Biology subjects

Fernandez, R.

Publications and source records attributed to Fernandez, R..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

ERGA-BGE genome of Pinctada radiata (Leach, 1814): one of the first Lessepsian migrants

Pinctada radiata, commonly known as the Gulf pearl oyster, is a species of pearl oyster found primarily in the warm waters of the Red Sea, the Persian Gulf, and parts of the Indian Ocean. Pinctada radiata contributes to marine ecosystems by filtering water, which helps maintain water quality and supports other marine life. This species is the first bivalve Lessepsian migrant, having migrated from the Red Sea to the Mediterranean Sea via the Suez Canal. The reference genome of Pinctada radiata could help identify genes enabling adaptation to varying temperatures and salinities, facilitating survival in diverse and newly colonized habitats allowing comparisons with other bivalves to uncover shared and unique genetic adaptations. Additionally, the genome could support targeted management practices and conservation initiatives, such as habitat restoration and selective breeding, ensuring the long-term sustainability of P. radiata. The entirety of the genome sequence was assembled into 14 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 0.93 Gb, composed of 220 contigs and 44 scaffolds, with contig and scaffold N50 values of 8.1 Mb and 63.8 Mb, respectively.

genomics↗

bioRxiv2025

ERGA-BGE genome of Stigmatoteuthis arcturi Robson, 1948: the jewelled squid

The Stigmatoteuthis arcturi reference genome offers a valuable resource for understanding the evolutionary patterns of oceanic squids, who perform important ecological roles as both predators and prey in mesopelagic and deep-sea environments, while their genomes remain understudied. The entirety of the genome sequence was assembled into 46 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 3.25 Gb, composed of 1,268 contigs and 497 scaffolds, with contig and scaffold N50 values of 11.0 Mb and 74.6 Mb, respectively.

genomics↗

bioRxiv2025

A proteo-transcriptomic investigation of toxin evolution in planarians and their role in flatworm terrestrialization

The transition from aquatic to terrestrial environments represents a major evolutionary transition in animals, requiring significant adaptations in physiology and defense mechanisms to the challenges presented by the harsh terrestrial environment. Platyhelminthes, which include both aquatic and terrestrial species with a single terrestrialization event in the family Geoplaniidae, serve as excellent model organisms for studying the evolutionary adaptations required for terrestrialization. This study investigates the evolutionary dynamics of toxin orthologous groups (as a proxy to gene families) in aquatic and terrestrial flatworms, together with mucus composition, focusing on their role in terrestrialization from a molecular ecology perspective. Using a proteo-transcriptomic approach, we predicted and identified a broader toxin gene repertoire in terrestrial flatworms compared to freshwater ones. Although most toxins in flatworms arose before terrestrial planarian diversification--gaining a novel evolutionary origin at the Tricladida and Continenticola nodes--the mucus protein repertoire appears to have a far older evolutionary origin in both species. Moreover, distinct orthologous groups underpin the toxin gene repertoire and mucus composition in each lineage, highlighting the contrasting evolutionary trajectories of these two functional components. While toxin families in both aquatic and terrestrial flatworms revealed overall common functions, including cytokine modulation and ion channel regulation, terrestrial flatworms exhibited specific expansions of lectin-like proteins and pro-inflammatory responses, highlighting their potential key role to respond to land-based threats. This study provides new insights into the differential evolutionary trajectories of toxin and mucus proteins in planarians, offering a deeper understanding of the genetic innovations that facilitated flatworm terrestrialization.

evolutionary biology↗

bioRxiv2025

Genomic exaptation and regulatory landscape shifts as key mechanisms enabling flatworm terrestrialization

Understanding the genomic toolkit that facilitated animal terrestrialization--the transition from aquatic to terrestrial environments--is crucial for unravelling the evolutionary processes behind the origin and diversification of terrestrial biodiversity. Despite its significance, the genomic foundations driving the physiological and metabolic adaptations required for life on land remain largely unexplored across most terrestrial animal phyla. Planarians (phylum Platyhelminthes) represent an ideal model for studying terrestrialization, as only one terrestrial lineage, the family Geoplanidae (order Tricladida) is known to exist. Here, we used an integrative approach combining genomics, transcriptomics, and proteomics to investigate the genetic underpinnings potentially facilitating adaptation to terrestrial environments. Our analysis revealed a significant burst of gene gain preceding the diversification of terrestrial planarians and their split from freshwater relatives, in the branch leading to Tricladida. Upon exposure to abiotic stress, terrestrial and freshwater planarians exhibited distinct genetic toolkits: most differentially expressed genes emerged in orthologous groups gained specifically in the branch leading to Tricladida, over half of which showed signs of strong directional selection in terrestrial flatworms, indicating their adaptive importance for land colonization. Transcriptomic analyses further revealed contrasting stress responses: terrestrial planarians upregulated ancient genes whose origin predates the Geoplanidae lineage to cope with abiotic stress, while freshwater planarians downregulated a separate set of ancestral genes. Our genomic, transcriptomic, and proteomic data consistently show that the genetic toolkit for abiotic stress response in terrestrial planarians is highly differentiated from that of their freshwater counterparts, with significant regulatory shifts as well. Overall, our findings suggest a burst of gene gain in the Tricladida lineage, with co-option of these genes, rather than clade-specific innovations, playing a critical role in the origin and diversification of terrestrial flatworms. This underscores genomic exaptation and regulatory landscape shifts as key mechanisms enabling terrestrialization within Platyhelminthes. This study offers the first genome-wide insight into the genetic toolkit underlying flatworm terrestrialization and contributes broadly to understanding the genomic basis of animal terrestrialization.

evolutionary biology↗

bioRxiv2025

Disentangling the evolutionary history of terrestrial planarians through phylogenomics

Triclads (Platyhelminthes, Tricladida) are found in marine, freshwater, and terrestrial habitats worldwide except Antarctica. Terrestrial planarians are grouped into the family Geoplanidae, which is subdivided into the subfamilies Geoplaninae, Bipaliinae, Rhynchodeminae, and Microplaninae. Some of these subfamilies result from taxonomic rearrangements based on molecular phylogenies inferred from a few molecular markers. However, the diagnosis of Rhynchodeminae was not aligned with the morphology of all its representatives. While the subfamilies are recovered as monophyletic in recent molecular phylogenies, robust hypotheses regarding the relationships between them remain unknown. In this study, we employ for the first time a phylogenomic framework to investigate the evolutionary relationships among the subfamilies, starting by obtaining the first transcriptomes for 15 species of terrestrial planarians. A total of 16 different datasets, comprising nearly two thousand single-copy genes inferred from transcriptomic data, were analyzed using various phylogenetic inference methods. We recovered, for the first time, a well-supported topology of phylogenetic relationships among Geoplanidae subfamilies, positioning Bipaliinae and Microplaninae as a clade sister to Rhynchodeminae + Geoplaninae. Internal relationships within the genus Microplana were not supported in our analyses. The subfamily Rhynchodeminae, represented in our phylogeny by species from the tribes Rhynchodemini and Caenoplanini, is re-diagnosed to align with previous taxonomic rearrangements. This study not only represents a significant step forward in the phylogenetic resolution of Geoplanidae but also provides important insights into the broader evolutionary dynamics shaping land planarian diversity. HighlightsO_LIFirst transcriptomes of multiple terrestrial planarians sequenced. C_LIO_LIFirst molecular phylogeny of terrestrial planarians at subfamily level based on transcriptomic data. C_LIO_LIHighly supported topology for phylogenetic interrelationship among terrestrial planarians subfamilies. C_LIO_LIUnclear interrelationships between species from the genus Microplana. C_LIO_LIThe subfamily Rhynchodeminae is re-diagnosed at the morphological level. C_LI

evolutionary biology↗

bioRxiv2024

Protein aggregation capture assisted profiling of the thiol redox proteome

Oxidative damage is critical in various diseases, including cardiovascular and neurological conditions. Thiol redox reactions, acting as oxidative stress sensors, influence protein structure and function. Redox proteomics based on differential alkylation of reduced and oxidized Cys forms using mass spectrometry enables comprehensive analysis of thiol redox status in cells and tissues. We introduce PACREDOX, an innovative redox proteomics approach based on the Protein Aggregation Capture (PAC) protocol and we demonstrate its compatibility with library free data-independent acquisition (DIA). PACREDOX reduces preparation time and costs compared to traditional methods, such as FASILOX, while maintaining thiol and proteome coverage. To enable library-free DIA, we corrected in silico spectral libraries in DIA-NN using experimental retention time data from beta-methylthiol-modified peptides. PACREDOX with DIA quantified 4,000 protein groups and [~]45,000 modified peptides in myocardial tissue from a porcine model of atrial fibrillation, including over 8,000 cysteine-containing peptides, 30% of which were reversibly oxidized. Benchmarking PACREDOX and DIA against FASILOX in a myocardial infarction model reflects the potential and efficiency of this methodology to study oxidative damage. Overall, PACREDOX offers a high-throughput, cost-effective strategy for thiol redox proteome analysis, compatible with label-free quantitative workflows.

systems biology↗

bioRxiv2024

ERGA-BGE Reference Genome of the Striped Field Mouse (Apodemus agrarius), a Widespread and Abundant Species in Central and Eastern Europe

The reference genome of Apodemus agrarius provides a valuable resource for phylogenetic studies of rodents, particularly mice, and for understanding factors that influence the geographical distribution of the species across East Asia and East Europe. A total of 25 contiguous chromosomal pseudomolecules were assembled from the genome sequence (23 autosomes and 2 sex chromosomes). This chromosome-level assembly encompasses 2.6 Gb, composed of 242 contigs and 60 scaffolds, with contig and scaffold N50 values of 35 Mb and 119 Mb, respectively.

genomics↗

bioRxiv2024

ERGA-BGE Reference Genome of the Northern chamois (Rupicapra rupicapra): Europe's most abundant mountain ungulate

The reference genome of Rupicapra rupicapra (subsp. rupicapra) provides insights into the genetic makeup that enabled this iconic mountain ungulate to adapt to its harsh environment, including its ability to survive in extreme weather and high altitudes--factors that are increasingly important in the face of climate change. A total of 29 contiguous chromosomal pseudomolecules were assembled from the genome sequence. This chromosome-level assembly encompasses 2.62 Gb, composed of 124 contigs and 76 scaffolds, with contig and scaffold N50 values of 77 Mb and 101 Mb, respectively.

genomics↗

bioRxiv2024

ERGA-BGE genome of Valencia hispanica (Valenciennes, 1826): a critically endangered Iberian toothcarp

The reference genome of Valencia hispanica, a critically endangered actinopterygian species endemic to the Iberian Peninsula, is key to unravelling its genetic architecture and adaptation to freshwater ecosystems. This genomic resource will enable targeted conservation efforts and shed light on the species essential role in ecological dynamics, including its contributions to algal biomass regulation and role in the aquatic food web while also highlighting the challenges it faces from habitat degradation and invasive species. Furthermore, it offers opportunities to gain valuable insights into the evolutionary paths within the Valenciidae family, significantly advancing our comprehension of genetic diversity and adaptability in aquatic ecosystems. The entirety of the genome sequence was assembled into 24 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 1.29Gb, composed of 99 contigs and 28 scaffolds, with contig and scaffold N50 values of 38.3Mb and 56.9Mb, respectively.

evolutionary biology↗

bioRxiv2024

Chromosome-level genome assembly and annotation of Corallium rubrum: a Mediterranean coral threatened by overharvesting and climate change.

Reference genomes are key resources in biodiversity conservation. Yet, sequencing efforts are not evenly distributed in the tree of life questioning our true ability to enlighten conservation with genomic data. Good quality reference genomes remain scarce in octocorals while these species are highly relevant target for conservation. Here, we present the first annotated reference genome in the red coral, Corallium rubrum (Linnaeus, 1758), a habitat-forming octocoral from the Mediterranean and neighboring Atlantic, impacted by overharvesting and anthropogenic warming-induced mass mortality events. Combining long reads from Oxford Nanopore Technologies (ONT), Illumina paired-end reads for improving the base accuracy of the ONT-based genome assembly and Arima Hi-C contact data to place the sequences into chromosomes, we assembled a genome of 475 Mb (21 chromosomes, 326 scaffolds) with contig and scaffold N50 of 1.6 Mb and 16.2 Mb, respectively. Fifty percent of the sequence (L50) was contained in eight superscaffolds. The consensus quality (QV) of the final assembly was 42 and the gene completeness reported by BUSCO was 74% (metazoa_odb10 database). We annotated 39,114 protein-coding genes and 32,678 non-coding transcripts. This annotated chromosome-level genome assembly, one of the first in octocorals, is currently used in a project based on whole genome re-sequencing dedicated to the conservation and management of C. rubrum. Significance StatementThe Mediterranean red coral, Corallium rubrum, is critically impacted by overharvesting and by mass mortality events linked to marine heat waves. Accordingly, C. rubrum is increasingly receiving conservation efforts. Previous population genetics studies based on microsatellites contributed to improving our knowledge of the species ecology. Yet, crucial questions regarding, admixture among lineages, demographic history, effective population sizes and local adaptation, are still open owing to a lack of genomic resources. Here, we present the first chromosome-level genome assembly for the species with high contiguity, good completeness and protein-coding genes and repeat sequence annotations. This genome, one of the first in octocorals, will pave the way for the integration of population genomics data into ongoing interdisciplinary conservation efforts dedicated to C. rubrum.

genomics↗

bioRxiv2024

A punctuated burst of massive genomic rearrangements by chromosome shattering and the origin of non-marine annelids

The genomic basis of cladogenesis and adaptive evolutionary change has intrigued biologists for decades. Here, we show that the tectonics of genome evolution in clitellates, a clade composed of most freshwater and all terrestrial species of the phylum Annelida, is characterised by extensive genome-wide scrambling that resulted in a massive loss of macrosynteny between marine annelids and clitellates. These massive rearrangements included the formation of putative neocentromeres with newly acquired transposable elements and preceded a further period of genome-wide reshaping events, potentially triggered by the loss of genes involved in genome stability and homeostasis of cell division. Notably, while these rearrangements broke short-range interactions observed between Hox genes in marine annelids, they were reformed as long-range interactions in clitellates. Our findings reveal extensive genomic reshaping in clitellates at both the linear (2D) and three-dimensional (3D) levels, suggesting that, unlike in other animal lineages where synteny conservation constrains structural evolution, clitellates exhibit a remarkable tolerance for chromosomal rearrangements. Our study thus suggests that the genomic landscape of Clitellata resulted from a rare burst of genomic changes that ended a long period of stability that persists across large phylogenetic distances.

evolutionary biology↗

bioRxiv2024

A cell-free workflow for detecting and characterizing RiPP recognition element-precursor peptide interactions

Post-translational modifications (PTMs) are important for the stability and function of many therapeutic proteins and peptides. Current methods for studying and engineering PTM installing proteins often suffer from low-throughput experimental techniques. Here we describe a generalizable, in vitro workflow coupling cell-free protein synthesis (CFPS) with AlphaLISA for the rapid expression and testing of PTM installing proteins. We apply our workflow to two representative classes of peptide and protein therapeutics: ribosomally synthesized and post-translationally modified peptides (RiPPs) and conjugate vaccines. First, we demonstrate how our workflow can be used to characterize the binding activity of RiPP recognition elements, an important first step in RiPP biosynthesis, and be integrated into a biodiscovery pipeline for computationally predicted RiPP products. Then, we adapt our workflow to study and engineer oligosaccharyltransferases (OSTs) involved in conjugate vaccine production, enabling the identification of mutant OSTs and sites within a carrier protein that enable high efficiency production of conjugate vaccines. In total, we expect that our workflow will accelerate design-build-test cycles for engineering PTMs.

synthetic biology↗

bioRxiv2024

CRISPR-Cas9 editing efficiency in fission yeast is not limited by homology search and is improved by combining gap-repair with fluoride selection

Protocols for CRISPR-Cas9 editing have been implemented in most model organisms, including fission yeast, for which some improvements have also been later described. Here, we report an improvement to the CRISPR-Cas9 protocol in fission yeast, as we combine a cloning free gap-repair method with our previously described fluoride selection marker, which speeds up genome editing. We also report a wide variability of editing efficiencies at different loci along the genome, and we demonstrate that this variability cannot be explained by the location of the edited sequences in the genome. Lastly, our attempt at improving editing efficiency by targeting the donor DNA to the cut site using a HaloTag strategy to link the donor DNA to two proteins of the homologous recombination repair machinery (Rad51 or Rad52) fell short, which shows that editing efficiency in fission yeast is likely not limited by homology search.

cell biology↗

bioRxiv2024

Illuminating the functional landscape of the dark proteome across the Animal Tree of Life through natural language processing models

Functional annotation is crucial in biology, but many protein-coding genes remain uncharacterized, especially in non-model organisms. FANTASIA (Functional ANnoTAtion based on embedding space SImilArity) integrates protein language models for large-scale functional annotation. Applied to [~]1,000 animal proteomes, it predicts functions to virtually all proteins, revealing previously uncharacterized functions that enhance our understanding of molecular evolution. FANTASIA is available on GitHub at https://github.com/CBBIO/FANTASIA.

evolutionary biology↗

bioRxiv2024

MATEdb2, a collection of high-quality metazoan proteomes across the Animal Tree of Life to speed up phylogenomic studies

Recent advances in high throughput sequencing have exponentially increased the number of genomic data available for animals (Metazoa) in the last decades, with high-quality chromosome-level genomes being published almost daily. Nevertheless, generating a new genome is not an easy task due to the high cost of genome sequencing, the high complexity of assembly, and the lack of standardized protocols for genome annotation. The lack of consensus in the annotation and publication of genome files hinders research by making researchers lose time in reformatting the files for their purposes but can also reduce the quality of the genetic repertoire for an evolutionary study. Thus, the use of transcriptomes obtained using the same pipeline as a proxy for the genetic content of species remains a valuable resource that is easier to obtain, cheaper, and more comparable than genomes. In a previous study, we presented the Metazoan Assemblies from Transcriptomic Ensembles database (MATEdb), a repository of high-quality transcriptomic and genomic data for the two most diverse animal phyla, Arthropoda and Mollusca. Here, we present the newest version of MATEdb (MATEdb2) that overcomes some of the previous limitations of our database: (1) we include data from all animal phyla where public data is available, (2) we provide gene annotations extracted from the original GFF genome files using the same pipeline. In total, we provide proteomes inferred from high-quality transcriptomic or genomic data for almost 1000 animal species, including the longest isoforms, all isoforms, and functional annotation based on sequence homology and protein language models, as well as the embedding representations of the sequences. We believe this new version of MATEdb will accelerate research on animal phylogenomics while saving thousands of hours of computational work in a plea for open, greener, and collaborative science.

evolutionary biology↗

bioRxiv2024

Decoding proteome functional information in model organisms using protein language models.

Protein language models have been tested and proved to be reliable when used on curated datasets but have not yet been applied to full proteomes. Accordingly, we tested how two different machine learning based methods performed when decoding functional information from the proteomes of selected model organisms. We found that protein Language Models are more precise and informative than Deep Learning methods for all the species tested and across the three gene ontologies studied, and that they better recover functional information from transcriptomics experiments. The results obtained indicate that these Language Models are likely to be suitable for large scale annotation and downstream analyses, and we recommend a guide for their use.

bioinformatics↗

bioRxiv2023

Unveiling the Hidden Viromes Across the Animal Tree of Life: Insights from a Taxonomic Classification Pipeline Applied to Invertebrates of 31 Metazoan Phyla

Invertebrates constitute the majority of animal species on Earth, including most disease-causing agents or vectors, with more diverse viromes when compared to vertebrates. Recent advancements in high-throughput sequencing have significantly expanded our understanding of invertebrate viruses, yet this knowledge remains biased toward a few well-studied animal lineages. In this study, we analyze invertebrate DNA and RNA viromes for 31 phyla using 417 publicly available RNA-Seq datasets from diverse environments in the marine-terrestrial and marine-freshwater gradients. This study aims to (i) estimate virome compositions at the family level for the first time across the Animal Tree of Life, including the first exploration of the virome in several phyla, (ii) quantify the diversity of invertebrate viromes and characterize the structure of invertebrate-virus interaction networks, and (iii) investigate host phylum and habitat influence on virome differences. Results showed that a set of few viral families of eukaryotes, comprising Retroviridae, Flaviviridae and several families of giant DNA viruses, were ubiquitous and highly abundant. Nevertheless, some differences emerged between phyla, revealing for instance a less diverse virome in Ctenophora compared to the other animal phyla. Compositional analysis of the viromes showed that the host phylum explained over five times more variance in composition than its habitat. Moreover, significant similarities were observed between the viromes of some phylogenetically related phyla, which could highlight the influence of co-evolution in shaping invertebrate viromes. ImportanceThis study significantly enhances our understanding of the global animal virome by characterizing the viromes of previously unexamined invertebrate lineages from a large number of animal phyla. It showcases the great diversity of viromes within each phylum and investigates the role of habitat shaping animal viral communities. Furthermore, our research identifies dominant virus families in invertebrates and distinguishes phyla with analogous viromes. This study sets the road towards a deeper understanding of the virome across the Animal Tree of Life.

ecology↗

bioRxiv2023

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

A global genome database of all of Earths species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all [~]1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.

genomics↗