Identifying nematodes to the species level is known to be complicated due to their morphological plasticity and limited number of taxonomically important characters. This is especially apparent in the genus Panagrolaimus , which comprises many cryptic species that are morphologically difficult to distinguish but differ genetically. These roundworms are particularly notable for their adaptation to extreme environments that are inhospitable to many other forms of life. Traditional morphological identification methods often fail at distinguishing genetically divergent populations due to high morphological plasticity in Panagrolaimus , limiting the efficacy of species discovery. High-quality genome assemblies overcome these challenges, offering a comprehensive blueprint of an organism's genetic structure that can be used for species identification. The analysis of ultra-conserved elements across multiple loci harvested from genome assemblies provides robust phylogenetic resolution. In this study, we integrate genome sequencing, ultra-conserved element analysis, and morphological assessment to identify and describe three novel species: Panagrolaimus einhardi sp. nov., formerly Panagrolaimus sp. ES5 from Germany; Panagrolaimus shuimeiren sp. nov. from the Namib Desert; and Panagrolaimus nebliphilus sp. nov. from the Atacama Desert. P. einhardi sp. nov. is named after Prof. Einhard Schierenberg, a renowned expert in roundworm development and cherished member of the nematode community, who isolated this species himself. All three species originate from different geographical locations, and their respective identification are supported by high-quality genome assemblies from either PacBio HiFi or Oxford Nanopore long-read data. The P. einhardi sp. nov. genome was scaffolded using Hi-C technology, which resulted in a 116 Mb collapsed assembly composed of 44 scaffolds (N50: 28 Mb). P. shuimeiren sp. nov. has an assembly size of 69 Mb with 49 scaffolds and a N50 of 13 Mb. P. nebliphilus sp. nov. assembly is 70 Mb with 24 scaffolds (N50: 13 Mb). The capacity of Panagrolaimus to adapt to extreme environments is driving research into their survival mechanisms, requiring comprehensive genomic resources. By combining morphology and genomics, we can gain a more comprehensive understanding of the rich biological diversity in lineages with numerous cryptic species, such as the Panagrolaimidae, thereby clarifying relationships where morphological data alone are ambiguous or confounded. ### Competing Interest Statement The authors have declared no competing interest. Deutsche Forschungsgemeinschaft, https://ror.org/018mejw64, 268236062

We present a genome assembly from an individual nematode Ostertagia ostertagi (Rhabditida, Trichostrongylidae). The genome sequence has a total length of 407.17 megabases. Most of the assembly sequence (99.3%) was assigned to 6 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled, with a length of 14.49 kilobases.

Abstract Background Xenarthrans, comprising sloths, anteaters, and armadillos, represent one of the most morphologically and physiologically specialized mammalian clades, yet the genomic basis of their adaptations remains poorly understood. Here, we present chromosome-level genomes for the two-toed sloth (Choloepus didactylus) and the southern anteater (Tamandua tetradactyla) and investigate how retrotransposon-mediated gene duplications (retrocopies) have shaped genome evolution in these and other species in Xenarthra. Results Comparative analyses revealed that the xenarthran genomes analyzed here harbour the highest number of retrocopies reported among mammals, with lineage-specific insertion dynamics. Anteater and armadillo genomes contain older LINE1 repertoires and species-specific older retrocopy insertions. In contrast, sloths retain both an abundance of young LINE1s and thousands of young retrocopies, alongside a large shared set that originated from an evolutionary burst of retroduplication in the branch leading to their last common ancestor (~ 30 Mya). In C. didactylus, 49% of retrocopies were found to be expressed in five tissues, compared with 27% in Dasypus novemcinctus in three tissues. Evolutionary analyses identified 38 retrocopies with strong hallmarks of domestication in C. didactylus. Many of these retrocopies derive from parental genes involved in mitochondrial and metabolic processes, suggesting a potential genomic contribution to the physiological specializations of sloths. Conclusions Altogether, our findings identify retrotransposition as a major contributor to the genomic architecture of the xenarthrans presented here and highlight retrocopy origination as a mechanism for generating lineage-specific novelty and, possibly, distinctive biological specializations.

We present a genome assembly of Thelazia callipaeda (nematode; Nematoda; Chromadorea; Rhabditida; Thelaziidae). The genome sequence has a total length of 117.59 megabases. Most of the assembly (75.82%) is scaffolded into 4 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has been assembled, with a length of 13.66 kilobases.

We present a genome of Echinomermella matsi (Nematoda: Plectida: Benthimermithidae), a body cavity parasite of the green sea urchin Strongylocentrotus spp. commonly found along the coast of Central and Northern Norway. Three assemblies were generated, 1 from multiple individuals using Oxford Nanopore long-read data and 2 from 2 individuals using PacBio long-read data. The genome of Echinomermella matsi is 65 Mb long consisting of 7 chromosomes, with nematode Benchmarking Using Single Copy Orthologue (BUSCO odb12) completeness reaching 96%. The E. matsi chromosome complement corresponds to the proposed Rhabditida ancestral linkage groups. Phylogenetic analyses using newly generated 18S rRNA genes and a multigene dataset consisting of BUSCO protein-coding genes, supported by morphological observations of juveniles, firmly place Echinomermella within the nematode order Plectida, alongside nematode parasitoids of marine invertebrates, Trophomera or Neocamacolaimus. As a result, the generally free-living order Plectida includes at least 3 independently evolved lineages of nematodes symbiotic with various groups of aquatic and terrestrial invertebrates and with unicellular organisms. This, and the fact that Plectida is the closest sister lineage to Rhabditida as a whole, and 1 node away from the exclusively animal parasitic Spirurina, makes this lineage a valuable model for study of evolution of animal parasitism in the aquatic environment.

The Gambusia holbrooki (eastern mosquitofish) reference genome will offer a crucial resource for understanding the evolution and adaptation of invasive freshwater fish species. The genome of G. holbrooki was assembled into two haplotypes through a phased assembly approach; however, only the primary haplotype was designated as the reference genome for annotation and downstream analyses. The entirety of the genome sequence was assembled into 24 contiguous chromosomal pseudomolecules and 1 mitochondrial genome. This chromosome-level assembly encompasses 0.67 Gb, composed of 421 contigs and 318 scaffolds, with contig and scaffold N50 values of 15.9 Mb and 29.6 Mb, respectively.

We present a genome assembly of Thelazia callipaeda (nematode; Nematoda; Chromadorea; Rhabditida; Thelaziidae). The genome sequence has a total length of 117.59 megabases. Most of the assembly (75.82%) is scaffolded into 4 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has been assembled, with a length of 13.66 kilobases.

In recent years, many high-quality reference genome sequences for arthropod species have been generated. Although most genome papers describe their protocols and metrics, no consensus exists on the data that should be included in genome reports. Here, we review current standards across seven key stages of an arthropod genome project (budgeting, sourcing and vouchering, sample preparation and sequencing, genome assembly, analysis reproducibility, databasing, and genome annotation) and identify persistent gaps in standards as well as their implementation. To assess current standards reporting in the community, we surveyed 100 arthropod genome papers published in 2024. The use of long reads to assemble highly contiguous arthropod genomes is now standard practice when adequate input DNA is available, and basic assembly contiguity and conserved gene content statistics are consistently reported. However, there is less standardization in pre- and post-assembly procedures and metrics. When comparing Darwin Tree of Life (DToL) genome notes to other journals, publications from the latter group were less likely to describe compliance with ethical collection practices, sample vouchering, post-assembly curation steps, and assembly quality metrics beyond basic contiguity and completeness values. Genome annotation practices are highly variable: some genome note formats do not explicitly require annotation, and while the reporting rate of protein-coding gene annotations is higher in non-DToL publications, the submission rate of annotations to centralized sequence databases is much lower. Our findings highlight critical opportunities to harmonize reporting standards and promote their dissemination, ensuring that future arthropod genomes are both comparable and maximally reusable for large-scale comparative and applied research.

How do sex chromosomes evolve in the transition to asexuality? So far, species that depart from canonical sexual reproduction-for example, parthenogens with rare sex or species where the paternal genome is set aside-have been found to carry either no sex chromosomes or sex chromosomes but no male-specific sex chromosome (i.e. no Y). Here we reveal that, in Mesorhabditis nematodes, a new Y chromosome evolved once, from sexual ancestors, in species that have transitioned into an unconventional mode of reproduction called autopseudogamy. In this reproductive system, females produce clonal females plus rare (∼10%) males that are needed for fertilization but that do not contribute to the female genome. Analyzing the Y chromosomes of two autopseudogamous species, we found high levels of degeneration, most likely due to loss of recombination, and two additional conserved features: (i) they accumulated male-beneficial genes, and (ii) they display a strong fertilization drive, in that mainly Y-bearing sperm fertilize female oocytes. Both features are likely evolutionarily favorable in the context of autopseudogamy. Our results suggest that male-specific chromosomes can still be maintained in systems with rare, and possibly "genetically useless," males.

The Biodiversity Genomics Europe (BGE) Project has the overarching aim of accelerating the use of genomic science to enhance understanding of biodiversity, monitor biodiversity change, and guide interventions to address its decline. The BGE Project comprises activities focused on DNA Barcoding (Barcoding Stream) and Reference Genome Generation (Genomes Stream) for eukaryotic species across Europe, bringing together two European networks: the International Barcode of Life in Europe (iBOL Europe) and the European Reference Genome Atlas (ERGA). This publication is an abridged version of the successful grant proposal developed jointly by iBOL Europe and ERGA in response to the Horizon Europe call HORIZON-CL6-2021-BIODIV-01-01. Two key strands of genomic science form the basis of this proposal: DNA barcoding - sequencing short, standardised genomic regions to tell the world’s species apart, transforming the speed of completion of the inventory of life on Earth and providing the foundations of a global bio-surveillance system for biodiversity; and genome sequencing - generating high-quality complete reference genomes for all species on Earth, transforming understanding of biodiversity at the genetic level, and delivering fundamental knowledge of how biological systems function and how species respond and adapt to environmental change. The BGE Project objectives are focused on (i) Capacity: To establish functioning biodiversity genomics networks at the European level to connect and grow community capacity to use genomic tools to tackle the biodiversity crisis; (ii) Production: To establish and implement large-scale biodiversity genomic data generation pipelines for Europe to accelerate the production and accessibility of genomic data for biodiversity characterisation, conservation, and biomonitoring; and (iii) Application: To apply genomic tools to enhance understanding of pan-European biodiversity and biodiversity declines to improve the efficacy of management interventions and biomonitoring programmes.

Hirudo verbana Carena, 1820, commonly known as the southern medicinal leech, is one of several European medicinal leeches, whose full diversity has just recently started to be uncovered. Historically, it has been widely used as a medicinal leech and for centuries it was treated erroneously under the specific name of Hirudo medicinalis L. 1758. Recent molecular and taxonomic analyses have revealed subspecific diversity within the morphospecies H. verbana. Hirudo verbana is a blood-feeding species sucking blood from amphibians, fish, and mammals. It occupies freshwater habitats, typically shallow ponds and lakes. Studies show that this leech species has a "naturally limited microbiome", suggesting it may serve as a powerful model system for the study of gut microbiota. We expect this chromosome-level assembly of H. verbana to serve as a high-quality genomic resource for this most famous leech genus and to serve as a foundation to the study of the diversification and biodiversity of European medicinal leeches, as well as their gut-associated symbionts. The genome of H. verbana was assembled into two haplotypes through a phased assembly approach; however, only the primary haplotype was designated as the reference genome for annotation and downstream analyses. The entirety of the primary haplotype was assembled into 14 contiguous chromosomal pseudomolecules, including the mitogenome. This chromosome-level assembly encompasses 0.18 Gb, composed of 277 contigs and 27 scaffolds, with contig and scaffold N50 values of 1.3 Mb and 13.4 Mb, respectively.

Abstract Tropical rainforests, and Amazonia in particular, contain more tree species than anywhere else, most of which arose through rapid evolutionary radiations 1–3 . Rapid radiations are often catalysed by ecological opportunity 4–6 , which in rainforest trees is presented by intense insect herbivore pressure, spurring the evolution of novel plant defence chemistry to escape it 7 . However, we do not understand how long-lived trees can adapt quickly enough to keep pace with rapidly-evolving insect herbivores. Here we show that hybridisation in rainforest trees, which was considered rare, allows exchange of gene clusters used in chemical defence against herbivore attack, facilitating rapid adaptation and diversification. Using genome sequencing for 461 individuals from the genus Inga , a characteristic Amazonian tree radiation, we find that regional tree communities form syngameons - networks of closely related, co-occurring species connected by gene flow. Integrating these genomes with herbivore abundance data from the same communities across the tropical Americas, we show that herbivore compositional turnover coincides with local, recurrent interspecific transfer of defence gene clusters that are retained by balancing selection, consistent with fluctuating selective pressure imposed by shifting herbivore communities. Together, our results demonstrate that hybridisation allows long-lived tropical trees to rapidly evolve chemical defences, fuelling adaptation to the relentless insect herbivory that structures the world’s most species-rich forests.

The reference genome of the Eurasian Woodcock (Scolopax rusticola) is an important resource to investigate population structure across the wide breeding range of this iconic game species and the conservation status of specific management units, such as the isolated Macaronesian populations. The genome sequence was assembled into 45 contiguous chromosomal pseudomolecules and 2 sex chromosomes (W and Z). This chromosome-level assembly encompasses 1.2 Gb, composed of 1,613 contigs and 935 scaffolds, with contig and scaffold N50 values of 5.9 Mb and 34.2 Mb, respectively.

Lichens are symbiotic associations between filamentous fungi and photosynthetic micro-organisms, such as green algae and/or cyanobacteria, that result in a single anatomically complex structure that can thrive in environments inhospitable to most organisms, including arctic tundra, high mountains, and deserts. Recent evidence suggests that lichens may be even more complex than previously appreciated, containing multiple microbial constituents, but how genomes of the principal fungal symbiont (which provides the majority of biomass in lichen tissue) have been shaped during evolution is largely unexplored. Recently, giant transposable elements called Starships have been found in many genomes of filamentous fungi, but to which extent they occur in lichen-forming fungi is not known. In this report, we describe a Starship element from the lichen fungus Xanthoria parietina . This element, named Tangerine , contains several genes that have signatures of horizontal gene transfer from nonlichen-forming fungi, most likely from black yeasts of the Chaetothyriales, that are often lichen-associated. Repetitive sequences carried by Tangerine , and found in other sites in Xanthoria genomes, are affected by repeat-induced point mutation, a mechanism of genome defense against transposable elements, consistent with fungal sexual reproduction which always precedes new lichen formation by X. parietina . Tangerine ’s “captain” belongs to a newly defined family of tyrosine recombinases specific to lichen-forming Lecanoromycetes. Several other captain clades have signatures of horizontal gene transfer between distantly related lichen-forming fungi and nonmycobiont lichen-associated fungi. We speculate that Starships may play a significant, yet hitherto unrecognized role, in lichen genome evolution and provide a roadmap for further investigation.

Biodiversity is declining in many parts of the world. Biological diversity measurement and monitoring are fundamental to the assessment of the causes and consequences of environmental changes, identification of key areas for the protection of biodiversity or ecosystem services, determining the effectiveness of actions, and the creation of decision-support tools critical to maintaining a sustainable planet. Biodiversity measurement is rapidly changing due to advances in citizen science, image recognition, acoustic monitoring, environmental DNA, genomics, remote sensing, and AI. In this perspective, we outline the exciting opportunities these developments offer but also consider the challenges. Our key recommendations are to 1) Capitalize on the ability of novel technology to integrate data sources 2) agree to standard methods for data collection 3) ensure new technologies are calibrated with existing data; 4) fill data gaps by using emerging technologies and increasing capacity, especially in the tropics; 5) create living safeguarded databases of trusted information to reduce the risk of poisoning by AI hallucinated, or false, information; 6) ensure data generation is valued; 7) ensure respectful incorporation of Indigenous Knowledge; 8) ensure measurements enable the quantification of effectiveness of actions, and 9) increase the resilience of global datasets to technical and societal change. Radical new collaborations are needed between computer scientists, engineers, molecular biologists, data scientists, field ecologists, citizen scientists, Indigenous peoples, policymakers, and local communities to create the rigorous, resilient, accessible biodiversity information systems required to underpin policies and practices that ensure the maintenance and restoration of ecological systems.

Hirudo verbana Carena, 1820, commonly known as the southern medicinal leech, is one of several European medicinal leeches, whose full diversity has just recently started to be uncovered. Historically, it has been widely used as a medicinal leech and for centuries it was treated erroneously under the specific name of Hirudo medicinalis L. 1758. Recent molecular and taxonomic analyses have revealed subspecific diversity within the morphospecies H. verbana. Hirudo verbana is a blood-feeding species sucking blood from amphibians, fish, and mammals. It occupies freshwater habitats, typically shallow ponds and lakes. Studies show that this leech species has a "naturally limited microbiome", suggesting it may serve as a powerful model system for the study of gut microbiota. We expect this chromosome-level assembly of H. verbana to serve as a high-quality genomic resource for this most famous leech genus and to serve as a foundation to the study of the diversification and biodiversity of European medicinal leeches, as well as their gut-associated symbionts. The genome of H. verbana was assembled into two haplotypes through a phased assembly approach; however, only the primary haplotype was designated as the reference genome for annotation and downstream analyses. The entirety of the primary haplotype was assembled into 14 contiguous chromosomal pseudomolecules, including the mitogenome. This chromosome-level assembly encompasses 0.18 Gb, composed of 277 contigs and 27 scaffolds, with contig and scaffold N50 values of 1.3 Mb and 13.4 Mb, respectively.

Abstract Identifying nematode species is challenging due to morphological plasticity and few diagnostic characters, especially in Panagrolaimus, which has many genetically distinct but morphologically similar cryptic species adapted to extreme environments. Morphology-based methods often fail to distinguish divergent Panagrolaimus, limiting discovery. Genome assemblies address these challenges by providing a detailed genetic blueprint for identification. We combined genome sequencing, phylogenetic analyses using 18S rRNA and ultra-conserved elements, and morphology to describe three novel species: Panagrolaimus einhardi sp. nov. (formerly Panagrolaimus sp. ES5, Rhineland, Germany), Panagrolaimus shuimeiren sp. nov. (Namib Desert, Namibia), and Panagrolaimus nebliphilus sp. nov. (Atacama Desert, Chile). Panagrolaimus einhardi is named after Prof. Einhard Schierenberg, a renowned expert and valued member of the nematode community, who isolated the species himself. The identifications are supported by high-quality assemblies from PacBio HiFi or Oxford Nanopore long reads. The P. einhardi assembly was scaffolded using Hi-C, yielding a 116 Mb collapsed assembly with 44 scaffolds (N50: 28 Mb). Panagrolaimus shuimeiren has an assembly size of 69 Mb (49 scaffolds, N50: 13 Mb), and P. nebliphilus an assembly size of 70 Mb (24 scaffolds, N50: 13 Mb). Integrating morphology and genomics clarifies biological diversity in cryptic-rich lineages like Panagrolaimidae, resolving relationships where morphology alone is ambiguous.

Acrobeloides nanus is a species of widely distributed bacteria-feeding nematodes belonging to the family Cephalobidae. It reproduces parthenogenetically, making it a valuable system for studying the consequences of obligate asexuality, and exhibits early developmental processes that differ significantly from the model organism Caenorhabditis elegans. Additionally, the species has demonstrated remarkable resistance in extreme conditions, surviving near-complete desiccation through anhydrobiosis. This new chromosome-level genome assembly provides a high-quality reference to study these traits. Combining Nanopore, amplified PacBio HiFi, and Hi-C sequencing, we generated a chromosome-level assembly spanning 188.9 Mb over six chromosomes. The genome features a 48.1% repeat content, dominated by Mutator-like elements, and contains 24,912 predicted genes. Structural analysis reveals the conservation of ancestral nematode linkage groups. This resource significantly improves upon previous fragmented assemblies, offering a new framework for identifying genomic adaptations in the family Cephalobidae.

Assembly quality is frequently assessed using independent measures of assembly span, contiguity, sequence composition, and completeness. Among contiguity metrics, contig, and scaffold N50 have perhaps gained the most traction, despite well-known limitations. Several authors have suggested considering the complete Nx curve rather than just the N50 value, but while using N90 values or considering the area under the Nx curve with auN statistics provide more complete measures of contiguity, they share the limitation of being unsuited to direct comparison across a range of genome sizes. We introduced snail plots to provide a genome-size-independent way to summarize a range of commonly used assembly metrics. Here, we demonstrate that easily learnt visual differences between snail plots allow simultaneous consideration of metrics across several key areas of assembly quality to rapidly identify high- and low-quality assemblies. We show that prominent features in snail plots of high-quality assemblies effectively highlight N50, N90, and auN contiguity statistics. As the presentation is scaled to the longest scaffold, we also show that plots can be compared effectively across a wide range of taxa and assembly sizes. We use the core features of a snail plot to derive a proportional measure of assembly quality based on auN, adjusted for non-ATGC bases and scaled to the length of the longest scaffold. We show that this "snail score" value corresponds closely to a qualitative assessment of overall assembly quality from visual interpretation of a snail plot and supports corrections for expected genome size.

LepEU, the European Lepidopteran Population Genomics Consortium, was launched in 2023 to coordinate continental-scale collections and generate population-level genomic data for butterflies and moths across Europe. Its whole-genome resequencing strategy takes advantage of the growing availability of reference genomes for Lepidoptera. LepEU supports scalable, standardized sampling and sequencing to quantify genetic diversity and population resilience. These data will allow addressing long-standing questions about geographic patterns of biodiversity in this iconic clade for evolutionary ecology, while also filling critical gaps in biodiversity monitoring and conservation. The consortium's first in-person workshop was held in Montpellier (France) in 2025 and was supported by the COST Action 10kLepGenomes. It gathered 23 researchers from 10 countries, including experts in Lepidoptera ecology, evolution, and population genomics. Building on 2 years of video conferencing, the workshop enabled participants to draw a roadmap for trans-continental standardized sampling, isolate DNA of specimens collected during 2024, outline key research questions for LepEU, and discuss an outreach strategy to engage additional stakeholders. LepEU is coordinating with other international networks and consortia to develop a collaborative platform for tracking European lepidopteran biodiversity and evolution. Looking ahead, LepEU is focused on training and mentoring the next generation of scientists, empowering them to integrate genomic analyses with phenotypic and ecological data to address ecological, evolutionary, and conservation questions.