In forest tree populations, the timing of budbreak (TBB) depends on several factors, both environmental and genetic. The genomic architecture underlying this trait is still not fully characterized. So far, common garden experiments have highlighted a few genomic regions with little heritability, while the whole spectrum of TBB variation observed in the wild still remains unexplored. We performed an in situ genome-wide association study (GWAS) to investigate the genetic and environmental bases of phenotypic variation in budbreak in two wild range-edge populations of the temperate continental tree, European beech (Fagus sylvatica L.) surveyed in two consecutive years. We found distinct significant loci between populations and among years, suggesting that local adaptation has occurred and that genotype-by-environment interactions contribute to the observed variation. The phenotypic variance explained by the significant loci is between 0.2% and 54% for field data and 0% to 59% for modelled data, which suggests that while some traits are polygenic, some others are influenced by a few loci with large effects in the population, which demonstrates the relevance of conducting in situ GWAS in multiple populations. Our findings provide novel insights into the complex genetic architecture of TBB in forest trees. The genetic diversity of budbreak control provides opportunities for selection that could be used through assisted migration to help prepare beech forests to face climate change.

Dendarus foraminosus Mulsant and Rey, 1855 is a darkling beetle in the family Tenebrionidae and one of the many Dendarus species endemic to the island of Crete. Dendarus foraminosus is a commonly found species and is widespread in the lowland and montane phrygana and maquis of central Crete. The species is classified as Least Concern (LC) by the IUCN Red List. The reference genome of Dendarus foraminosus will enable phylogenetic, population, and evolutionary research regarding this endemic species and its close relatives. A total of 11 contiguous chromosomal pseudomolecules (sex chromosomes included) were assembled from the genome sequence. This chromosome-level assembly encompasses 0.59 Gb, composed of 430 contigs and 415 scaffolds, with contig and scaffold N50 values of 24.4 Mb and 51.9 Mb, respectively.

Dendarus foraminosus Mulsant and Rey, 1855 is a darkling beetle in the family Tenebrionidae and one of the many Dendarus species endemic to the island of Crete. Dendarus foraminosus is a commonly found species and is widespread in the lowland and montane phrygana and maquis of central Crete. The species is classified as Least Concern (LC) by the IUCN Red List. The reference genome of Dendarus foraminosus will enable phylogenetic, population, and evolutionary research regarding this endemic species and its close relatives. A total of 11 contiguous chromosomal pseudomolecules (sex chromosomes included) were assembled from the genome sequence. This chromosome-level assembly encompasses 0.59 Gb, composed of 430 contigs and 415 scaffolds, with contig and scaffold N50 values of 24.4 Mb and 51.9 Mb, respectively.

The main genetic diversity observed in cultivated citrus results from a reticulate evolution involving four ancestral taxa whose radiation occurred in allopatry. In such context, GWAS analysis, genome diversity and transcriptomic studies will be significantly enhanced through pangenome approaches. We report the implementation of a super-pangenome for cultivated citrus, established with de novo assemblies of C. medica, C. reticulata and C. micrantha, released for the first time alongside a published chromosome-scale assembly of C. maxima. Repetitive element annotation revealed that half of each genome consisted of transposable elements or DNA-satellites. The new genome assemblies display strong synteny and collinearity, while discrepancies are observed with the C. maxima assembly. Resequencing information from 55 accessions helped to explore the intra- and interspecific diversity of the ancestral taxa and their relationships with horticultural groups. Diagnostic SNPs of the ancestral taxa revealed interspecific introgressions in several representative accessions of C. reticulata, C. maxima and C. medica as well as insights into the origin and phylogenomic structures of horticultural groups. PAV analysis revealed a gene whose absence or presence was specific to one of the ancestral taxa. Diagnostic PAV analysis uncovered a large chloroplastic introgression in C. medica chromosome 4. The analysis of the functional enrichment and species-specific adaptations in the citrus super-pangenome revealed distinct functional specialisations. This highlights the evolutionary paths that have shaped species, contributing to the diversity in the citrus super-pangenome while maintaining a shared foundation of essential biological processes. We established a Genome Hub, offering a platform for continuous genomic research.

Oceanian citrus species, including wild taxa native to Australia and Papua New Guinea, form a genetically distinct clade within the Citrus L. (1753) genus. These species remain largely underexplored, despite their adaptation to diverse environments and relevance for citrus improvement. To support their use in breeding and evolutionary studies, we generated a high-quality, Chromosome-scale genome assembly of an Australian finger lime accession (SRA 1002), a natural interspecific hybrid. The genome was assembled using long-read sequencing, optical mapping, and a high-density genetic map, resulting in nine pseudomolecules covering over 97% of the genome. Using this reference, we analyzed whole-genome resequencing data from 132 accessions representing the diversity of Asian and Oceanian citrus. Variant calling across the dataset produced a high-resolution catalogue of single nucleotide polymorphisms (SNPs) and derived database of SNP fully discriminant of 20 Citrus species (DSNPs), enabling detailed exploration of inter- and intra-specific diversity. The data reveal a strong population structure within the group with clear heterozygosity variation between ancestral species and admixed accessions, reflecting their complex evolutionary history and hybridization patterns. This study provides the first integrated genomic framework for Oceanian citrus diversity, offering essential tools for downstream applications in citrus breeding, conservation, and evolutionary genomics. The resources generated lay the groundwork for future association studies and the targeted introgression of beneficial traits into cultivated citrus.

Arca noae, also known as the Noah's Ark clam, is a bivalve mollusk found in the shallow coastal waters of the Mediterranean Sea and the eastern Atlantic Ocean. This species plays a crucial ecological role by filtering plankton and organic particles from the water, helping maintain water quality and supporting nutrient cycling in marine ecosystems. It is also an important food source for various marine predators, including fish and crustaceans, thereby contributing to the coastal food web. Arca noae is notably resilient to environmental stressors, such as temperature fluctuations, changes in salinity, and pollution, making it a valuable model species for studying how bivalves adapt and respond to stress. While it is not commonly harvested commercially, Arca noae is of great interest to marine researchers due to its ability to thrive in diverse coastal habitats. The reference genome of Arca noae will thus provide important evolutionary insights. The entirety of the genome sequence was assembled into 19 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 1.5 Gb, composed of 257 contigs and 119 scaffolds, with contig and scaffold N50 values of 20.5 Mb and 84.7 Mb, respectively. ### Competing Interest Statement The authors have declared no competing interest.

Dendarus foraminosus Mulsant and Rey, 1855 is a darkling beetle in the family Tenebrionidae and one of the many Dendarus species endemic to the island of Crete. Dendarus foraminosus is a commonly found species and is widespread in the lowland and montane phrygana and maquis of central Crete. The species is classified as Least Concern (LC) by the IUCN Red List. The reference genome of Dendarus foraminosus will enable phylogenetic, population, and evolutionary research regarding this endemic species and its close relatives. A total of 11 contiguous chromosomal pseudomolecules (sex chromosomes included) were assembled from the genome sequence. This chromosome-level assembly encompasses 0.59 Gb, composed of 430 contigs and 415 scaffolds, with contig and scaffold N50 values of 24.4 Mb and 51.9 Mb, respectively.

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.

Most of the rich genetic diversity observed in cultivated citrus results from a reticulate evolution involving four ancestral taxa, C. medica, C. reticulata, C. maxima and C. micrantha, whose radiation occurred in allopatry. In such an evolutive context, genome diversity studies, GWAS analysis and transcriptomic studies will be significantly enhanced through pangenome approaches. We report the implementation of a super-pangenome for cultivated citrus, established with de novo assemblies in pseudochromosomes of C. medica (346 Mb), C. reticulata (332 Mb) and C. micrantha (333 Mb), released for the first time alongside a previously published chromosome-scale assembly of C. maxima. Gene annotation of these four genome assemblies revealed 28,090, 29,477, 29,258 and 30,101 genes, respectively, with a focus on pattern recognition receptors. Repetitive element annotation revealed that nearly half of each genome consisted of transposable elements or DNA-satellites. The 3 new genome assemblies display strong synteny and collinearity, while significant discrepancies are observed with the C. maxima assembly. Resequencing information (single nucleotide polymorphisms [SNPs], small indels and gene presence-absence variation [PAV]) from 55 accessions were used to explore the intra- and interspecific diversity of the four ancestral taxa and their relationships with the main horticultural groups resulting from reticulate evolution. Diagnostic SNPs of the ancestral taxa, all over the four genomes assemblies, revealed interspecific introgressions in several accessions representative of C. reticulata, C. maxima and C. medica as well as insights into the origin and phylogenomic structures of modern horticultural groups. PAV analysis revealed a gene whose absence or presence was specific to one of the ancestral taxa (dPAV). Interestingly, diagnostic PAV (dPAV) analysis uncovered a large chloroplastic introgression in chromosome 4 of C. medica, inherited in horticultural groups and recent hybrids having this species as the male parent. Implementing the super-pangenome combined the identification of orthologous genes across the four genome assemblies and the PAV information from the resequencing data. Significant inter- and intraspecific variations were highlighted, including 25,291 core, 2,431 soft-core and 5,171 dispensable genes. The analysis of the functional enrichment and species-specific adaptations in the citrus super-pangenome revealed distinct functional specializations. This highlights the evolutionary paths that have shaped each species, contributing to the diversity in the citrus super-pangenome while maintaining a shared foundation of essential biological processes. The development of this super-pangenome is a significant milestone in citrus genomics, providing a comprehensive resource that captures the extensive genetic diversity of modern cultivated citrus. Additionally, we established a dedicated Genome Hub, offering a platform for continuous genomic research and allowing for ongoing updates and future inclusion of additional ancestral species. ### Competing Interest Statement The authors have declared no competing interest.

High-quality annotation of microsporidian genomes is essential for understanding the biological processes that govern the development of these parasites. Here we present an improved structural annotation method using transcriptional DNA signals. We apply this method to re-annotate four previously annotated genomes, which allow us to detect annotation errors and identify a significant number of unpredicted genes. We then annotate the newly sequenced genome of Anncaliia algerae. A comparative genomic analysis of A. algerae permits the identification of not only microsporidian core genes, but also potentially highly expressed genes encoding membrane-associated proteins, which represent good candidates involved in the spore architecture, the invasion process and the microsporidian-host relationships. Furthermore, we find that the ten-fold variation in microsporidian genome sizes is not due to gene number, size or complexity, but instead stems from the presence of transposable elements. Such elements, along with kinase regulatory pathways and specific transporters, appear to be key factors in microsporidian adaptive processes.

Tetraodon nigroviridis is a freshwater puffer fish with the smallest known vertebrate genome. Here, we report a draft genome sequence with long-range linkage and substantial anchoring to the 21 Tetraodon chromosomes. Genome analysis provides a greatly improved fish gene catalogue, including identifying key genes previously thought to be absent in fish. Comparison with other vertebrates and a urochordate indicates that fish proteins have diverged markedly faster than their mammalian homologues. Comparison with the human genome suggests ∼900 previously unannotated human genes. Analysis of the Tetraodon and human genomes shows that whole-genome duplication occurred in the teleost fish lineage, subsequent to its divergence from mammals. The analysis also makes it possible to infer the basic structure of the ancestral bony vertebrate genome, which was composed of 12 chromosomes, and to reconstruct much of the evolutionary history of ancient and recent chromosome rearrangements leading to the modern human karyotype.

Acinetobacter sp. strain ADP1 is a nutritionally versatile soil bacterium closely related to representatives of the well-characterized Pseudomonas aeruginosa and Pseudomonas putida. Unlike these bacteria, the Acinetobacter ADP1 is highly competent for natural transformation which affords extraordinary convenience for genetic manipulation. The circular chromosome of the Acinetobacter ADP1, presented here, encodes 3325 predicted coding sequences, of which 60% have been classified based on sequence similarity to other documented proteins. The close evolutionary proximity of Acinetobacter and Pseudomonas species, as judged by the sequences of their 16S RNA genes and by the highest level of bidirectional best hits, contrasts with the extensive divergence in the GC content of their DNA (40 versus 62%). The chromosomes also differ significantly in size, with the Acinetobacter ADP1 chromosome <60% of the length of the Pseudomonas counterparts. Genome analysis of the Acinetobacter ADP1 revealed genes for metabolic pathways involved in utilization of a large variety of compounds. Almost all of these genes, with orthologs that are scattered in other species, are located in five major 'islands of catabolic diversity', now an apparent 'archipelago of catabolic diversity', within one-quarter of the overall genome. Acinetobacter ADP1 displays many features of other aerobic soil bacteria with metabolism oriented toward the degradation of organic compounds found in their natural habitat. A distinguishing feature of this genome is the absence of a gene corresponding to pyruvate kinase, the enzyme that generally catalyzes the terminal step in conversion of carbohydrates to pyruvate for respiration by the citric acid cycle. This finding supports the view that the cycle itself is centrally geared to the catabolic capabilities of this exceptionally versatile organism.

Microsporidia are obligate intracellular parasites infesting many animal groups1. Lacking mitochondria and peroxysomes, these unicellular eukaryotes were first considered a deeply branching protist lineage2 that diverged before the endosymbiotic event that led to mitochondria. The discovery of a gene for a mitochondrial-type chaperone3,4,5 combined with molecular phylogenetic data6,7,8,9 later implied that microsporidia are atypical fungi that lost mitochondria during evolution. Here we report the DNA sequences of the 11 chromosomes of the ∼2.9-megabase (Mb) genome of Encephalitozoon cuniculi (1,997 potential protein-coding genes). Genome compaction is reflected by reduced intergenic spacers and by the shortness of most putative proteins relative to their eukaryote orthologues. The strong host dependence is illustrated by the lack of genes for some biosynthetic pathways and for the tricarboxylic acid cycle. Phylogenetic analysis lends substantial credit to the fungal affiliation of microsporidia. Because the E. cuniculi genome contains genes related to some mitochondrial functions (for example, Fe–S cluster assembly), we hypothesize that microsporidia have retained a mitochondrion-derived organelle.