Comparing prairie voles (Microtus ochrogaster), a species that forms lasting pair bonds and exhibits biparental care, with meadow voles (Microtus pennsylvanicus), a non-monogamous species showing maternal care only, provides a framework to examine the genomic basis of behavioral divergence over short evolutionary time. Here, we develop a simplified assembly approach combining PacBio HiFi and CiFi sequencing in a single library and run, producing high-quality contiguous chromosome-scale diploid prairie and meadow vole genomes (2.3 Gbp). Comparative analysis reveals substantial differences, including near-complete Y chromosome divergence and a prairie-vole-specific duplication of Avpr1a, a vasopressin receptor gene implicated in social bonding and autism in humans. These extensive genomic changes suggest rapid chromosome evolution as a driver of the dramatic Microtus radiation, generating ∼60 vole species in >2 million years. This single-library approach facilitates a simplified and more affordable assembly workflow, producing near-complete genomes of diverse species using one sequencing platform.

Scleractinia (stony corals) are a diverse taxonomic order within the phylum Cnidaria, comprising more than 1,600 species described to date. Most of these corals play a key role as reef builders by secreting calcium carbonate, forming rigid skeletons that provide the structural foundation of tropical coral reef ecosystems. Through colonial growth and symbioses with their photosynthetic microalgae (Symbiodiniaceae) and a suite of other microorganisms, scleractinian corals support high primary productivity and underpin the vast biodiversity of coral reefs. Corals are under severe pressure from climate change, including ocean warming and acidification, which threaten their survival and, consequently, the persistence of coral reef systems globally. In recent years, significant efforts have been made to increase the number of sequenced genomes from scleractinian corals, thereby providing crucial insights into their biology, evolution, resilience, and vulnerability. However, there are few high-quality reference genomes for Scleractinia, and many available genomes remain unannotated, creating barriers to collaboration and scientific insight. Annotation outcomes also vary depending on the methods and software utilised. To address these issues, we applied a standardised pipeline for generating high-quality gene models to 40 scleractinian genomes, spanning 22 genera across 13 families. These genomes, produced through the Aquatic Symbiosis Genomics (ASG) Project, are publicly available. This curated resource of annotated quality genomes will provide essential molecular tools at a critical time for coral reef conservation.

We present here a high-quality genome assembly of a male mountain hare ( Lepus timidus Linnaeus), from Ilomantsi, Eastern Finland, utilizing an isolated fibroblast cell line as the source for high quality DNA and RNA. Following the previously published brown hare reference genome assembly, the mountain hare is the second Finnish pilot species for the European Reference Genome Atlas (ERGA) initiative, a collaborative effort to generate reference genomes for European biodiversity. The genome was assembled using 21x PacBio HiFi sequencing data and scaffolded using the Hi-C chromosome structure capture approach. After manual curation, the primary assembly length was 2,695,305,354 bp with N50 125,755,317 bp. The largest scaffold was 181 Mbp and the scaffold N50 127 Mbp, contributing to a primary assembly consisting of 85 scaffolds and an alternate assembly with 109 scaffolds. The scaffolds include 23 autosomes, numbered according to their size, as well as X and Y chromosomes, matching the known karyotype. Telomeric regions were present on at least one end of 19 of the chromosomes. The genome has a high degree of completeness based on the BUSCO score (mammalia_odb10 database), Complete: 95.1 % [Single copy: 92.3 %, Duplicated: 2.7 %], Fragmented 0.8 %, and Missing 4.1 %. The mitochondrial genome of the cell line was sequenced and assembled separately. The assembly meets the Earth BioGenome Project criteria for a reference-standard genome assembly. Compared to the previous pseudo-reference genome assembly of L. timidus ssp. hibernicus Bell, assembled using the rabbit genome, this new reference genome represents the nominate subspecies and the species-specific chromosomal conformation. The published genome assembly will provide a solid foundation for future genomic research on Lagomorpha, including the insights into the genomic basis of adaptations to snowy and cold environments. Furthermore, it opens opportunities for experimental analysis of mountain hare gene functions.

Somion occarium is a wood-decaying bracket fungus belonging to an order known to be rich in useful chemical compounds. Despite its widespread distribution, S. occarium has been assessed as endangered on at least 1 national Red List, presumably due to loss of old-growth forest habitat. Here, we present a near-complete, annotated nuclear genome assembly for S. occarium consisting of 31 Mbp arranged in 11 pseudochromosomes-9 of which are telomere-to-telomere-as well as a complete mitochondrial genome assembly of 112.9 Kbp. We additionally performed phylogenomic analysis and annotated carbohydrate-active enzymes (CAZymes) to compare gene and CAZyme content across closely related species. This genome was sequenced as the representative for Kingdom Fungi in the European Reference Genome Atlas Pilot Project.

We present a genome assembly from an individual female Culex pipiens sensu stricto (the northern house mosquito; Arthropoda; Insecta; Diptera; Culicidae), from a wild population in Sweden. The genome sequence is 533 megabases in span. Most of the assembly is scaffolded into three chromosomal pseudomolecules. The complete mitochondrial genome was also assembled and is 15.6 kilobases in length.

The Danioninae subfamily of teleost fishes boasts up to four hundred distinct species that have evolved to display a stunning diversity of morphological forms. Here we use newly assembled genome sequences of four laboratory and wild zebrafish strains as well as eleven species of the Danio and Danionella genera to explore their phylogenetic history and the genetic basis of pigment pattern diversification. Phylogenomic analyses uncover extensive introgression and incomplete lineage sorting that have obscured phylogenetic relationships within Danio and corroborate an ancient hybrid origin of zebrafish. Whereas D. rerio inherited ancestral horizontal stripes, relatives repeatedly evolved spots and vertical bars. Interspecific complementation tests reveal functional divergence of the adhesion molecule gene igsf11 and the gap junction gene gja5b between the striped zebrafish and Danio species with divergent patterns. Comparative genomic and transcriptomic analyses suggest that protein and regulatory evolution have accompanied pigment pattern diversification. Our analyses elucidate complex genetic changes underlying the phylogenetic history and morphological diversification in the Danio genus. Resolved phylogenetic relationships, available genome assemblies, transcriptomes, and genetic tractability establish Danio fish species as excellent models for biomedical research in vertebrates.

Bread wheat (Triticum aestivum) is a vital staple crop, with an urgent need for increased production to help feed the world’s growing population. Aegilops mutica (2n = 2x = 14; T genome) is a diploid wild relative of wheat carrying valuable agronomic traits resulting in its extensive exploitation for wheat improvement. This paper reports a chromosome-scale, haplotype-resolved genome assembly of Ae. mutica using HiFi reads and Omni-C data. The final lengths for the curated genomes were ~4.65 Gb (haplotype 1) and 4.56 Gb (haplotype 2), featuring a contig N50 of ~4.35 Mb and ~4.60 Mb, respectively. Genome annotation predicted 96,723 gene models and repeats. In summary, the genome assembly of Ae. mutica provides a valuable resource for the wheat breeding community, facilitating faster and more efficient pre-breeding of wheat to enhance food security.

While sex-determining mechanisms have been extensively characterized in many vertebrates, they have not been explored in chondrichthyan fishes until relatively recently. In the present study, we used high-quality whole genome reference assemblies to examine the putative sex chromosomes of 14 elasmobranch species spanning nine orders. We describe four newly assembled reference genomes belonging to the white shark Carcharodon carcharias , the Atlantic stingray Hypanus sabinus , the smalltooth sawfish Pristis pectinata , and the zebra shark Stegostoma tigrinum . We conducted sex chromosome identification and verification using short-read sequence data collected for multiple individuals for three of the species. This revealed putative pseudoautosomal regions (PARs) and, in one instance, a candidate sex chromosome reassignment. A synteny analysis revealed an ancient and shared origin of the chromosomes within elasmobranchs considerably older than any previously proposed scenario, and a potential candidate gene involved in sex determination shared across all examined species. The synteny analysis also revealed a historical fusion and the formation of neo-Y chromosomes between two myliobatiform species. Our results show that there has been strong conservation and homology of the X chromosomes among elasmobranchs in spite of their varied features and different evolutionary histories. ### Competing Interest Statement The authors have declared no competing interest.

We present a genome assembly from an individual female Culex pipiens sensu stricto (the northern house mosquito; Arthropoda; Insecta; Diptera; Culicidae), from a wild population in Sweden. The genome sequence is 533 megabases in span. Most of the assembly is scaffolded into three chromosomal pseudomolecules. The complete mitochondrial genome was also assembled and is 15.6 kilobases in length.

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 serve as a resource 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. ### Competing Interest Statement The authors have declared no competing interest.

A major question in evolutionary biology is what drives the diversification of lineages. Rapid, recent radiations are ideal systems for addressing how new species arise because they may preserve key morphological and ecological adaptations associated with speciation. Melinaea and Mechanitis are two classic examples of rapidly radiating Neotropical butterfly genera of the tribe Ithomiini. They were models for early studies of Amazonian biogeography and colour pattern mimicry and have been proposed as biodiversity indicators. We generated reference genomes for five species of each genus, and whole-genome resequencing data of most species and subspecies covering a wide geographic range to assess phylogeographic relationships, patterns of hybridisation and chromosomal rearrangements. We find rampant evidence of hybridisation within both radiations, which may have facilitated their rapid diversification. Our data also provide evidence for a putative hybrid species that combines traits of both parental species. Moreover, many chromosomal fusions and fissions were identified, even between sister species. Our data also help resolve the classification of these notoriously taxonomically challenging butterflies. We conclude that interactions between geography, hybridisation and chromosomal rearrangements have contributed to these two rapid radiations in the highly diverse Neotropical region. ### Competing Interest Statement The authors have declared no competing interest.

The atomic force microscope is a versatile tool for assessing the topography, friction, and roughness of a broad spectrum of surfaces, encompassing anti-bacterial nanostructure arrays. Measuring and comparing all these values with one instrument allows clear comparisons of many nanomechanical reactions and anomalies. Increasing nano-Newton-level forces through the cantilever tip allows for the testing and measuring of failure points, damage behavior, and functionality under unfavorable conditions. Subjecting a grade 5 titanium alloy to hydrothermally etched nanostructures while applying elevated cantilever tip forces resulted in the observation of irreversible damage through atomic force microscopy. Despite the damage, a rough and non-uniform morphology remained that may still allow it to perform in its intended application as an anti-bacterial implant surface. Utilizing an atomic force microscope enables the evaluation of these surfaces before their biomedical application.

We present genome assembly from individual female An. coustani (African malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae) from Lopé, Gabon. The genome sequence is 270 megabases in span. Most of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled for both species. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.

We present a genome assembly from an individual female Anopheles marshallii (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae) from Lopé, Gabon. The genome sequence is 225.7 megabases in span. Most of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.

A genomic database of all Earth's eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.

The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance to cancer. To further this and other blue whale-related research, we report a reference-quality, long-read-based genome assembly of this fascinating species. We assembled the genome from PacBio long reads and utilized Illumina/10X, optical maps, and Hi-C data for scaffolding, polishing, and manual curation. We also provided long read RNA-seq data to facilitate the annotation of the assembly by NCBI and Ensembl. Additionally, we annotated both haplotypes using TOGA and measured the genome size by flow cytometry. We then compared the blue whale genome with other cetaceans and artiodactyls, including vaquita (Phocoena sinus), the world’s smallest cetacean, to investigate blue whale’s unique biological traits. We found a dramatic amplification of several genes in the blue whale genome resulting from a recent burst in segmental duplications, though the possible connection between this amplification and giant body size requires further study. We also discovered sites in the insulin-like growth factor-1 gene correlated with body size in cetaceans. Finally, using our assembly to examine the heterozygosity and historical demography of Pacific and Atlantic blue whale populations, we found that the genomes of both populations are highly heterozygous and that their genetic isolation dates to the last interglacial period. Taken together, these results indicate how a high-quality, annotated blue whale genome will serve as an important resource for biology, evolution, and conservation research.

The threat of infection during implant placement surgery remains a considerable burden for millions of patients worldwide. To combat this threat, clinicians employ a range of anti -infective strategies and practices. One of the most common interventions is the use of prophylactic antibiotic treatment during implant placement surgery. However, these practices can be detrimental by promoting the resilience of biofilm-forming bacteria and enabling them to persist throughout treatment and re-emerge later, causing a life -threatening infection. Thus, it is of the utmost importance to elucidate the events occurring during the initial stages of bacterial surface attachment and determine whether any biological processes may be targeted to improve surgical outcomes. Using gene expression analysis, we identified a cellular mechanism of S. aureus which modifies its cell surface charge following attachment to a medical grade titanium surface. We determined the upregulation of two systems involved in the D-alanylation of teichoic acids and the lysylation of phosphatidylglycerol. We supported these molecular findings by utilizing synchrotron -sourced attenuated total reflection Fourier -transform infrared microspectroscopy to analyze the biomolecular properties of the S. aureus cell surface following attachment. As a direct consequence, S. aureus quickly becomes substantially more tolerant to the positively charged vancomycin, but not the negatively charged cefazolin. The present study can assist clinicians in rationally selecting the most potent antibiotic in prophylaxis treatments. Furthermore, it highlights a cellular process that could potentially be targeted by novel technologies and strategies to improve the outcome of antibiotic prophylaxis during implant placement surgery. Statement of significance The antibiotic tolerance of bacteria in biofilm is a well -established phenomenon. However, the physiological adaptations employed by Staphylococcus aureus to increase its antibiotic tolerance during the early stages of surface attachment are poorly understood. Using multiple techniques, including gene expression analysis and synchrotron -sourced Fourier -transform infrared microspectroscopy, we generated insights into the physiological response of S. aureus following attachment to a medical grade titanium surface. We showed that this phenotypic transition enables S. aureus to better tolerate the positively charged vancomycin, but not the negatively charged cefazolin. These findings shed light on the antibiotic tolerance mechanisms employed by S. aureus to survive prophylactically administered antibiotics and can help clinicians to protect patients from infections. (c) 2024 The Authors. Published by Elsevier Ltd on behalf of Acta Materialia Inc. This is an open access article under the CC BY license ( http://creativecommons.org/licenses/by/4.0/ )

We present a genome assembly from an individual female Anopheles gambiae (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae), Ifakara strain. The genome sequence is 264 megabases in span. Most of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.

Theory predicts that compensatory genetic changes reduce negative indirect effects of selected variants during adaptive evolution, but evidence is scarce. Here, we test this in a wild population of Hawaiian crickets using temporal genomics and a high-quality chromosome-level cricket genome. In this population, a mutation, flatwing, silences males and rapidly spread due to an acoustically-orienting parasitoid. Our sampling spanned a social transition during which flatwing fixed and the population went silent. We find long-range linkage disequilibrium around the putative flatwing locus was maintained over time, and hitchhiking genes had functions related to negative flatwing-associated effects. We develop a combinatorial enrichment approach using transcriptome data to test for compensatory, intragenomic coevolution. Temporal changes in genomic selection were distributed genome-wide and functionally associated with the population’s transition to silence, particularly behavioural responses to silent environments. Our results demonstrate how ‘adaptation begets adaptation’; changes to the sociogenetic environment accompanying rapid trait evolution can generate selection provoking further, compensatory adaptation.

We present a genome assembly from an individual female Anopheles gambiae (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae), Ifakara strain. The genome sequence is 264 megabases in span. Most of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.