years, skipping the sexual phase. Clustering analysis identified a group of multilocus lineages that displayed all hallmarks of the genetic consequences of asexual reproduction, including highly negative and large variance among loci of the inbreeding coefficient (FIS). This indirect evidence for asexual reproduction was confirmed by the direct observation of these asexual lineages being repeatedly sampled across multiple years. This result demonstrates the coexistence of these lineages with their sexual counterparts in the same ecological niche, challenging conventional assumptions about geographical sorting of reproductive modes. These considerations are of paramount importance for understanding the contemporary evolution of major pathogen species. This switch from sexual to asexual reproduction has contributed to devastating epidemics worldwide.

evolutionary biology↗