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The Tyrrhenian tree frog ( Hyla sarda ) is a small cryptically coloured amphibian found in Corsica, Sardinia, and the Tuscan Archipelago. Investigation into the species’ evolutionary history has revealed phenotypic changes triggered by glaciation-induced range expansion, but understanding the genetic basis of this trait variation has been hampered by the lack of a reference genome. To address this, we assembled a chromosome-level genome of Hyla sarda using PacBio HiFi long reads, Bionano optical maps, and Hi-C data. The assembly comprises 13 assembled chromosomes, spanning a total length of 4.15 Gb with a scaffold N50 of 385 Mb, a BUSCO completeness of 94.60%, and a k -mer completeness of 98.30%. Approximately 75% of the genome consists of repetitive elements. We annotated 22,847 protein-coding genes with a BUSCO completeness of 94.60% and an OMArk completeness of 93.74%. This high-quality assembly provides a valuable resource for studying phenotypic evolution and its genomic basis during range expansion, and will assist future investigations into the population and conservation genomics of Hyla sarda .

Sorex araneus, the Eurasian common shrew, has seasonal brain size plasticity (Dehnel's phenomenon) and abundant intraspecific chromosomal rearrangements. Genomic contributions to these traits, however, remain unknown. We couple a chromosome-scale genome assembly with seasonal brain transcriptomes to discover relationships between molecular changes and both traits. While positively selected genes enriched the Fanconi anemia DNA repair pathway (FANCI, FAAP100), which is likely involved in chromosomal rearrangements by preventing the accumulation of chromosomal aberrations, genes under positive selection or showing seasonal differential expression in the brain implicate neurogenesis (PCDHA6, SOX9, Notch signaling) and metabolic regulation (VEGFA, SPHK2) as key mechanisms underlying Dehnel's phenomenon. We also find that both positively selected and differentially expressed genes in the hippocampus are overrepresented near Sor. araneus evolutionary breakpoints. This relates both positive selection and differential expression to accessible chromatin configuration, suggesting that chromosomal rearrangements are integral to adaptive evolution and the regulation of brain size plasticity.Sorex araneus, the Eurasian common shrew, has seasonal brain size plasticity (Dehnel's phenomenon) and abundant intraspecific chromosomal rearrangements. Genomic contributions to these traits, however, remain unknown. We couple a chromosome-scale genome assembly with seasonal brain transcriptomes to discover relationships between molecular changes and both traits. While positively selected genes enriched the Fanconi anemia DNA repair pathway (FANCI, FAAP100), which is likely involved in chromosomal rearrangements by preventing the accumulation of chromosomal aberrations, genes under positive selection or showing seasonal differential expression in the brain implicate neurogenesis (PCDHA6, SOX9, Notch signaling) and metabolic regulation (VEGFA, SPHK2) as key mechanisms underlying Dehnel's phenomenon. We also find that both positively selected and differentially expressed genes in the hippocampus are overrepresented near Sor. araneus evolutionary breakpoints. This relates both positive selection and differential expression to accessible chromatin configuration, suggesting that chromosomal rearrangements are integral to adaptive evolution and the regulation of brain size plasticity.

Abstract Sorex araneus, the Eurasian common shrew, has seasonal brain size plasticity (Dehnel's phenomenon) and many intraspecific chromosomal rearrangements. Genomic contributions to these traits, however, remain unknown. We couple a chromosome-scale genome assembly with seasonal brain transcriptomes to discover relationships between molecular evolution and both traits. While Positively Selected Genes (PSGs) enriched the Fanconi anemia DNA repair pathway (FANCI, FAAP100), which is likely involved in chromosomal rearrangements by preventing the accumulation of chromosomal aberrations, genes under positive selection or showing seasonal differential expression in the brain implicate neurogenesis (PCDHA6, SOX9, Notch signaling) and metabolic regulation (VEGFA, SPHK2) as key mechanisms underlying Dehnel's phenomenon. We also find that both positively selected and differentially expressed genes in the hippocampus are overrepresented near S. araneus evolutionary breakpoints. This relates both positive selection and differential expression to accessible chromatin configuration, suggesting that chromosomal rearrangements are integral to adaptive evolution and the regulation of brain size plasticity.

The European mink Mustela lutreola (Mustelidae) ranks among the most endangered mammalian species globally, experiencing a rapid and severe decline in population size, density, and distribution. Given the critical need for effective conservation strategies, understanding its genomic characteristics becomes paramount. To address this challenge, the platinum-quality, chromosome-level reference genome assembly for the European mink was successfully generated under the project of the European Mink Centre consortium. Leveraging PacBio HiFi long reads, we obtained a 2586.3 Mbp genome comprising 25 scaffolds, with an N50 length of 154.1 Mbp. Through Hi-C data, we clustered and ordered the majority of the assembly (>99.9%) into 20 chromosomal pseudomolecules, including heterosomes, ranging from 6.8 to 290.1 Mbp. The newly sequenced genome displays a GC base content of 41.9%. Additionally, we successfully assembled the complete mitochondrial genome, spanning 16.6 kbp in length. The assembly achieved a BUSCO (Benchmarking Universal Single-Copy Orthologs) completeness score of 98.2%. This high-quality reference genome serves as a valuable genomic resource for future population genomics studies concerning the European mink and related taxa. Furthermore, the newly assembled genome holds significant potential in addressing key conservation challenges faced by M. lutreola. Its applications encompass potential revision of management units, assessment of captive breeding impacts, resolution of phylogeographic questions, and facilitation of monitoring and evaluating the efficiency and effectiveness of dedicated conservation strategies for the European mink. This species serves as an example that highlights the paramount importance of prioritizing endangered species in genome sequencing projects due to the race against time, which necessitates the comprehensive exploration and characterization of their genomic resources before their populations face extinction.

The European mink Mustela lutreola (Mustelidae) ranks among the most endangered mammalian species globally, experiencing a rapid and severe decline in population size, density, and distribution. Given the critical need for effective conservation strategies, understanding its genomic characteristics becomes paramount. To address this challenge, the platinum-quality, chromosome-level reference genome assembly for the European mink was successfully generated under the project of the European Mink Centre consortium. Leveraging PacBio HiFi long reads, we obtained a 2586.3 Mbp genome comprising 25 scaffolds, with an N50 length of 154.1 Mbp. Through Hi-C data, we clustered and ordered the majority of the assembly (>99.9%) into 20 chromosomal pseudomolecules, including heterosomes, ranging from 6.8 to 290.1 Mbp. The newly sequenced genome displays a GC base content of 41.9%. Additionally, we successfully assembled the complete mitochondrial genome, spanning 16.6 kbp in length. The assembly achieved a BUSCO (Benchmarking Universal Single-Copy Orthologs) completeness score of 98.2%. This high-quality reference genome serves as a valuable genomic resource for future population genomics studies concerning the European mink and related taxa. Furthermore, the newly assembled genome holds significant potential in addressing key conservation challenges faced by M. lutreola. Its applications encompass potential revision of management units, assessment of captive breeding impacts, resolution of phylogeographic questions, and facilitation of monitoring and evaluating the efficiency and effectiveness of dedicated conservation strategies for the European mink. This species serves as an example that highlights the paramount importance of prioritizing endangered species in genome sequencing projects due to the race against time, which necessitates the comprehensive exploration and characterization of their genomic resources before their populations face extinction.

Reference genomes from representative species across families provide the critical infrastructure for research and conservation. The Cetacean Genomes Project (CGP) began in early 2020 to facilitate the generation of near error-free, chromosome-resolved reference genomes for all cetacean species. Towards that goal, and using the methods, goals and genome assembly quality standards of the Vertebrate Genomes Project (VGP), we generated 13 new reference genomes across eight of the 14 cetacean families. Additionally, we summarize the genome assembly characteristics for 18 species, including these newly-generated and five published genome assemblies that meet the completeness and quality standards. We infer ancestral linkage groups (ALG) for cetaceans, showing that the ancestral karyotype of 22 ALGs is largely conserved in extant species, except for Ziphiidae, and for Balaenidae and Kogiidae, which exhibit similar independent fusions. Gene annotation, characterization of historical demography, heterozygosity and runs of homozygosity (ROH) reveal important information for conservation applications. By comparing the new reference genomes to previous draft assemblies, we show that the reference genomes have enhanced characteristics that will support and promote scientific research. Specifically, the genomes improve resolution and characterization of repetitive elements, provide validation (or exclusion) of genes linked to complex traits, and allow more complete characterization of gene regions such as the highly complex Major Histocompatibility Complex (MHC) Class I and II gene clusters that are important for population health.

Advances in DNA sequencing and assembly technologies are spurring a shift from haploid reference genomes to sample-specific diploid assemblies. Here, we generated the first telomere-to-telomere (T2T) diploid reference for the widely used human embryonic stem cell (hESC) line, H9 (WAe009-A). This haplotype-resolved assembly is highly accurate with comprehensive annotation of genes, segmental duplications, methylation, and chromatin conformation. Pangenomic and phased-locus inference point to H9's mixed ancestry with a predominant European component. H9-specific genomic features include near-perfect telomeres ∼1.65-fold longer than other T2T assemblies, consistent with telomerase activity during pluripotency; chromosome 17 inversions that can predispose offspring to neurological syndromes; and expansions of ncRNA clusters, with overall genomic stability maintained despite extensive culturing. Mapping multi-omic datasets to the genome, we demonstrate the power of this resource for allele-specific, high-precision transcriptomic, genetic, and epigenetic analyses, with far-reaching implications for human development and disease.

Bird genomes are the smallest among amniotes, but remain challenging to assemble due to their structural complexity. This study presents the first fully phased, diploid, telomere-to-telomere (T2T) reference genome for the zebra finch ( ), a model organism for neuroscience and evolutionary genomics. Combining multiple sequencing strategies resulted in closing nearly all gaps, adding ~90 Mbp of previously missing sequence (7.8%). This includes T2T assemblies for all microchromosomes, including dot chromosomes, and the previously almost entirely missing chr16. The T2T genome is comprehensively annotated for genes, repeats, structural variants, and long-read methylation calls. Complete centromeric structures were assembled and annotated along with kinetochore binding sites. Relative to the previous high-quality reference of the Vertebrate Genomes Project, 2,778 (8.51%) previously unassembled or unannotated genes were identified, of which 9% overlap with segmental duplications. This first complete genome of a songbird, now the new public reference, illuminates avian genome architecture and function.

The Brazilian merganser (Mergus octosetaceus) is a critically endangered bird, with fewer than 250 mature individuals remaining in fragmented populations of the Cerrado biome in Brazil. It is an ecologically demanding species that requires clear water of fast-flowing rivers for diving and foraging, and riverside cavities for nesting. Technical and logistical challenges have restricted sampling and research to few genetic studies so far. The genetic results consistently revealed a low genetic diversity and high inbreeding in the species. Besides, the lack of a reference genome has precluded deeper evolutionary and conservation genetic analyses for the species. We generated the first high-quality, chromosome-level genome assembly for Mergus octosetaceus using PacBio HiFi long reads and Arima Hi-C data from a female specimen. The assembly is 1.25 Gb in length, is highly complete, scoring 98.9% of BUSCO completeness, and includes both sex chromosomes (Z and W). Annotated repetitive elements comprise 18.94% of the genome, with evidence of recent activity, particularly among LINEs and LTRs retrotransposons. We also produced and annotated the complete mitochondrial genome, identifying 37 genes and the control region. Comparative synteny analysis with other Anatidae species revealed strong chromosomal conservation, with several inversion events in macrochromosomes. Demographic history reconstruction indicated fluctuations in effective population size, with significant reductions overlapped by major temperature changes, highlighting potential climate sensitivity of this lineage. This reference genome provides a fundamental resource for M. octosetaceus, enabling insights into genome evolution, chromosomal dynamics within Anatidae, and past population history. It is a remarkable foundation for future research and conservation strategies for managing and restoring this critically endangered species.