Biology subjects

Fernandez, R.

Publications and source records attributed to Fernandez, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Sea stickleback genome reveals repeated chromosomal rearrangements in sticklebacks

Sticklebacks (Gasterosteidae) encompass model organisms which are of particular interest for evolutionary and ecological genomics. Within Gasterosteidae, chromosome number is variable (2n=40-46) and independent fusions of homologous chromosomes have been proposed. The sea stickleback (or fifteen-spined stickleback, Spinachia spinachia ) has the lowest known number of chromosomes (2n=40) and hence is crucial in understanding chromosome evolution among sticklebacks, but is so far missing in genomic datasets. Here, we present a high-quality diploid genome assembly of S. spinachia. PacBio HiFi and Hi-C reads were assembled into a genome of 407.5 Mb in size, consisting of 20 chromosomes, with an N50 of 6.6 Mb and 98.96% complete single-copy BUSCO genes. A phylogenetic tree inferred across five stickleback species and four outgroup genomes from 19,156 genes, alongside synteny analyses and ancestral chromosome reconstructions, confirms S. spinachia as the sister species to the four-spined stickleback (Apeltes quadracus) and not as the sister group to all other sticklebacks as once thought. It has one species-specific chromosome fusion and shares two fusions with the three-spined stickleback (Gasterosteus aculeatus), none of which are present in its sister species. One of these fusions is also present in Pungitius, leading to reinterpretion of this fusion as ancestral to Gasterosteidae, with subsequent fission in Apeltes. This implies a lower ancestral chromosome number in Gasterosteidae (2n=44) than previously thought. The other fusion shared with G. aculeatus presents a case of convergence. Our results suggest that karyotype evolution in Gasterosteidae has been shaped by ancestral chromosome fusion, convergent fusion, and secondary fission.

evolutionary biology↗

bioRxiv2026

ERGA-BGE reference genomes of Hyalomma lusitanicum and its obligate Francisella endosymbiont as a genomic resource for One Health research

Hyalomma lusitanicum is a characteristic tick species of the western Mediterranean region, with a well-established distribution across the Iberian Peninsula. It is strongly associated with wild ungulates, particularly red deer, as well as livestock, to which it can transmit a wide range of pathogens, including viruses, bacteria, and protozoa. Here, we present three genomic resources for H. lusitanicum: a scaffold-scale nuclear genome, the complete mitochondrial genome, and the complete genome of its associated Francisella bacterial endosymbiont. The nuclear genome assembly spans 1.81 Gb and comprises 59 scaffolds, with a scaffold N50 of 153.6 Mb (L50 = 5) and no gaps, indicating high contiguity and completeness with a gene annotation completeness BUSCO score of 97.1 %. Genome annotation of the nuclear assembly identified 20,638 protein-coding genes, 1,422 non-coding genes, and 5,775 pseudogenes. A total of 18 scaffolds were assembled as putative chromosomes, exceeding the 11 chromosomes inferred as ancestral; however, synteny analyses suggest that several scaffolds likely represent fragmented portions of the same chromosome, probably due to incomplete Hi-C scaffolding. Despite this, the assembly represents one of the most complete tick nuclear genomes generated to date. In addition, we report the complete genome of a Francisella endosymbiont (1.51 Mb, 1,679 genes), characterized by a high proportion of pseudogenes and reduced genome size, consistent with patterns of genome reduction associated with obligate symbiosis. Together, these genomic resources provide a framework to investigate local adaptation and host-symbiont evolution, and to support improved surveillance, control, and management strategies for species of public health relevance.

genomics↗

bioRxiv2026

LINGUINE: a phylogeny-aware, orthogroup-based framework for robust ancestral linkage group inference

Reconstructing the chromosomal architecture of ancestral genomes is a central challenge in comparative genomics, yet existing methods for ancestral linkage group (ALG) inference struggle in clades with rapid genome evolution. Current approaches rely predominantly on single-copy orthologous genes to anchor linkage groups between species, limiting marker density and lacking mechanisms to resolve paralogy, which leads to systematic inflation of inferred ALG counts and propagates structural artifacts in downstream analyses. Here we present LINGUINE (LINkage GroUps INfErence), a phylogeny-aware pipeline for robust ALG reconstruction addressing these limitations. LINGUINE uses orthogroups to maximise marker density, employs a Hidden Markov Model to delineate syntenic blocks while accommodating gene loss, rearrangements, and assembly fragmentation, and incorporates an explicit paralogy resolution step prior to ancestral reconstruction. Ancestral states are inferred through iterative post-order traversal of the species tree, progressively integrating information from all descendants. Using GARLIC (Genome reARrangement simuLator for Inferring Chromosomal landscapes), we characterise the limits of synteny signal detectability and define the conditions under which ALG reconstruction remains reliable. Benchmarking on nematodes demonstrates concordant performance with existing tools while incorporating a substantially larger fraction of the gene repertoire. Applied to clitellate annelids, a clade with highly rearranged genomes, LINGUINE recovers biologically coherent ancestral architectures that existing methods fail to resolve. These results establish LINGUINE as a flexible framework for ancestral genome reconstruction in clades where traditional approaches lose resolution. LINGUINE and GARLIC are open source and available in GitHub (https://github.com/MetazoaPhylogenomicsLab/Vargas-Chavez-Fernandez_2026_LINGUINE, and https://github.com/MetazoaPhylogenomicsLab/Vargas-Chavez-Fernandez_2026_GARLIC).

evolutionary biology↗

bioRxiv2026

Lungfish comparative genomics reveals ancient gene networks co-opted for life on land

The transition from water to land was a defining event in vertebrate evolution, requiring major changes in physiology and gene regulation. Lungfish, the closest extant relatives of tetrapods, offer a unique window into this process through their capacity for estivation, a physiological state that mirrors key demands of terrestrial life. Here, we constructed and compared gene co-expression networks across five vertebrate species using multi-tissue transcriptomic data. Focusing on estivating lungfish tissues, we identified conserved modules enriched in core functions, including metabolic regulation, RNA processing, and protein turnover. We further show that a subset of retained ohnologs from the vertebrate 2R-WGD act as network hubs under directional selection in key phylogenetic branches. These genes, involved in membrane trafficking, cytoskeletal regulation, water balance, and stress response, illustrate how duplicated, dosage-sensitive genes were co-opted to meet the physiological demands of terrestrial adaptation. Together, our findings support a model in which ancient whole-genome duplications supplied raw material later shaped by selection and network rewiring to enable extreme physiological adaptations such as estivation. TeaserAncient duplicated gene networks in lungfish estivation reveal how vertebrates repurposed genomic toolkits to adapt to land.

evolutionary biology↗

bioRxiv2026

Transformer-Based Phenotyping of Rice Root Aerenchyma Across Environments Enables Climate-Smart Rice Selection

Quantification of root anatomical traits such as cortical aerenchyma is key to understanding rice adaptation to diverse water regimes. Recently, the role of aerenchyma in regulating methane emissions has been demonstrated, making it a target for climate change mitigation. Despite its importance, breeding for root anatomical traits remains limited because manual analysis of root cross-sections is labor-intensive, inconsistent, and poorly scalable, and analysis pipelines do not generalize across heterogeneous imaging conditions. We present a deep learning pipeline based on a recent vision transformer architecture to automatically segment rice root anatomical structures and quantify aerenchyma. The model was trained on a multi-environment dataset of 1,760 annotated rice root cross-sections acquired across growth stages, cultivation systems, and countries, using a collaboratively defined annotation protocol. The model achieved high segmentation performance (mean Intersection-over-Union > 0.92) and near-perfect aerenchyma ratio quantification (R2 = 0.98), and was evaluated by two experts as performing on par with, and in some cases better than, expert annotators. Delivered as open-source software with an online interactive demonstrator, the pipeline revealed differences in aerenchyma across genotypes, water regimes, environments, and developmental stages. Overall, this work demonstrates that transformer-based segmentation enables high-throughput anatomical phenotyping, supporting scalable and climate-smart rice breeding. HIGHLIGHTSO_LITransformer-based segmentation enables robust aerenchyma phenotyping across environments C_LIO_LIA SegFormer model achieves expert-level accuracy on diverse rice root cross-sections C_LIO_LIAutomated analysis delivers near-perfect lacuna-to-cortex ratio quantification (R2 {approx} 0.98) C_LIO_LIOur online demonstrator supports scalable, climate-smart rice breeding applications C_LI

physiology↗

bioRxiv2026

Atlas-Based Spatio-temporal MRI Phenotyping of 3D Fungal Spread in Grapevine Wood

In perennial crops, inner wood degradation by pathogens often escapes detection until irreversible damage has occurred. Grapevine trunk disease (GTD) is a well-known example in viticulture that alters plants from within, years before foliar symptoms arise, making early assessment difficult. To overcome this limitation, we present a novel non-destructive 3D + t pipeline for Magnetic Resonance Imaging (MRI) spatial quantification and monitoring of early internal tissue degradation resulting from fungal colonization. This pipeline integrates (i) anatomical alignment and rigid time-series registration of volumetric MRI scans, (ii) a generalized cylindrical coordinate transformation for cross-sectional trunk anatomy normalization, (iii) supervised classification to segment water-depleted (diseased/non-functional) regions, and (iv) population-level statistical analyses including construction of population mean images, probabilistic atlases of lesions, and 3D lesion descriptors. Applied to multiple Vitis vinifera cultivars inoculated with a fungal trunk pathogen, our approach enables time-lapse comparisons between cultivar and treatment in vivo. The results reveal consistent early degradation signals across individuals and cultivar-dependent lesion differences. By combining high-resolution MRI with advanced image processing and statistical atlas tools, this method provides a new paradigm for 3D plant phenotyping of internal disease progression. This methodological innovation allows non-invasive quantification of disease development and comparative assessment of host responses in woody plants, demonstrating its potential to advance understanding and management of GTDs.

bioinformatics↗

bioRxiv2025

Parallel genomic remodeling associated with independent terrestrialization events in arthropods

The repeated transition from aquatic to terrestrial environments (terrestrialization) has shaped the evolutionary trajectory of many animal lineages, yet the genomic basis of this ecological shift remains incompletely understood. Arthropods, with multiple independent terrestrialization events, provide a powerful system to investigate whether parallel genomic changes underlie adaptation to land. Here, we present a phylum-wide comparative phylogenomic analysis of 309 arthropod species representing aquatic and terrestrial lineages, using gene family evolutionary dynamics and directional selection analyses to uncover shared genomic strategies associated with life on land. We identified thousands of orthogroups showing parallel expansions or contractions across the three main lineages that colonized land (Arachnida, Myriapoda, and Hexapoda), of which a significant proportion also exhibited lineage-specific shifts in selective pressure. Functional enrichment of these orthogroups revealed functional convergence on processes such as oxidative stress response, transmembrane transport, energy metabolism, exoskeleton formation, and moulting regulation. Notably, parallel evolution in aquaporins, solute carriers, cytochrome P450s, superoxide dismutases, and heat shock proteins suggests that a conserved terrestrialization toolkit underlies independent colonization events. Additionally, parallel remodeling of key developmental and immune signaling pathways highlights the role of regulatory and structural innovations in adapting to terrestrial challenges. Our results provide the first large-scale genomic evidence of parallel molecular evolution driving arthropod terrestrialization and emphasize the power of comparative genomics to reveal shared solutions to ecological transitions across deep evolutionary timescales.

evolutionary biology↗

bioRxiv2025

Independent genomic trajectories shape adaptation to life on land across animal lineages

How animals repeatedly adapted to life on land is a central question in evolutionary biology. While terrestrialisation occurred independently across animal phyla, it remains unclear whether shared genomic mechanisms underlie these transitions. Here, we combine large-scale comparative genomics, machine learning, and multi-omics data, including proteomics and transcriptomics from stress experiments relevant to terrestrial environmental challenges in 17 species, to investigate the genomic basis of animal terrestrial adaptation. Gene co-expression networks reveal that genes relevant to stress are largely lineage-specific, yet converge in function through the co-option of gene families pre-dating terrestrialisation events. Phylogenomic and machine learning analyses support a dominant role for early-evolving genes, enriched in stress-related functions, paired with a higher gene loss than gain at terrestrialisation nodes. Our findings support a model of lineage-specific genomic changes involving mostly conserved genes that converged at the functional level during the independent transitions to terrestrial life.

evolutionary biology↗

bioRxiv2025

An evaluation of clustering and assembly strategies from Iso-Seq data in the absence of reference genomes in non-model animals

Transcriptome assembly enables the recovery of expressed genes and isoforms, but the optimal strategy for reconstructing transcriptomes from long-read sequencing remains unresolved. In particular, establishing best practices for generating accurate gene models and selecting representative isoforms is essential for comparative genomics, since orthology inference typically requires only the longest isoform per gene model. Here, we systematically compare clustering and de novo assembly methods using PacBio Iso-Seq data from diverse invertebrate lineages with the goal of identifying the most optimal methodology for isoform selection in the absence of dedicated pipelines. We evaluate four approaches: IsoSeq3 (isoseq3 cluster), CD-HIT, RNA-Bloom2 and isONform, all benchmarked against short-read Trinity assemblies. Assembly quality was assessed using BUSCO completeness, short-read mapping rates, coding sequence recovery, longest isoform prediction, and SQANTI3 structural classification. Our results show that CD-HIT clustering at high similarity thresholds ([≥]99%) yields the most complete and coding-rich long-read transcriptomes, rivaling Trinity while avoiding its high redundancy. SQANTI3 classification further confirms that CD-HIT 99 recovers the highest number of full-splice-match transcripts among all methods. Consensus-based methods such as IsoSeq3 and isONform recover fewer single-copy orthologs (mirrored in a lower BUSCO score) and achieve lower mapping rates, while RNA-Bloom2 provides intermediate performance with reduced duplication. Together, these findings establish, to date, CD-HIT as a robust and practical strategy for transcriptome reconstruction from long-read data when genomic references are unavailable. This work provides practical guidance for deriving high-quality gene models and selecting representative isoforms for orthology inference in non-model species.

evolutionary biology↗

bioRxiv2025

PAN-CANCER ANALYSES IDENTIFY ONCOGENIC DRIVERS, EXPRESSION SIGNATURES, AND THERAPEUTIC VULNERABILITIES IN RHO GTPase PATHWAY GENES

RHO family GTPases are key regulators of cancer-related processes such as cytoskeletal dynamics, cell migration, proliferation, and survival. Despite this, a comprehensive understanding of RHO signaling alterations across tumors is still lacking. Here, we present a pan-cancer analysis of 484 genes encoding RHO GTPases, regulators, proximal effectors, distal downstream signaling elements, and components of their proximal interactomes using data from over 10,000 tumor samples and 33 tumor types present in The Cancer Genome Atlas (TCGA). In addition, we have utilized available data from genome-wide functional dependency screens performed in more than 1,000 gene-edited cancer cell lines. This study has uncovered positively selected mutations in both well-known and previously uncharacterized RHO pathway genes. Transcriptomic profiling reveals widespread and tumor-specific differential expression patterns, some of them correlating with copy number changes. Interestingly, certain regulators exhibit consistent expression profiles across tumors opposite to those predicted from their canonical roles. Coexpression and gene set enrichment analyses highlight coordinated transcriptional programs involving some RHO GTPase pathway genes and their linkage to key cancer hallmarks, including extracellular matrix reorganization, cell motility, cell cycle progression, cell survival, and immune modulation. Functional screens further identify context-specific dependencies on several deregulated RHO GTPase pathway genes. Altogether, this study provides a comprehensive map of RHO GTPase pathway alterations in cancer and identifies new oncogenic drivers, expression-based signatures, and therapeutic vulnerabilities that could guide future mechanistic and translational research.

cancer biology↗

bioRxiv2025

Microbiome Dynamics During Translocation of the Critically-Endangered Frog Craugastor ranoides

O_LIAmphibian populations are declining and species going extinct due to habitat loss, climate change and emerging infectious disease, prompting the increasing use of translocations as a conservation tool. C_LIO_LISkin-associated microbial communities play a key role in amphibian health, particularly in protecting hosts from pathogenic infection. However, to date we know relatively little about the impact of translocation on the dynamics of skin-associated microbes, or the consequences of translocation-mediated disturbance of the microbiome for amphibian health. C_LIO_LIWe investigated the skin microbiome of the critically endangered frog Craugastor ranoides, now restricted to a fraction of its historical range in Costa Rica. We first conducted a multi-population survey to characterise among-population variation in skin bacterial communities. We then translocated individuals to a new site, using radio tracking to monitor them over time and assess individual-level changes in body mass, microbiome composition, and predicted microbial function. C_LIO_LIWe found limited among-population variation in skin microbiome composition across three different populations of C. ranoides. Response of the microbiome to translocation was highly individual-specific; some frogs demonstrated relatively stable community richness and composition, whilst others exhibited marked turnover in bacterial membership and predicted function. Body mass showed similar dynamics, but several of the recaptured frogs had gained mass after several days in the translocation site. C_LIO_LISynthesis and Applications: Our findings highlight the importance of considering microbiome dynamics in threatened species translocations to optimize individual health. This includes considering whether individuals should be prioritised for translocation based on their initial microbiome composition, and understanding how shifts in microbiome post-translocation may alter overall success of translocation efforts. These insights extend beyond amphibians, offering a broader framework for integrating long-term monitoring of host microbiomes and health into conservation efforts. C_LI

ecology↗

bioRxiv2025

Reactivation of threat conditioning memory in humans: disentangling the effects on emotional memory and cognitive biases.

Learning to detect and respond to threats is fundamental for survival and is often modeled through threat conditioning (TC) paradigms. While these paradigms reliably produce implicit memories that elicit physiological and behavioral responses to conditioned stimuli (CS), less is explored about how TC influences cognitive and emotional biases, particularly those implicated in anxiety disorders, such as threat overestimation and negative stimulus representation. In this study, we investigated the dynamic interaction between the reactivation of the implicit threat memory and these cognitive biases using a validated TC paradigm in humans. In Experiment 1, participants underwent TC on Day 1, followed by a memory reactivation session (incomplete reminder: one unreinforced CS+) and a highly demanding working memory (HWM) task, used as an amnesic manipulation, or a control condition on Day 2. On Day 3, memory retention was tested using a simplified, single-trial protocol (one CS+, one CS-, and one neutral CS), followed by tasks assessing threat valuation and representation. Results indicated that the HWM task administered post-reactivation significantly reduced skin conductance responses (SCRs) and attenuated cognitive biases, without altering expectancy of the unconditioned stimulus (US). In Experiment 2, we evaluated the effect of varying reactivation frequency (none, one, or two reminders) on implicit memory and cognitive biases. While repeated reactivations generalized the conditioned response to other stimuli, cognitive and emotional biases remained stable, suggesting a dissociation between memory generalization and evaluative processing. These findings demonstrate that implicit threat memories can be selectively modified through post-reactivation interventions, affecting both physiological and cognitive-emotional domains. Importantly, the distinct effects of memory reactivation and reconsolidation on physiological versus cognitive outcomes support the existence of temporally and functionally dissociable mechanisms. This research highlights the need to consider cognitive biases alongside physiological responses when evaluating memory-based interventions and offers novel insight into mechanisms underlying anxiety maintenance and treatment.

neuroscience↗

bioRxiv2025

Lizards on a sky archipelago: Genomic approaches to the evolution of the mountain genus Iberolacerta

The mountain-dwelling lizards of the genus Iberolacerta inhabit several isolated massifs across central and southwestern Europe. Their restricted and fragmented ranges, coupled with high altitude specialization in most species, entail a significant threat in the context of climate change for this group of lizards that has attracted interest from different fields. On the one hand, the alpine confinement of these relict species precedes the Pleistocene glacial cycles, and a few hypotheses have been proposed to explain it: from competitive exclusion by the wall lizards of the genus Podarcis, to adaptations to either cold or hypoxia, that would prevent them from expanding into lowlands. On the other hand, extensive research on chromosome evolution has shown Iberolacerta karyotypes to fairly differ from other lacertid lizards, exhibiting reductions in chromosome numbers and multiple sex chromosome determination systems. Here we present a chromosome-level genome assembly for Iberolacerta aurelioi, an Endangered rock lizard endemic to the Pyrenees. This genome has shed light on a genome architecture shaped by chromosome fusions, whose adaptive potential we discuss, as well as on expression shifts towards a hemoglobin isoform of enhanced oxygen affinity, as an adaptation to altitudinal hypoxia. In addition, medium coverage whole-genome sequencing data from 12 representatives encompassing all species and subspecies within the genus allowed us to address phylogenomic relationships, unveiling introgression events, gathering evidence in support of the competitive exclusion hypothesis through past demographic inference, and providing insights into homozygosity burdens, which offer valuable information for conservation efforts.

genomics↗

bioRxiv2025

A chromosome-level genome of the King penguin (Aptenodytes patagonicus): an emerging model-in-the-wild for studying evolution

The King penguin (Aptenodytes patagonicus) is an iconic species of the Southern Ocean and is currently being developed as a model-in-the-wild for understanding evolution. We present a high-quality, haplotype-resolved 1.35 Gb chromosome-level genome of an adult female King penguin - Pen/Se-guin - from the Crozet Archipelago, assembled using PacBio HiFi long-read sequencing and Hi-C proximity data. 94.93% of the assembly is assigned to 34 chromosomes (32 autosomes, plus the Z and W chromosomes), with a BUSCO completeness of 97.2%, a k-mer completeness of 99.7%, and a quality value (QV) of 63.8. We also assembled a circularised mitogenome (20,520 bp), which includes the avian tandem duplication (TD). Annotation of repetitive sequences revealed that 16.3% of the genome comprises repetitive elements, with LINEs being the most abundant transposable element class (5.6%). Gene prediction using an extensive multi-tissue RNA-seq dataset resulted in 18,081 predicted protein-coding genes, of which 17,081 were functionally annotated, with a BUSCO completeness of 98.4% and an OMArk completeness of 97.3%. The presented assembly substantially improves the quality of a previous draft genome, showing a 28-fold increase in assembly contiguity and a significantly improved genome annotation, exceeding the standards of the Earth BioGenome Project (EBP) and Vertebrate Genomes Project (VGP). This high-quality genome will enable ongoing and future studies harnessing the King penguin as a model-in-the-wild to test hypotheses on the genotype-to-fitness link, ageing, life-history trait evolution, and adaptation.

genomics↗

bioRxiv2025

ERGA-BGE genome of Noah's Ark shell (Arca noae Linnaeus, 1758), a Mediterranean bivalve species

Arca noae, also known as the Noahs Ark clam, is a bivalve mollusk found in the shallow coastal waters of the Mediterranean Sea and the eastern Atlantic Ocean. This species plays a crucial ecological role by filtering plankton and organic particles from the water, helping maintain water quality and supporting nutrient cycling in marine ecosystems. It is also an important food source for various marine predators, including fish and crustaceans, thereby contributing to the coastal food web. Arca noae is notably resilient to environmental stressors, such as temperature fluctuations, changes in salinity, and pollution, making it a valuable model species for studying how bivalves adapt and respond to stress. While it is not commonly harvested commercially, Arca noae is of great interest to marine researchers due to its ability to thrive in diverse coastal habitats. The reference genome of Arca noae will thus provide important evolutionary insights. The entirety of the genome sequence was assembled into 19 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 1.5 Gb, composed of 257 contigs and 119 scaffolds, with contig and scaffold N50 values of 20.5 Mb and 84.7 Mb, respectively.

genomics↗

bioRxiv2025

ERGA-BGE genome of Coenonympha oedippus: an IUCN endangered European butterfly species occurring in two ecotypes

The reference genome of the False ringlet (Coenonympha oedippus) will serve as a valuable resource for uncovering the genetic mechanism underlying the species' adaptability to two ecologically distinct habitats. Through this genome we might be able to determine whether (i) each ecotype is monophyletic, indicating that the ecological divergence represents an early stage of speciation, (ii) the ecotypes have evolved through divergent evolution of habitat preference, or (iii) the differences between ecotypes are solely due to phenotypic plasticity or epigenetic variation. This reference genome is also a prerequisite for the planning, design, and implementation of conservation measures for this endangered species, taking into account its intraspecific diversity. Furthermore, it holds broader implications for population genomic studies of the species-rich genus Coenonympha, which includes some of the most endangered butterfly taxa in Europe. The complete genome sequence was assembled into 30 contiguous chromosomal pseudomolecules (sex chromosomes included). This chromosome-level assembly encompasses 0.39 Gb, composed of 385 contigs and 62 scaffolds, with contig and scaffold N50 values of 2.8 Mb and 14.2 Mb, respectively.

genomics↗

bioRxiv2025

ERGA-BGE Reference Genome of Loboptera subterranea: a cave adapted cockroach endemic to the Canary Islands

Species of the genus Loboptera from the Canary Islands are adapted to life in subterranean environments, except Loboptera canariensis and Loboptera decipiens which inhabit epigean, often influenced by human activities. The genome of Loboptera subterranea provides a valuable resource for understanding the genetic basis of how the Canarian Loboptera species evolved and thrived in subterranean environments. A total of 14 contiguous chromosomal pseudomolecules were assembled from the genome sequence. This chromosome-level assembly encompasses 2.7 Gb, composed of 486 contigs and 90 scaffolds, with contig and scaffold N50 values of 13.1 Mb and 202.7 Mb, respectively.

genomics↗

bioRxiv2025

ERGA-BGE genome of Cheirolophus tagananensis: an IUCN endangered shrub endemic to the Canary Islands

The reference genome of Cheirolophus tagananensis, locally known as the Cabezon de Taganana, will provide an exceptional opportunity to establish a new framework to develop comparative genomic tools. These tools will help uncover the genetic basis of rapid plant radiations and microevolutionary adaptation processes of insular species on oceanic islands. This genomic resource will also contribute to facilitate the establishment of better informed in situ and ex-situ conservation strategies for this narrow endemic in the face of potential habitat degradation, and support taxonomic studies to better understand genetic diversity at the population, species, and genus levels. A total of 16 contiguous chromosomal pseudomolecules were assembled from the genome sequence. This chromosome-level assembly encompasses 0.62 Gb, composed of 421 contigs and 235 scaffolds, with contig and scaffold N50 values of 4.0 Mb and 36.5 Mb, respectively.

genomics↗