Biology subjects

Escudero, M.

Publications and source records attributed to Escudero, M..

7 recordsLinked to original sources

bioRxiv2026

Multi-Omics analysis provides crucial insights into ecological adaptation to dryland of a dominant grass (Psammochloa villosa, Poaceae) in Northwest China

Desertification exerts dramatic selection pressures on the evolution of plants. Despite the key role of ecological adaptation by natural selection to arid grasslands and subsequent intraspecific divergence, specific mechanisms driving this process remain poorly understood. Psammochloa villosa, a perennial forage grass endemic to the arid grasslands in Northwest China, where it thrives in shifting and semi-fixed sand land due to its exceptional drought tolerance, provides an ideal system to study adaptive evolution to aridity. In our study, we assembled a high-quality, chromosome-scale genome and conducted genomic resequencing of 42 populations across its major distribution. The genome assembly, which is approximately 1.55 Gb in size, has a super-scaffold N50 of 66.79 Mb, with 75.84% of the sequences identified as transposable elements. Coalescent phylogeny and genomic collinearity analyses strongly supported that P. villosa and Neotrinia splendens, as the closest taxa, shared a recent whole-genome duplication (WGD) event occurring approximately 18-20 Mya and followed by their divergence around ~11.2 Mya. Based on ancestral grass karyotype (AGK) reconstruction from synteny analysis, our results suggest that, relative to the AGK after the {rho}-WGD event, P. villosa and N. splendens underwent similar chromosomal restructuring and lineage-specific retention of numerous copies, providing a genomic basis for potential ecological adaptation and intraspecific diversification. The expanded XTH family, which encodes enzymes mediating xyloglucan endotransglucosylation and hydrolysis and thereby regulating xyloglucan remodeling, showed strong transcriptional responses under PEG-6000 treatment, suggesting that retained copies may be associated with xerophytic adaptation in P. villosa. Together, these findings suggest that WGD-derived gene retention created a delayed reservoir of genetic diversity that was later shaped by desertification and Qinghai-Xizang Plateau environmental changes, contributing to climate-associated genomic islands and intraspecific differentiation.

genomics↗

bioRxiv2026

A Modular Synthetic Hydrogel with Cell-scale Micropores Modulates Osteocyte-like Morphogenesis and Osteogenic Differentiation In Vitro

One crucial step during early osteogenesis is the embedding of osteoblasts within a collagen-rich extracellular matrix (osteoid), where they subsequently differentiate into a functional network of osteocytes. However, reconstructing 3D osteocyte networks in vitro remains a major challenge. We recently developed a synthetic microporous hydrogel to support the in vitro culture of 3D bone cell networks. Although matrix biodegradability facilitates cell-material interactions, the influence of micropores on bone tissue morphogenesis and differentiation remains poorly understood. Here, we investigate the effect of cell-scale micropores on bone cell morphogenesis and osteogenic differentiation in vitro. By exploiting polymerization-induced phase separation (PIPS) between 4-arm polyethylene glycol vinyl sulfones and dextran in the presence of hyaluronan, we generated matrix metalloproteinase-sensitive hydrogels with cell-scale micropores. Increasing the dextran concentration enlarged the average pore size from 4 m to 8 m, accompanied by a slight decrease in mechanical stiffness. Following encapsulation within these hydrogels, primary human osteoblasts remained highly viable. Hydrogels with larger pores supported extensive 3D cell network formation, whereas hydrogels with smaller pores exhibited enhanced osteogenic differentiation following 21 days of osteogenic culture. Together, these findings highlight that bone cells are sensitive to microporous physical cues and even minor changes over pore sizes can make an impact on osteocyte-like morphogenesis and differentiation in vitro.

bioengineering↗

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

Genomic insights into the karyotypic radiation of a narrow endemic holocentric plant Carex helodes

Holocentric chromosomes allow rapid genome changes through chromosomal rearrangements such as fissions, fusions, inversions or translocations. The plant genus Carex shows one of the highest rates of karyotypic evolution among holocentric organisms. We studied the genomic patterns underlying chromosomal rearrangements in the karyotypic radiation of the narrow endemic species Carex helodes (2n = 68-75). Comparing genome assemblies of C. helodes from the two karyologically distinct extremes of its European distribution, revealed a striking number of eight chromosomal rearrangements including fusions, translocations and inversions. Genomic breakpoints are gene-poor and TE-rich, corroborating findings in other species and suggesting common genomic characteristics that facilitate the evolution and establishment of chromosomal rearrangements. We identified a chromosomal inversion exhibiting patterns of purifying selection and enrichment in functional genes that potentially mediate rearrangement tolerance. Conversely, another inversion displayed elevated sequence divergence and enrichment in response to temperature stress and phosphate limitation, matching key environmental variables that differ between the study localities. The establishment of chromosomal rearrangements along Carex helodes European populations was likely driven by demographic bottlenecks and distinct genomic features at breakpoints. Our findings provide preliminary evidence on the rearrangement role in population differentiation either as reproductive barriers or as genomic islands of differentiation.

genomics↗

bioRxiv2025

Chromosome Size as a Universal Predictor of Recombination Rate: Insights from Holocentric and Monocentric Systems

Recombination is a fundamental evolutionary process essential for generating genetic diversity, facilitating adaptation, and driving speciation. However, direct measurement of recombination rate remains challenging, as standard methods--such as chiasma counts or genetic linkage maps--are labor-intensive and often infeasible for non-model species. In this study, we identify chromosome number and mean chromosome size as practical proxies for genome-wide recombination rate by analyzing genetic map data from 73 insect species and supplementary analyses of 157 monocentric flowering plants. We confirm the long-standing hypothesis that monocentric species have nearly twice as many crossovers per chromosome as holocentric species, reflecting structural constraints imposed by diffuse centromeres. Using both ordinary and phylogenetically informed Bayesian regression models, we show that recombination rate increases with chromosome number and decreases with mean chromosome size. Crucially, mean chromosome size is a significantly better predictor, particularly in holocentric species. This insight enables recombination rate estimation in thousands of species with known genome and chromosome sizes, thereby allowing hypothesis testing at scales previously unattainable. Building on these results, we present predictive models applicable to poorly studied holocentric plants. Overall, our study highlights the pivotal role of chromosome architecture in recombination evolution and provides an accessible framework for evolutionary genomic research across diverse lineages. Article summaryWhy do some species have more genetic shuffling than others? We investigated 73 insect species with detailed genetic maps and found that mean chromosome size is the best predictor of genome-wide recombination rate, not the number of chromosomes. This means we can now estimate recombination rates even in species where genetic maps are unavailable, using only genome size and chromosome number. We also show that chromosome structure matters--species with a single centromere per chromosome (monocentric) have nearly double the recombination compared to those with diffuse centromeres (holocentric). These insights open new doors for studying evolution across many organisms.

genetics↗

bioRxiv2024

Identifying conservation priorities of a pantropical plant lineage: a case study in Scleria (Cyperaceae)

Scleria is a pantropical genus of annual and perennial herbs and the sixth largest genus in the Cyperaceae family with around 261 species. In this study, we produced preliminary extinction risk assessments for the [~]30% of Scleria species that do not yet have a global Red List assessment and followed the Evolutionarily Distinct and Globally Endangered (EDGE2) and Ecologically Distinct and Globally Endangered (EoDGE) protocols to identify evolutionary and ecologically unique Scleria species at greatest risk of extinction and hotspots of rare and endangered species. Our results indicate that 38 of the 78 Scleria species not yet included in the Red List, and 26% of species in the genus, are potentially threatened with extinction. The risk of extinction is not equally distributed across the phylogeny, and the Afrotropics and the Neotropics accumulate most threatened species. Eleven ecoregions mostly from four African (Madagascar, D.R. Congo, Zambia and Tanzania) and two South American (Brazil, Venezuela) countries accumulate almost half of Scleria species and stand out in terms of their sum of EDGE2 scores. Phylogenetic and functional distinctiveness metrics were largely uncorrelated, and the EcoDGE metric mostly points towards South American countries as reservoirs of ecologically distinctive and endangered species: Brazil, Venezuela, Bolivia, Peru, Colombia, Guyana and Dominican Republic. Recent methodological advances in the identification of species at-risk of extinction and the novel EDGE2 framework emerge as powerful tools to identify conservation priorities.

ecology↗

bioRxiv2023

Global analysis of Poales diversification - parallel evolution in space and time into open and closed habitats

O_LIPoales are one of the most species-rich, ecologically and economically important orders of plants and often characterise open habitats, enabled by unique suites of traits. We test the hypotheses that Poales species are assembled into distinct phyloregions, with centres of high phylogenetic diversity and endemism clustered in tropical regions, and that cosmopolitan families show parallel transitions into open and closed habitats at different times. C_LIO_LIWe sampled 42% of Poales species and obtained taxonomic and biogeographic data from the World Checklist of Vascular Plants database, which was combined with open/closed habitat data scored by taxonomic experts. A dated supertree of Poales was constructed. We integrated spatial phylogenetics with regionalization analyses, historical biogeography, ancestral state estimations, and models of contingent evolution. C_LIO_LIDiversification in Poales and assembly of open and closed habitats result from dynamic evolutionary processes that vary across lineages, time, space, and traits, most prominently in tropical and southern latitudes. Our results reveal parallel and recurrent patterns of habitat and trait transitions in the species-rich families Poaceae and Cyperaceae, yet other smaller families display unique evolutionary trajectories. C_LIO_LIThe Poales have achieved global dominance via parallel evolution in open habitats, with notable, spatially and phylogenetically restricted divergences into strictly closed habitats. C_LI

ecology↗