Judit Salces-Ortiz

The king penguin (Aptenodytes patagonicus) is a long-lived seabird of the Southern Ocean that is emerging as a promising model in the wild for studying evolution. We present a high-quality, haplotype-resolved 1.35 Gb chromosome-level genome of an adult female king penguin - ‘Pen/Se-guin’ - assembled using PacBio HiFi long-reads and Hi-C proximity data. A total of 95% of the assembly is assigned to 34 chromosomes (32 autosomes, plus the Z and W chromosomes). The primary haplotype has a BUSCO completeness of 97.2%, and across both haplotypes the assembly has a k-mer completeness of 99.7% and a quality value of 63.8. We also assembled a circularised mitogenome (20,520 bp) containing the avian tandem duplication. Repetitive sequence annotation showed that 16.3% of the genome comprises repetitive elements, with LINEs representing 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%. Compared with the previous draft genome, the presented genome shows a 30-fold increase in assembly contiguity and a substantially improved genome annotation, exceeding the standards of the Earth BioGenome Project and Vertebrate Genomes Project. This genome provides a foundation for ongoing and future studies using the king penguin to investigate genotype–fitness relationships, ageing, life-history evolution, and adaptation.

Corema album is a perennial, dioecious shrub endemic to the Atlantic coast of the Iberian Peninsula and the Azores. It inhabits coastal dune ecosystems from Galicia to the Strait of Gibraltar, where it plays an important ecological role. The goal of this study was to assemble and annotate a chromosome-level reference genome for C. album. The entirety of the genome sequence was assembled into 13 contiguous chromosomal pseudomolecules, one mitochondrial, and one chloroplast genome. This chromosome-level assembly encompasses 548 Mb, composed of 96 contigs and 68 unplaced scaffolds, with contig and scaffold N50 values of 23.7 Mb and 40.9 Mb, respectively. Structural annotation revealed that 51% of the genome of C. album consists of repeats, identified 53,794 genes and encompassed 94.6% of the Viridiplantae BUSCO genes set, confirming a high gene representativeness in the assembly.

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.

Phorcus turbinatus (turbinate monodont; Mollusca, Trochidae) is widely used as a biomarker of water quality and numerous scientific studies rely on this species for environmental and genomic research. Consequently, the generation of a chromosome-level assembly for P. turbinatus is of substantial scientific interest. Most of the genome sequence was assembled into 18 contiguous chromosomal pseudomolecules and the mitochondrial genome. This chromosome-level assembly encompasses 0.95 Gb, composed of 104 contigs and 103 scaffolds, with a contig and scaffold N50 of 50.6 Mb.

Understanding the genomic toolkit that enabled animal terrestrialization, the shift from aquatic to terrestrial habitats, is key to uncovering the evolutionary origins of land biodiversity. Yet, the genomic basis of the physiological and metabolic adaptations required for life on land remains poorly understood across most terrestrial animal phyla. Planarians (Platyhelminthes) offer a powerful model, as only one terrestrial lineage, the Geoplanidae (order Tricladida), is known. Here, we integrated genomics, transcriptomics, and proteomics to explore the genetic changes potentially supporting terrestrial adaptation. We identified a major burst of gene gain in the lineage leading to Tricladida, preceding the radiation of terrestrial planarians. Upon abiotic stress exposure, terrestrial and freshwater species exhibited distinct responses: most differentially expressed genes belonged to orthogroups gained in Tricladida, with over half under strong directional selection in terrestrial flatworms, suggesting their adaptive relevance. Transcriptomic profiles revealed divergent strategies: terrestrial species upregulated ancient genes, while freshwater species downregulated a separate set of ancestral genes. Across all datasets, the abiotic stress–response toolkit in terrestrial planarians was markedly different from freshwater relatives, with significant regulatory divergence. Our results highlight gene gain and co-option, rather than lineage-specific innovations, as key drivers of terrestrial flatworm evolution, emphasizing genomic exaptation and regulatory shifts as central to terrestrialization in Platyhelminthes. This study provides the first genome-wide view of the genetic basis of flatworm terrestrialization and sheds light on broader patterns of animal terrestrial adaptation.

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 characterized 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 homoeostasis of cell division. Notably, whereas 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.

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.

Reference genomes are key resources in biodiversity conservation. Yet, sequencing efforts are not evenly distributed across the tree of life raising concerns over our ability to enlighten conservation with genomic data. Good-quality reference genomes remain scarce in octocorals while these species are highly relevant targets 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 532 Mb (20 chromosomes, 309 scaffolds) with contig and scaffold N50 of 1.6 and 18.5 Mb, respectively. Fifty percent of the sequence (L50) was contained in seven superscaffolds. The consensus quality value of the final assembly was 42, and the single and duplicated gene completeness reported by BUSCO was 86.4% and 1%, respectively (metazoa_odb10 database). We annotated 26,348 protein-coding genes and 34,548 noncoding transcripts. This annotated chromosome-level genome assembly, one of the first in octocorals and the first in Scleralcyonacea order, is currently used in a project based on whole-genome resequencing dedicated to the conservation and management of C. rubrum.

A global genome database of all of Earth's 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 34 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.

The advent of long-read sequencing technologies has allowed the generation of multiple high-quality de novo genome assemblies for multiple species, including well-known model species such as Drosophila melanogaster. Genome assemblies for multiple individuals of the same species are key to discover the genetic diversity present in natural populations, especially the one generated by transposable elements, the most common type of structural variant. Despite the availability of multiple genomic data sets for D. melanogaster populations, we lack an efficient visual tool to display different genome assemblies simultaneously. In this work, we present DrosOmics, a population genomic-oriented browser currently containing 52 high-quality reference genomes of D. melanogaster, including annotations from a highly reliable set of transposable elements, and functional transcriptomics and epigenomics data for 26 genomes. DrosOmics is based on JBrowse 2, a highly scalable platform, which allows the visualization of multiple assemblies at once, key to unraveling structural and functional features of D. melanogaster natural populations. DrosOmics is an open access browser and is freely available at http://gonzalezlab.eu/drosomics.