Biology subjects

Sargheini, N.

Publications and source records attributed to Sargheini, N..

6 recordsLinked to original sources

bioRxiv2026

Dynamic holocentric genomes facilitate divergent evolutionary paths through chromosomal rearrangements, hybrid dysfunction, and recombination suppression

Theory predicts chromosomal rearrangements (CRs) to promote reproductive isolation and local adaptation by disrupting meiosis and altering recombination landscapes. These processes are especially important in holocentric organisms, whose diffuse centromeres facilitate CRs. Here, we investigated the genomic origins and evolutionary consequences of CRs in the holocentric sedge Carex laevigata, a species with extreme intraspecific chromosome-number variation (2n = 69-84). Establishing chromosome-scale genome assemblies, experimental crosses involving more than one thousand living plants throughout three generations and eight years, linkage mapping, and Quantitative Trait Loci (QTL) analyses, we identified extensive CRs among karyotypically distinct populations. Breakpoint regions of CRs were enriched in GC-rich and repetitive sequences, particularly LTR-Gypsy elements, suggesting recurrent genomic regions prone to structural instability. Inter-cytotype hybrids formed complex meiotic configurations and showed reduced germination success, consistent with hybrid dysfunction associated with increasing chromosomal divergence. Rearranged chromosomes exhibited strong recombination suppression and segregation distortion near breakpoint regions and within inverted segments. QTL analyses further identified fitness-related loci associated with both rearranged and collinear chromosomes. Together, our results corroborate theoretical predictions providing novel empirical evidence that CRs arise preferentially in structurally fragile genomic regions and contribute to genomic divergence through hybrid dysfunction and recombination suppression.

plant biology↗

bioRxiv2026

Holocentromere diversity in Cyperaceae: contrasting repeat organisation in Mapanioideae and Cyperoideae

Centromeres ensure accurate chromosome segregation and are typically confined to a single, localised region in monocentric chromosomes. In contrast, holocentric chromosomes exhibit kinetochore activity distributed along the chromosome length. Although holocentricity is widespread in Cyperaceae, the composition and organisation of these centromeres, as well as their evolutionary diversification, remain poorly understood. Here, we investigated centromere organisation in representatives of the subfamilies Mapanioideae (Hypolytrum schraderianum Nees) and Cyperoideae (Cladium mariscus (L.) Pohl) by combining genome assemblies, repeatome characterisation (RepeatExplorer), fluorescence in situ hybridisation (FISH), and immunolocalisation. Comparative synteny analyses incorporating the genomes of Rhynchospora breviuscula (n = 5) and Carex littledalei (n = 29) identified conserved blocks, eventually expanding almost whole chromosomes of H. schraderianum (n = 30) and Cl. mariscus (n = 39), despite divergent chromosome numbers and deep evolutionary distances within Cyperaceae. Mobile elements showed very low abundances and were uniformly dispersed, with Ty1/Copia Angela being the most abundant in both species. In Cl. mariscus, holocentromeres showed an extended distribution of centromere- and kinetochore-associated proteins along the chromosomes, largely colocalised with two satellite DNA repeats that form dispersed clusters. In contrast, H. schraderianum also displayed kinetochore signals along chromatids, but the most abundant satellite DNA family was enriched in distal and interstitial chromosomal regions rather than interspersed along the chromatids. Together, these results reveal different genomic architectures underlying holocentric organisation in phylogenetically distinct Cyperaceae lineages, suggesting that holocentromeres in this family have diversified with variation in centromere organisation in regard to its association with repetitive DNA.

evolutionary biology↗

bioRxiv2026

Proteogenomics of Blumeria hordei supports RNA and protein coding innovative potential derived from transposable elements

Some filamentous plant-pathogenic fungi have comparably large genome sizes within the fungal kingdom due to the proliferation of transposable elements (TEs). Blumeria hordei (Bh), the causal agent of the powdery mildew disease on barley, is a filamentous obligate biotrophic fungus. Compared to other ascomycetes, it contains a low number of genes but a high genomic TE content of approximately 75%. Yet, a comprehensive understanding of the contribution of TEs to the RNA and protein landscape of Bh is lacking. Here, we use Bh as a model to study transcripts and proteins derived from genes and individual TEs. Therefore, we created two high-quality genome assemblies of the German Bh isolate TUM1 and the Australian Bh isolate AUS1. We applied deep proteomics with mass spectrometry, long-read and short-read sequencing on both DNA and RNA. Based on these multi-omic resources, we completed nearly gapless genome assemblies, new gene and TE annotations, and effector predictions. Using long-read RNA sequencing, we detected extensive co-transcription of TEs and genes as TE-gene chimeric transcripts. We identified previously unpredicted splice variants or genes, partially supported by proteomics. The intergenic and TE genomic space of Bh TUM1 gives rise to thousands of transcripts and several novel TE-derived proteins that lack from previous TE protein predictions. Together, this supports an existing potential for expression of novel transcripts and proteins from highly abundant TEs in the Bh genome.

plant biology↗

bioRxiv2026

A holocentric pangenome links karyotype evolution to meiotic recombination

Chromosomal fissions, fusions and whole-genome duplications propel genome evolution, yet their impact on meiotic recombination is obscured by the centromere constraint, since in monocentric species most large rearrangements are lethal1-4. Holocentric organisms, which distribute kinetochore activity along the entire chromosome, overcome this barrier and therefore offer a unique window onto the interplay between karyotype change and crossover control2. We assembled chromosome-scale genomes for 20 holocentric Rhynchospora species (including 56 haplotypes), representing all major clades of the genus, featuring satellite-based holocentromeres5,6, and integrated single-gamete crossover maps, high-resolution meiotic synapsis immunocytochemistry and Hi-C chromatin architecture. Breakpoint analysis shows that holocentromeric Tyba satellite arrays6,7 are recurrent hotspots for both chromosome fusions and fissions, contributing to the genuss extraordinary chromosome number variation from 2n = 4 to 36. Crossover landscapes group into two apparent modes: strongly distal-biased versus irregularly distributed, which is correlated with divergent patterns of synapsis elongation. Moreover, crossover number scales with chromosome count and meiotic axis length. In contrast, crossover density per megabase is inversely related to chromosome length and to chromatin-loop size. We propose that chromosome fissions create karyotypes with smaller chromosomes folded into shorter loops, thereby increasing the axial substrate accessible for double-strand break formation and elevating recombination frequency. Together, our results provide a structural link between large-scale structural chromosome evolution and meiotic recombination through coupled changes in chromosome number, size, loop geometry, and synapsis dynamics.

genomics↗

bioRxiv2026

Sex without crossovers mimics clonal reproduction in the holocentric plant Rhynchospora tenuis

Meiotic recombination ensures accurate chromosome segregation and promotes genetic diversity by generating crossovers between homologous chromosomes1. While essential in most sexually reproducing organisms, recombination is variably regulated and can be absent in some lineages, a condition known as achiasmy2. However, obligate achiasmy in both sexes of a sexual species has not been previously documented. Here, we investigate the beak-sedge Rhynchospora tenuis, a holocentric plant with the lowest known chromosome number among flowering plants (n = 2) and inverted meiosis3. Using chromosome-scale genome assemblies from nine accessions, molecular cytogenetics, immunocytochemistry, high-throughput single-gamete sequencing and whole-genome sequencing of controlled crosses, we show that R. tenuis undergoes obligate, genome-wide achiasmy in both male and female meiosis. Despite normal early meiotic axis formation, synapsis fails, crossovers are not detected cytologically or genetically, and univalents persist at metaphase I. Extensive haplotype-specific accumulation of transposable elements (TEs) generates segregation distortion (e.g. meiotic drive), favouring the transmission of larger, TE-rich chromosomes. Remarkably, sexual reproduction is retained with fertilisation producing viable seeds only when translocation-compatible gametes meet, indicating strong post-meiotic selection that eliminates incompatible homozygous combinations. As a result, all surviving offspring are genetically identical to the maternal genotype, effectively restoring heterozygosity each generation and mimicking clonal reproduction. We propose that the combined effects of recombination loss, low chromosome number, holocentricity, inverted meiosis, and selective transmission of longer chromosomes enable faithful segregation and clonal-like inheritance despite sexual reproduction. These findings challenge the boundary between sex and clonality, revealing a unique evolutionary strategy linking genome architecture, recombination loss, and transmission bias.

evolutionary biology↗

bioRxiv2025

A high-quality reference genome for the Ural Owl (Strix uralensis) enables investigations of cell cultures as a genomic resource for endangered species

BackgroundReference genomes have a wide range of applications. Yet, we are from a complete genomic picture for the tree of life. We here contribute another piece to the puzzle by providing a high-quality reference genome for the Ural Owl (Strix uralensis), a species of conservation concern and efforts affected by habitat destruction and climate change. ResultsWe generated a reference genome assembly for the Ural Owl based on high-fidelity (HiFi) long reads and chromosome conformation capture (Hi-C) data. It figures amongst the best avian genome assemblies currently available (BUSCO completeness of 99.94 %). The primary assembly had a size of 1.38 Gb with a scaffold N50 of 90.1 Mb, while the alternative assembly had a size of 1.3 Gb and a scaffold N50 of 17.0 Mb. We show an exceptionally high repeat content (21.07 %) that is different from those of other bird taxa with repeat extensions. We confirm a Strix characteristic chromosomal fusion and support the observation that bird microchromosomes have a higher density of genes, associated with a reduction in gene length due to shorter introns. An analysis of gene content provides evidence of changes in the keratin gene repertoire as well as modifications of metabolism genes of owls. This opens an avenue of research if this is related to flight adaptations. The population size history of the Ural Owl decreased over long periods of time with increases during the Eemian interglacial and stable size during the last glacial period. Ever since it is declining to its currently lowest effective population size. We also investigated cell culture of progressive passages as a tool for genetic resources. Karyotyping of passages confirmed no large variants, while a SNP analysis revealed a low presence of short variants across cell passages. ConclusionsThe established reference genome is a valuable resource for ongoing conservation efforts, but also for (avian) comparative genomics research. Further research is needed to determine whether cell culture passages can be safely used in genomic research.

genomics↗