Rosa Fernández

The paper presents the chromosome-level genome assembly of Valencia hispanica, a critically endangered fish, to support conservation and ecological studies.

The paper presents a high-quality genome assembly of the sea stickleback and reveals chromosomal fusions and fissions that reshape understanding of karyotype evolution in sticklebacks.

The paper investigates genomic mechanisms underlying independent transitions to terrestrial life across species, finding lineage-specific gene changes that converge functionally.

The paper presents genomic resources for Hyalomma lusitanicum and its Francisella endosymbiont, providing insights into host-symbiont evolution and disease transmission.

LINGUINE improves ancestral linkage group inference by using orthogroups and a Hidden Markov Model to handle gene loss and paralogy, outperforming existing methods in nematodes and clitellate annelids.

The paper identifies conserved gene networks in lungfish estivation that were co-opted for terrestrial adaptation through ancient gene duplications.

This study presents a chromosome-level genome assembly for Iberolacerta aurelioi and uses whole-genome sequencing to investigate phylogenomic relationships and adaptive traits in the genus Iberolacerta.

This study identifies parallel genomic changes across arthropod lineages that independently transitioned to land, revealing shared molecular strategies for terrestrial adaptation.

The paper evaluates clustering and assembly methods for Iso-Seq data in non-model animals without reference genomes, finding CD-HIT at 99% similarity provides the best transcriptome quality.

The paper presents the chromosome-level genome assembly of Stigmatoteuthis arcturi, providing insights into the evolutionary biology of deep-sea squids.

This paper introduces FANTASIA, a tool using protein language models to annotate functions for thousands of animal proteomes, uncovering previously unknown functions across species.

The paper shows that clitellates experienced a burst of genomic rearrangements leading to loss of macrosynteny with marine annelids and new chromosomal interactions.

This study uses phylogenomic analysis of transcriptomic data to resolve the evolutionary relationships among terrestrial planarian subfamilies, revealing a well-supported topology and re-diagnosing Rhynchodeminae.

The paper presents a high-quality chromosome-level genome of the king penguin, improving assembly contiguity and annotation for studying genotype-fitness relationships.

The paper presents the reference genome of Coenonympha oedippus, an endangered butterfly, to study genetic mechanisms of adaptation to two ecotypes and support conservation efforts.

The paper presents the chromosome-level genome assembly of Arca noae, a Mediterranean bivalve, providing evolutionary insights and genomic resources for studying environmental adaptation.

The paper presents the genome assembly of Loboptera subterranea, a cave-adapted cockroach, providing insights into its adaptation to subterranean environments.

This paper presents the first chromosome-level genome assembly and annotation for the red coral Corallium rubrum, providing genomic resources for conservation and population genomics studies.

The paper presents the reference genome of Cheirolophus tagananensis, providing tools for studying genetic adaptation and supporting conservation strategies.

The paper presents the genome of Pinctada radiata, a Lessepsian migrant, providing insights into its genetic adaptations to environmental changes and supporting conservation efforts.

This study identifies gene gain and regulatory shifts in terrestrial planarians as key mechanisms for terrestrialization, showing distinct stress response toolkits compared to freshwater relatives.

This study compares toxin and mucus protein evolution in aquatic and terrestrial flatworms, finding broader toxin gene repertoires and distinct functional expansions in terrestrial species.

The paper presents a chromosome-level reference genome for the striped field mouse, providing resources for phylogenetic studies and understanding its geographical distribution.

The paper presents a chromosome-level reference genome for the Northern chamois, providing insights into its genetic adaptation to extreme environments.

MATEdb2 provides high-quality proteomes for nearly 1000 animal species to enhance phylogenomic research by reducing computational effort and standardizing data formats.

The paper describes the European Reference Genome Atlas (ERGA) pilot project, which tests a decentralized model for producing high-quality reference genomes across 98 European species.

The paper describes the ERGA Pilot project's efforts to establish standards for sample collection and metadata gathering to support reference genome generation for European biodiversity.

This study compares protein language models and deep learning methods for decoding functional information from proteomes of model organisms, finding language models more precise and informative.

The paper presents a high-quality genome assembly for the ant Lasius platythorax using long-read sequencing and Hi-C, providing insights into the genomic basis of trait differentiation in ant species.

The paper investigates the role of recent gene duplications in the pea aphid Acyrthosiphon pisum, finding that most duplicates show asymmetric evolution with positive selection and gene expression divergence.