Biology subjects

Avila Robledillo, L.

Publications and source records attributed to Avila Robledillo, L..

6 recordsLinked to original sources

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↗

bioRxiv2026

Pangenome analysis reveals the evolutionary dynamics of repeat-based holocentromeres

Centromeres are essential for chromosome segregation, yet their organisation and evolution remain poorly understood in holocentric species, where kinetochore activity is distributed along entire chromosomes1,2. While monocentric centromeres are often structured by megabase-sized satellite arrays3-5, the role of repetitive DNA in holocentric systems remains enigmatic. Here, we analyse the dynamics of centromeric Tyba satellite DNA repeats and transposable elements across a chromosome-scale pangenome comprising 56 long-read haplotype assemblies from 20 Rhynchospora species6,7, a plant genus with repeat-based holocentromeres8,9. We identify over 4.6 million monomers of the Tyba satellite repeat, arranged into 43,400 discrete arrays that span all chromosomes. CENH3 ChIP-seq reveals that, unexpectedly, the same Tyba satellite defines holocentromere across the entire genus, demonstrating deep conservation of centromeric DNA over over 40 million years despite extensive karyotype evolution and centromere array turnover. We show that Tyba arrays function as modular centromeric units whose number and spacing, but not size, scale with chromosome length. Tyba sequence diversity recapitulates species phylogeny, while higher-order repeat formation and antagonism with transposable elements shape array turnover. A novel synteny-aware algorithm reveals rapid gain, loss, and rearrangement of arrays across homologous chromosomes. Using cytogenetics and polymer simulations, we demonstrate that inter-array spacing governs chromatin loop length and chromatid thickness, linking repeat-based holocentromere organisation directly to chromosome mechanics. Our findings uncover a scalable, modular logic for holocentromere function and establish a framework for understanding the plasticity of repeat-based centromere evolution and genome architecture in eukaryotes.

genomics↗

bioRxiv2025

Contrasting centromere structures in carnivorous sundews uncover a dynamic evolutionary trajectory shaped by polyploidy and chromosomal remodeling

Centromeres are essential for chromosome function, yet their role in shaping genome evolution in polyploid plants remains poorly understood. Allopolyploidy, where post-hybridization genome doubling merges parental genomes that may differ markedly in chromosomal architecture, has the potential to increase centromeric complexity and influence genomic plasticity. We explore this possibility in carnivorous Caryophyllales, a morphologically and chromosomally diverse plant lineage encompassing sundews, Venus flytraps, and Nepenthes pitcher plants. Focusing on sundews (Drosera), we generated chromosome-scale assemblies of holocentric D. regia and monocentric D. capensis, which share an allohexaploid origin but have diverged dramatically in genome structure. D. regia retains ancestral chromosomal fusions, dispersed centromeric repeats, and conserved synteny, whereas D. capensis exhibits extensive chromosomal reorganization and regionally localized centromeres after a lineage-specific genome duplication. Phylogenomic evidence traces D. regia to an ancient hybridization between sundew- and Venus flytrap-like ancestors, setting it apart within its infrageneric context. Genus-wide satellite DNA repeat profiling reveals rapid turnover and species-level variation in centromere organization. Together, these results establish sundews as a natural system for investigating how centromere dynamics interact with recurrent polyploidization and episodes of ecological innovation to shape genomic resilience.

genomics↗

bioRxiv2022

Assembly of the 81.6 Mb centromere of pea chromosome 6 elucidates the structure and evolution of metapolycentric chromosomes

Centromeres in the legume genera Pisum and Lathyrus exhibit unique morphological characteristics, including extended primary constrictions and multiple separate domains of centromeric chromatin. These so-called metapolycentromeres resemble an intermediate form between monocentric and holocentric types, and therefore provide a great opportunity for studying the transitions between different types of centromere organizations. However, because of the exceedingly large and highly repetitive nature of metapolycentromeres, highly contiguous assemblies needed for these studies are lacking. Here, we report on the assembly and analysis of a 177.6 Mb region of pea (Pisum sativum) chromosome 6, including the 81.6 Mb centromere region (CEN6) and adjacent chromosome arms. Genes, DNA methylation profiles, and most of the repeats were uniformly distributed within the centromere, and their densities in CEN6 and chromosome arms were similar. The exception was an accumulation of satellite DNA in CEN6, where it formed multiple arrays up to 2 Mb in length. Centromeric chromatin, characterized by the presence of the CENH3 protein, was predominantly associated with arrays of three different satellite repeats; however, five other satellites present in CEN6 lacked CENH3. The presence of CENH3 chromatin was found to determine the spatial distribution of the respective satellites during the cell cycle. Finally, oligo-FISH painting experiments, performed using probes specifically designed to label the genomic regions corresponding to CEN6 in Pisum, Lathyrus, and Vicia species, revealed that metapolycentromeres evolved via the expansion of centromeric chromatin into neighboring chromosomal regions and the accumulation of novel satellite repeats. However, in some of these species, centromere evolution also involved chromosomal translocations and centromere repositioning. SignificanceDespite their conserved function, plant centromeres exhibit considerable variation in their morphology and sequence composition. For example, centromere activity is restricted to a single region in monocentric chromosomes, but is distributed along the entire chromosome length in holocentric chromosomes. The principles of centromere evolution that led to this variation are largely unknown, partly due to the lack of high-quality centromere assemblies. Here, we present an assembly of the pea metapolycentromere, a unique type of centromere that represents an intermediate stage between monocentric and holocentric organizations. This study not only provides a detailed insight into sequence organization, but also reveals possible mechanisms for the formation of the metapolycentromere through the spread of centromeric chromatin and the accumulation of satellite DNA.

genomics↗

bioRxiv2019

Genome-wide characterization of satellite DNA arrays in a complex plant genome using nanopore reads

BackgroundAmplification of monomer sequences into long contiguous arrays is the main feature distinguishing satellite DNA from other tandem repeats, yet it is also the main obstacle in its investigation because these arrays are in principle difficult to assemble. Here we explore an alternative, assembly-free approach that utilizes ultra-long Oxford Nanopore reads to infer the length distribution of satellite repeat arrays, their association with other repeats and the prevailing sequence periodicities.\n\nResultsWe have developed a computational workflow for similarity-based detection and downstream analysis of satellite repeats in individual nanopore reads that led to genome-wide characterization of their properties. Using the satellite DNA-rich legume plant Lathyrus sativus as a model, we demonstrated this approach by analyzing eleven major satellite repeats using a set of nanopore reads ranging from 30 to over 200 kb in length and representing 0.73x genome coverage. We found surprising differences between the analyzed repeats because only two of them were predominantly organized in long arrays typical for satellite DNA. The remaining nine satellites were found to be derived from short tandem arrays located within LTR-retrotransposons that occasionally expanded in length. While the corresponding LTR-retrotransposons were dispersed across the genome, this array expansion occurred mainly in the primary constrictions of the L. sativus chromosomes, which suggests that these genome regions are favorable for satellite DNA accumulation.\n\nConclusionsThe presented approach proved to be efficient in revealing differences in long-range organization of satellite repeats that can be used to investigate their origin and evolution in the genome.

genomics↗