The era of reference genomes in conservation genomics

Draft genome of the endemic alpine ground beetle Carabus (Platycarabus) depressus (Coleoptera: Carabidae) from long-read sequencing of a frozen archived specimen

The rapid advancement of genomic technologies has enabled the production of highly contiguous reference genomes for nonmodel organisms. However, these methods often require exceptionally fresh material containing unfragmented high-molecular-weight nucleic acids. Researchers who preserve field-collected specimens in ethanol at ambient temperatures, prior to transferring them to long-term frozen archives, face challenges in applying advanced genomic approaches due to DNA and RNA fragmentation under suboptimal preservation conditions. To explore the potential of such preserved specimens as sources of reference genomes, we utilized Nanopore MinION technology to generate genomic data from a frozen archived specimen of the endemic alpine ground beetle Carabus (Platycarabus) depressus. Using a rapid in-house protocol for high-molecular-weight DNA extraction, followed by sequencing on a single flow cell, we produced 8.75 million raw reads with an N50 of 2.8 kb. The resulting assembly achieved remarkable completeness, recovering up to 98% of Benchmarking Universal Single-Copy Orthologs genes, despite a moderate N50 of 945 kb. This genome is only the second available for the taxonomically diverse genus Carabus, demonstrating the feasibility of using short-to-long-read sequencing on frozen archived specimens commonly housed in natural history collections. These findings open new avenues for advancing nonmodel organism genomics and its downstream applications.

Revealing extensive inbreeding and less efficient purging of deleterious mutations in wild Amur tigers in China

Inbreeding increases genome homozygosity within populations, which can exacerbate inbreeding depression by exposing homozygous deleterious alleles that are responsible for declines in fitness traits. In small populations, genetic purging that occurs under the pressure of natural selection acts as an opposing force, contributing to a reduction of deleterious alleles. Both inbreeding and genetic purging are paramount in the field of conservation genomics. The Amur tiger (Panthera tigris altaica) lives in small populations in the forests of Northeast Asia and is among the most endangered animals on the planet. Using genome-wide assessment and comparison, we reveal substantially higher and more extensive inbreeding in wild Amur tigers (FROH = 0.50) than in captive individuals (FROH = 0.24). However, a relatively reduced number of loss-of-function mutations in wild Amur tigers is observed compared to captive individuals, indicating genetic purging of inbreeding load with relatively large-effect alleles. The higher ratio of homozygous mutation load and number of fixed damaging alleles in the wild population indicates a less-efficient genetic purging, with purifying selection also contributing to this process. These findings provide valuable insights for the future conservation of Amur tigers.

Satellite-observed mountain greening predicts genomic erosion in a grassland medicinal herb over half a century

Mountains are biodiversity hotspots contributing essential benefits to human societies, but global environmental change is rapidly altering their habitats. During the past five decades, increasing temperatures and land-use change in montane and subalpine elevations facilitated the productivity and expansion of competitive vegetation, termed as "greening," with adverse effects on open grassland habitats. Although vegetation greening is well-documented through satellite observations, its impact on the populations and genomic integrity of affected species remains underexplored. Here, we address this challenge by integrating 40 years of remote sensing data with museum genomics and fieldwork to assess the impact of mountain greening on the genomic diversity of grassland plants in the southern Balkan peninsula. We sequenced the genomes of historical and modern populations of Ironwort, a plant of significant medicinal value, and demonstrate widespread genomic erosion across its populations. Our results show that, on average, 6% (0%-20%) of Ironwort's genome is affected by inbreeding accumulation over the past half century, indicating various degrees of population declines. Importantly, we show that genomic erosion is highly predictable by the normalized difference vegetation index (NDVI) rates of change. Our models suggest that faster increases in vegetation density are associated with higher population declines in this grassland species, revealing the negative impacts of increasing productivity in mountain ecosystems. By linking two independent and disparate monitoring indicators, we demonstrate the ability of remote sensing to predict the consequences of environmental change on temporal genomic change in mountain grassland species, with far-reaching implications for protecting natural resources in these fragile ecosystems.

The Genomics Revolution in Nonmodel Species: Predictions vs. Reality for Salmonids

The increasing feasibility of whole-genome sequencing has been highly anticipated, promising to transform our understanding of the biology of nonmodel species. Notably, dramatic cost reductions beginning around 2007 with the advent of high-throughput sequencing inspired publications heralding the 'genomics revolution', with predictions about its future impacts. Although such predictions served as useful guideposts, value is added when statements are evaluated with the benefit of hindsight. Here, we review 10 key predictions made early in the genomics revolution, highlighting those realised while identifying challenges limiting others. We focus on predictions concerning applied aspects of genomics and examples involving salmonid species which, due to their socioeconomic and ecological significance, have been frontrunners in applications of genomics in nonmodel species. Predicted outcomes included enhanced analytical power, deeper insights into the genetic basis of phenotype and fitness variation, disease management and breeding program advancements. Although many predictions have materialised, several expectations remain unmet due to technological, analytical and knowledge barriers. Additionally, largely unforeseen advancements, including the identification and management applicability of large-effect loci, close-kin mark-recapture, environmental DNA and gene editing have added under-anticipated value. Finally, emerging innovations in artificial intelligence and bioinformatics offer promising new directions. This retrospective evaluation of the impacts of the genomic revolution offers insights into the future of genomics for nonmodel species.

Synteny Enabled Upgrade of the Galapagos Giant Tortoise Genome Improves Inferences of Runs of Homozygosity

The utility and importance of whole-genome sequences are recognized across various fields, including evolution and conservation. However, for some taxa, like extinct species, using methods to generate contiguous genomes that rely on high-quality DNA is impossible. In such cases, an alternative may be to employ synteny-based methods using a genome from a closely related taxon to generate more complete genomes. Here we update the reference genome for the Pinta Island Galapagos giant tortoise (Chelonoidis abingdonii) without conducting additional sequencing through rescaffolding against the most closely related chromosome-level genome assembly, the Aldabra giant tortoise (Aldabrachelys gigantea). This effort resulted in a much more contiguous genome, CheloAbing_2.0, with an N50 that is two orders of magnitude longer and large reductions in L50 and the number of gaps. We then examined the impact of the CheloAbing_2.0 genome on estimates of runs of homozygosity (ROH) using genome resequencing data from 37 individual Galapagos giant tortoises from the 13 extant lineages to test the mechanisms by which a fragmented assembly may over- or underestimate the number and extent of ROH. The use of CheloAbing_2.0 resulted in individual estimates of inbreeding, including ROH proportion (FROH), number (NROH), and cumulative length (SROH), that were statistically different from those derived from the earlier genome assembly. This improved genome will serve as a resource for future efforts focusing on the ecology, evolution, and conservation of this species group. More broadly, our results highlight that synteny-based scaffolding is promising for generating contiguous genomes without needing additional data types.

High-quality genome assembly of the azooxanthellate coral Tubastraea coccinea (Lesson, 1829)

Coral reefs are among the most biodiverse and economically significant ecosystems globally, yet they are increasingly degrading due to global climate change and local human activities. The sun coral Tubastraea coccinea (T. coccinea) an obligate heterotroph lacking symbiotic zooxanthellae, exhibits remarkable tolerance to conditions that cause bleaching and mortality in zooxanthellate species. With its extensive low-latitude distribution across multiple oceans, T. coccinea has become a highly invasive species, adversely impacting native species, degrading local ecosystems, and causing significant socio-economic challenges that demand effective management. Despite substantial research efforts, the molecular biology of T. coccinea remains insufficiently characterized. To address this gap, we generated a draft genome assembly for T. coccinea using PacBio Hi-Fi long-read sequencing. The assembly spans 875.9 Mb with a scaffold N50 of 694.3 kb and demonstrates high completeness, with a BUSCO score of 97.4%. A total of 37,307 protein-coding sequences were identified, 95.2% of which were functionally annotated through comparisons with established protein databases. This reference genome provides a valuable resource for understanding the genetic structure of T. coccinea, advancing research into its adaptive mechanism to environmental changes, and informing conservation and management strategies to mitigate its invasive impact.

A chromosome-level genome assembly of the European green toad (Bufotes viridis)

The European green toad (Bufotes viridis) is geographically widely distributed. While the species global conservation status is labeled as of least concern by the IUCN, it is declining in many parts of its range where populations are fragmented and isolated. A high-quality reference genome is an important resource for conservation genomic researchers who are trying to understand and interpret the genomic signals of population decline, inbreeding, and the accumulation of deleterious mutations. Here, we assembled and annotated a chromosome-level reference genome for B. viridis as part of the European Reference Genome Atlas pilot project. The genome assembly, with a size of ∼3.89 Gb consists of 11 chromosomes and an additional 2,096 unplaced scaffolds. The final assembly had a scaffold N50 value of 478.39 Mb and covered 90.4% single copy tetrapod orthologs, and 46.7% repetitive elements. Finally, a total of 23,830 protein-coding genes matching a known gene, together with 56,974 mRNAs were predicted. This high-quality reference genome will benefit amphibian evolutionary genomics research and enable conservation genetic studies to inform practical conservation work on this species.

Genomic investigations of successful invasions: the picture emerging from recent studies

Invasion biology aims to identify traits and mechanisms that contribute to successful invasions, while also providing general insights into the mechanisms underlying population expansion and adaptation to rapid climate and habitat changes. Certain phenotypic attributes have been linked to successful invasions, and the role of genetics has been critical in understanding adaptation of invasive species. Nevertheless, a comprehensive summary evaluating the most common evolutionary mechanisms associated with successful invasions across species and environments is still lacking. Here we present a systematic review of studies since 2015 that have applied genomic tools to investigate mechanisms of successful invasions across different organisms. We examine demographic patterns such as changes in genomic diversity at the population level, the presence of genetic bottlenecks and gene flow in the invasive range. We review mechanisms of adaptation such as selection from standing genetic variation and de novo mutations, hybridisation and introgression, all of which can have an impact on invasion success. This comprehensive review of recent articles on the genomic diversity of invasive species led to the creation of a searchable database to provide researchers with an accessible resource. Analysis of this database allowed quantitative assessment of demographic and adaptive mechanisms acting in invasive species. A predominant role of admixture in increasing levels of genetic diversity enabling molecular adaptation in novel habitats is the most important finding of our study. The "genetic paradox" of invasive species was not validated in genomic data across species and ecosystems. Even though the presence of genetic drift and bottlenecks is commonly reported upon invasion, a large reduction in genomic diversity is rarely observed. Any decrease in genetic diversity is often relatively mild and almost always restored via gene flow between different invasive populations. The fact that loci under selection are frequently detected suggests that adaptation to novel habitats on a molecular level is not hindered. The above findings are confirmed herein for the first time in a semi-quantitative manner by molecular data. We also point to gaps and potential improvements in the design of studies of mechanisms driving rapid molecular adaptation in invasive populations. These include the scarcity of comprehensive studies that include sampling from multiple native and invasive populations, identification of invasion sources, longitudinal population sampling, and the integration of fitness measures into genomic analyses. We also note that the potential of whole genome studies is often not exploited fully in predicting invasive potential. Comparative genomic studies identifying genome features promoting invasions are underrepresented despite their potential for use as a tool in invasive species control.

Chromosome-Level Genome Assembly and Annotation of Corallium rubrum: A Mediterranean Coral Threatened by Overharvesting and Climate Change

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.

Allochrony in Atlantic Lumpfish: Genomic and Otolith Shape Divergence Between Spring and Autumn Spawners

Allochrony is a form of reproductive isolation characterized by differences in the timing of spawning and may play a crucial role in the genetic and phenotypic divergence within species. The Atlantic lumpfish (Cyclopterus lumpus) is known to spawn in spring and autumn. However, the role of allochrony on the genomic structure of this species has not been addressed. Here, by combining whole genome sequencing data and otolith shape of 64 specimens, we explore the evolutionary drivers of divergence in Atlantic lumpfish, focusing on spring and autumn spawners sampled at two well-separated spawning grounds along the Norwegian coast. Overall, we identified pronounced genomic and morphologic differences between the two spawning groups. Genomic differences between the two groups were concentrated in three chromosomes, with a region of chromosome 1 encompassing the same single nucleotide polymorphisms (SNPs) driving differential season spawning for both localities, suggesting parallel responses. The functional analysis of the SNPs in this region revealed genes associated with responses to environmental stressors, possibly adaptations to seasonal variations at high latitudes. The morphological analysis of otoliths supported these findings, showing differences compatible with adaptations to seasonal light availability. The presence of genomic islands of divergence, alongside a general lack of differentiation across the mitochondrial genome, suggest recent and rapid selection processes potentially modulated by ongoing gene flow. This study underscores the importance of considering temporal genetic structures, particularly for species with bimodal spawning time, in conservation and management strategies to prevent overexploitation and optimize breeding programs.

Enhancing inbreeding estimation and global conservation insights through chromosome-level assemblies of the Chinese and Malayan pangolin

A high-quality reference genome coupled with resequencing data is a promising strategy to address issues in conservation genomics. This has greatly enhanced the development of conservation plans for endangered species. Pangolins are fascinating animals with a variety of unique features. Unfortunately, they are the most trafficked wild animal in the world. In this study, we assembled a chromosome-scale genome with HiFi long reads and Hi-C short reads for the Chinese and Malayan pangolin and provided two new representative reference genomes for the pangolin species. We found a great improvement in the evaluation of genetic diversity and inbreeding based on these high-quality genomes and obtained different results for the detection of genome-wide extinction risks compared with genomes assembled using short reads. Moderate inbreeding and genetic diversity were reverified in these two pangolin species, except for one Malayan pangolin population with high inbreeding and low genetic diversity. Moreover, we identified a much higher inbreeding level (FROH = 0.54) in the Chinese pangolin individual from Taiwan Province compared with that from Mainland China, but more than 99.6% runs of homozygosity (ROH) fragments were restricted to less than 1 Mb, indicating that the high FROH in Taiwan Chinese pangolins may have accumulated from historical inbreeding events. Furthermore, our study is the first to detect relatively mild genetic purging in pangolin populations. These two high-quality reference genomes will provide valuable genetic resources for future studies and contribute to the protection and conservation of pangolins.

The nuclear and mitochondrial genomes of the bellicose bumblebee (Bombus bellicosus, Hymenoptera: Apidae), a threatened pollinator in a changing South American landscape

We present the first genome of a Brazilian bumblebee species, the bellicose bumblebee (Bombus bellicosus). This is an endemic species in southern South America facing local extinction due to habitat loss and climate change. During the COVID-19 social distancing in Brazil, we launched a citizen science initiative via social media to locate remaining bellicose bumblebee populations, leading to the collection of a specimen for genome sequencing. Analysis of the novel genome revealed lower genetic diversity in the bellicose bumblebee compared to a widespread related species (Bombus pascuorum). However, the absence of extensive runs of homozygosity indicated a lack of recent inbreeding, offering a promising perspective for the conservation of this species. Furthermore, demographic history analysis indicates population expansion during past glacial periods, in contrast to Palearctic bumblebees that suffered a stark decline during glaciations. Our findings provide invaluable information for the conservation of this species and for further studies about its biology and evolution, particularly under a scenario of rapid environmental change.

The Genetic Architecture of Local Adaptation and Reproductive Character Displacement in Scutiger boulengeri Complex (Anura: Megophryidae)

Speciation is a continuous process driven by barriers to gene flow. Based on genome-wide SNPs (single nucleotide polymorphisms) of 190 toads from 31 sampling sites of Scutiger boulengeri complex, we found evidence for monophyly which represented a continuous speciation process of at least six lineages in S. boulengeri, which radiated and exhibited varying degrees of divergence and gene flow. The SNP-based phylogenetic tree was largely discordant with the multilocus mitochondrial tree (i.e., S. mammatus and S. glandulatus nested in the lineages of S. boulengeri) published before. The Min Mountains (MM) and Qinghai-Tibet Plateau (QTP) lineages differ fundamentally in habitat (i.e., elevation) and morphology (i.e., SVL), we detected signatures of potential high-altitude and cold adaptation genes in QTP (vs. MM). We found the evidence of reproductive trait disparity (i.e., SVL and nuptial pads) is key to promoting sympatric rather than allopatric species pairs. In addition, we identified selection signals for genes related to sympatric character displacement, genes linked to obesity-related traits, nuptial spines morphology and enlarged chest nuptial pads in S. mammatus (vs. QTP group of S. boulengeri). Our study provided new insight and paradigm for a varied speciation pattern from local adaptation of allopatry to sympatric character displacement in the S. boulengeri complex.

A Genomic-Based Workflow for eDNA Assay Development for a Critically Endangered Turtle, Myuchelys georgesi

Environmental DNA (eDNA) analysis has become a popular conservation tool for detecting rare and elusive species. eDNA assays typically target mitochondrial DNA (mtDNA) due to its high copy number per cell and its ability to persist in the environment longer than nuclear DNA. Consequently, the development of eDNA assays has relied on mitochondrial reference sequences available in online databases, or in cases where such data are unavailable, de novo DNA extraction and sequencing of mtDNA. In this study, we designed eDNA primers for the critically endangered Bellinger River turtle (Myuchelys georgesi) using a bioinformatically assembled mitochondrial genome (mitogenome) derived from a reference genome. We confirmed the accuracy of this assembled mitogenome by comparing it to a Sanger-sequenced mitogenome of the same species, and no base pair mismatches were detected. Using the bioinformatically extracted mitogenome, we designed two 20 bp primers that target a 152-base-pair-long fragment of the cytochrome oxidase 1 (CO1) gene and a 186-base-pair-long fragment of the cytochrome B (CytB) gene. Both primers were successfully validated in silico, in vitro, and in situ.

De Novo Genome Assembly for an Endangered Lemur Using Portable Nanopore Sequencing in Rural Madagascar

As one of the most threatened mammalian taxa, lemurs of Madagascar are facing unprecedented anthropogenic pressures. To address conservation imperatives such as this, researchers have increasingly relied on conservation genomics to identify populations of particular concern. However, many of these genomic approaches necessitate high-quality genomes. While the advent of next-generation sequencing technologies and the resulting reduction in associated costs have led to the proliferation of genomic data and high-quality reference genomes, global discrepancies in genomic sequencing capabilities often result in biological samples from biodiverse host countries being exported to facilities in the Global North, creating inequalities in access and training within genomic research. Here, we present the first published reference genome for the endangered red-fronted brown lemur (Eulemur rufifrons) from sequencing efforts conducted entirely within the host country using portable Oxford Nanopore sequencing. Using an archived E. rufifrons specimen, we conducted long-read, nanopore sequencing at the Centre ValBio Research Station near Ranomafana National Park, in rural Madagascar, generating over 750 Gb of sequencing data from 10 MinION flow cells. Exclusively using this long-read data, we assembled 2.157 gigabase, 2980-contig nuclear assembly with an N50 of 101.6 Mb and a 17,108 bp mitogenome. The nuclear assembly had 30× average coverage and was comparable in completeness to other primate reference genomes, with a 96.1% BUSCO completeness score for primate-specific genes. As the first published reference genome for E. rufifrons and the only annotated genome available for the speciose Eulemur genus, this resource will prove vital for conservation genomic studies while our efforts exhibit the potential of this protocol to address research inequalities and build genomic capacity.

The Ribosomal Operon Database: A Full-Length rDNA Operon Database Derived From Genome Assemblies

Current rDNA reference sequence databases are tailored towards shorter DNA markers, such as parts of the 16/18S marker or the internally transcribed spacer (ITS) region. However, due to advances in long-read DNA sequencing technologies, longer stretches of the rDNA operon are increasingly used in environmental sequencing studies to increase the phylogenetic resolution. There is, therefore, a growing need for longer rDNA reference sequences. Here, we present the ribosomal operon database (ROD), which includes eukaryotic full-length rDNA operons fished from publicly available genome assemblies. Full-length operons were detected in 34.1% of the 34,701 examined eukaryotic genome assemblies from NCBI. In most cases (53.1%), more than one operon variant was detected, which can be due to intragenomic operon copy variability, allelic variation in non-haploid genomes, or technical errors from the sequencing and assembly process. The highest copy number found was 5947 in Zea mays. In total, 453,697 unique operons were detected, with 69,480 operon variant clusters remaining after intragenomic clustering at 99% sequence identity. The operon length varied extensively across eukaryotes, ranging from 4136 to 16,463 bp, which will lead to considerable polymerase chain reaction (PCR) bias during amplification of the entire operon. Clustering the full-length operons revealed that the different parts (i.e., 18S, 28S, and the hypervariable regions V4 and V9 of 18S) provide divergent taxonomic resolution, with 18S, the V4 and V9 regions being the most conserved. The ROD will be updated regularly to provide an increasing number of full-length rDNA operons to the scientific community.

Chromosome-Level Genome Assembly and Genetic Maker System of the Endangered Largemouth Bronze Gudgeon (Coreius guichenoti) with Focus on Conservation Applications

The largemouth bronze gudgeon (Coreius guichenoti), an endemic fish species, is distributed in the upper Yangtze River drainage. Due to anthropogenetic factors such as water pollution, overfishing, and dam construction, the wild populations of C. guichenoti have dramatically declined in recent decades. In this study, we generated a reference chromosomal-level genome assembly of C. guichenoti on the basis of PacBio HiFi sequencing and Hi-C scaffolding technologies. The final genome assembly was 1.10 Gb in length (contig N50: 28.64 Mb; scaffold N50: 42.39 Mb) with 25 chromosomes. The completeness score of the C. guichenoti genome was 96.4%, and high synteny was detected compared with Danio rerio and Ictalurus punctatus genomes. A total of 24 325 PCGs were annotated for the C. guichenoti genome. Comparative genomics analysis identified 986 expanded gene families in C. guichenoti, which were significantly enriched in GO items associated with the development and interaction of sperm and egg as well as immunity. Furthermore, positively selected genes (PSGs) detected in C. guichenoti were mainly associated with DNA repair, ATP binding, mitochondrion, and lipid homeostasis. Based on the reference genome and resequencing data, the polymorphic microsatellite (SSR) loci were comprehensively analyzed for C. guichenoti, and the top 15 tetra-nucleotide SSR loci were selected for the construction of the genetic maker system after validation through PCR and genotyping. All of these 15 tetra-nucleotide SSR loci without Hardy-Weinberg equilibrium (HWE) deviation showed high polymorphism, good amplification stability, and selective neutrality. The PID (sibs) curves revealed that the subset of four tetra-nucleotide SSR loci (cgui1, cgui5, cgui3, cgui13) was sufficient for accurate identification of C. guichenoti individuals (PIDsib < 0.01). These 15 tetra-nucleotide SSR loci could also serve as genetic markers in subsequent parentage identification and genetic diversity analysis. The chromosome-level genome assembly and findings laid solid foundations for molecular breeding, genomic research, and biological conservation of C. guichenoti.

A Faroese perspective on decoding life for sustainable use of nature and protection of biodiversity

Biodiversity is under pressure, mainly due to human activities and climate change. At the international policy level, it is now recognised that genetic diversity is an important part of biodiversity. The availability of high-quality reference genomes gives the best basis for using genetics and genetic diversity towards the global aims of (1) the protection of species, biodiversity, and nature, and (2) the management of biodiversity for achieving sustainable harvesting of nature. Protecting biodiversity is a global responsibility, also resting on small nations, like the Faroe Islands. Being in the middle of the North Atlantic Ocean and having large fisheries activity, the nation has a particular responsibility towards maritime matters. We here provide the reasoning behind the Genome Atlas of Faroese Ecology (Gen@FarE), a project based on our participation in the European Reference Genome Atlas consortium (ERGA). Gen@FarE has three major aims: (1) To acquire high-quality genomes of all eukaryotic species in the Faroe Islands and Faroese waters. (2) To establish population genetics for species of commercial or ecological interest. (3) To establish an information databank for all Faroese species, combined with a citizen science registration database, making it possible for the public to participate in acquiring and maintaining the overview of Faroese species in both terrestrial and marine environments. Altogether, we believe that this will enhance the society's interest in and awareness of biodiversity, thereby protecting the foundations of our lives. Furthermore, the combination of a wide and highly competent ERGA umbrella and more targeted national projects will help fulfil the formal and moral responsibilities that all nations, also those with limited resources, have in protecting biodiversity and achieving sustainability in harvesting from nature.

The genome sequence of the Violet Carpenter Bee, Xylocopa violacea (Linnaeus, 1785): a hymenopteran species undergoing range expansion

We present a reference genome assembly from an individual male Violet Carpenter Bee (Xylocopa violacea, Linnaeus 1758). The assembly is 1.02 gigabases in span. 48% of the assembly is scaffolded into 17 pseudo-chromosomal units. The mitochondrial genome has also been assembled and is 21.8 kilobases in length. The genome is highly repetitive, likely representing a highly heterochromatic architecture expected of bees from the genus Xylocopa. We also use an evidence-based methodology to annotate 10,152 high confidence coding genes. This genome was sequenced as part of the pilot project of the European Reference Genome Atlas (ERGA) and represents an important addition to the genomic resources available for Hymenoptera.

Evolutionary Genomics Provides Insights Into Endangerment and Conservation of a Wild Apple Tree Species, Malus sieversii

Understanding the evolutionary history of a species is essential for effective conservation management. Malus sieversii, a relict broad-leaf forest tree found in arid Central Asian mountains, has a narrow and fragmented distribution and is classified as an endangered species in China. This species is considered one of the ancestors of the domesticated apple trees. In the present study, we sampled five populations of M. sieversii and its wide-ranging congener M. baccata from China. Through deep whole-genome resequencing, we analyzed the population's genetic diversity, genetic structure, demographic history, fixation of deleterious mutations, and genomic divergence. Our results revealed that M. baccata exhibits a higher level of genetic diversity than M. sieversii. The effective population size of M. sieversii decreased, whereas that of M. baccata recovered after the bottleneck effect. In M. sieversii, the genetic structure of the Yili region was distinct from that of the Tacheng region. Populations at the rear edge of the Tacheng region showed a stronger fixation of deleterious mutations than those in the Yili region. Genomic divergence indicated that the positively selected genes were associated with physiological processes within the genomic islands between the Yili and Tacheng regions. Based on these findings, we recommend the establishment of two separate conservation units for the Yili and Tacheng lineages to preserve their genetic resources. Given the limited distribution range and high fixation rate of deleterious mutations, urgent protective measures are recommended for the Tacheng lineage.

Harnessing the Power of Next-Generation Sequencing in Wastewater-Based Epidemiology and Global Disease Surveillance

Wastewater-based epidemiology (WBE) has emerged as a valuable surveillance tool for SARS-CoV-2 and other pathogens globally, providing insights into community-level infections, including asymptomatic and pre-symptomatic cases. While most WBE programmes focus on quantitative pathogen assessment, next-generation sequencing (NGS) approaches have enabled more detailed analyses, including variant and recombinant genotype identification for viruses like SARS-CoV-2 and poliovirus. Despite recent NGS advancements allowing for the detection of known and novel viruses in wastewater, many of these tools remain underutilised in routine WBE. This short review critically evaluates the applicability of common NGS tools in routine WBE programmes, assessing their capability for identifying emerging threats with epidemic or pandemic potential. Here, we provide evidence-based recommendations for integrating NGS techniques into WBE and the use of results for informed decision-making within a One Health framework, aiming to enhance global infectious disease surveillance and pandemic preparedness.

Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe

Genomic resources are important for evaluating genetic diversity and supporting conservation efforts. The garden dormouse (Eliomys quercinus) is a small rodent that has experienced one of the most severe modern population declines in Europe. We present a high-quality haplotype-resolved reference genome for the garden dormouse, and combine comprehensive short and long-read transcriptomics data sets with homology-based methods to generate a highly complete gene annotation. Demographic history analysis of the genome reveal a sharp population decline since the last interglacial, indicating an association between colder climates and population declines before anthropogenic influence. Using our genome and genetic data from 100 individuals, largely sampled in a citizen-science project across the contemporary range, we conduct the first population genomic analysis for this species. We find clear evidence for population structure across the species' core Central European range. Notably, our data show that the Alpine population, characterized by strong differentiation and reduced genetic diversity, is reproductively isolated from other regions and likely represents a differentiated evolutionary significant unit (ESU). The predominantly declining Eastern European populations also show signs of recent isolation, a pattern consistent with a range expansion from Western to Eastern Europe during the Holocene, leaving relict populations now facing local extinction. Overall, our findings suggest that garden dormouse conservation may be enhanced in Europe through the designation of ESUs.

Harnessing genomic technologies for one health solutions in the tropics

BACKGROUND

The targeted application of cutting-edge high-throughput molecular data technologies provides an enormous opportunity to address key health, economic and environmental issues in the tropics within the One Health framework. The Earth's tropical regions are projected to contain > 50% of the world's population by 2050 coupled with 80% of its biodiversity however these regions are relatively less developed economically, with agricultural productivity substantially lower than temperate zones, a large percentage of its population having limited health care options and much of its biodiversity understudied and undescribed. The generation of high-throughput molecular data and bespoke bioinformatics capability to address these unique challenges offers an enormous opportunity for people living in the tropics. MAIN: In this review we discuss in depth solutions to challenges to populations living in tropical zones across three critical One Health areas: human health, biodiversity and food production. This review will examine how some of the challenges in the tropics can be addressed through the targeted application of advanced omics and bioinformatics and will discuss how local populations can embrace these technologies through strategic outreach and education ensuring the benefits of the One Health approach is fully realised through local engagement.

CONCLUSION

Within the context of the One Health framework, we will demonstrate how genomic technologies can be utilised to improve the overall quality of life for half the world's population.

Assembly and annotation of a chromosome-level reference genome for the endangered Colorado pikeminnow (Ptychocheilus lucius)

Advancements in genome sequencing technology have brought unprecedented accessibility of high-throughput sequencing to species of conservation interest. The potential knowledge gained from application of these techniques is maximized by availability of high-quality, annotated reference genomes for endangered species. However, these vital resources are often lacking for endangered minnows of North America (Cypriniformes: Leuciscidae). One such endangered species, Colorado pikeminnow (Ptychocheilus lucius), is the largest North American minnow and the top-level native aquatic predator in the Colorado River Basin of the southwestern United States and northwestern Mexico. Over the past century, Colorado pikeminnow has suffered habitat loss and population declines due to anthropogenic habitat modifications and invasive species introductions. The lack of genetic resources for Colorado pikeminnow has hindered conservation genomic study of this unique organism. This study seeks to remedy this issue by presenting a high-quality reference genome for Colorado pikeminnow developed from Pacific Biosciences HiFi sequencing and Hi-C scaffolding. The final assembly was a 1.1 Gb genome comprised of 305 contigs including 25 chromosome-sized scaffolds. Measures of quality, contiguity, and completeness met or exceeded those observed for Danio rerio (Danionidae) and 2 other Colorado River Basin leuciscids (Meda fulgida and Tiaroga cobitis). Comparative genomic analyses identified enrichment of gene families for growth, development, immune activity, and gene transcription; all of which are important for a large-bodied piscivorous fish living in a dynamic environment. This reference genome will provide a basis for important conservation genomic study of Colorado pikeminnow and help efforts to better understand the evolution of desert fishes.

Towards Reliable Detection of Introgression in the Presence of Among-Species Rate Variation

The role of interspecific hybridization has recently seen increasing attention, especially in the context of diversification dynamics. Genomic research has now made it abundantly clear that both hybridization and introgression-the exchange of genetic material through hybridization and backcrossing-are far more common than previously thought. Besides cases of ongoing or recent genetic exchange between taxa, an increasing number of studies report "ancient introgression"- referring to results of hybridization that took place in the distant past. However, it is not clear whether commonly used methods for the detection of introgression are applicable to such old systems, given that most of these methods were originally developed for analyses at the level of populations and recently diverged species, affected by recent or ongoing genetic exchange. In particular, the assumption of constant evolutionary rates, which is implicit in many commonly used approaches, is more likely to be violated as evolutionary divergence increases. To test the limitations of introgression detection methods when being applied to old systems, we simulated thousands of genomic datasets under a wide range of settings, with varying degrees of among-species rate variation and introgression. Using these simulated datasets, we showed that some commonly applied statistical methods, including the D-statistic and certain tests based on sets of local phylogenetic trees, can produce false-positive signals of introgression between divergent taxa that have different rates of evolution. These misleading signals are caused by the presence of homoplasies occurring at different rates in different lineages. To distinguish between the patterns caused by rate variation and genuine introgression, we developed a new test that is based on the expected clustering of introgressed sites along the genome and implemented this test in the program Dsuite.

Genetic diversity loss in the Anthropocene will continue long after habitat destruction ends

Genetic diversity within species is the basis for evolutionary adaptive capacity and has recently been included as a target for protection in the United Nations' Global Biodiversity Framework (GBF). However, there is a lack of reliable large-scale predictive frameworks to quantify how much genetic diversity has already been lost, let alone to quantitatively predict future losses under different conservation scenarios in the 21st century. Combining spatio-temporal population genetic theory with population genomic data of 18 plant and animal species, we studied the dynamics of genetic diversity after habitat area losses. We show genetic diversity reacts slowly to habitat area and population declines, but lagged losses will continue for many decades even after habitats are fully protected. To understand the magnitude of this problem, we combined our predictive method with species' habitat area and population monitoring reported in the Living Planet Index, the Red List, and new GBF indicators. We then project genetic diversity loss in 13,808 species with a short-term genetic diversity loss of 13-22% and long-term loss of 42-48% with substantial deviations depending on the level of habitat fragmentation. These results highlight that protection of only current habitats is insufficient to ensure the genetic health of species and that continuous genetic monitoring alone likely underestimates long term impacts. We provide an area-based spatio-temporal predictive framework to develop quantitative scenarios of global genetic biodiversity.

The last days of Aporia crataegi (L.) in Britain: Evaluating genomic erosion in an extirpated butterfly

Current rates of habitat degradation and climate change are causing unprecedented declines in global biodiversity. Studies on vertebrates highlight how conservation genomics can be effective in identifying and managing threatened populations, but it is unclear how vertebrate-derived metrics of genomic erosion translate to invertebrates, with their markedly different population sizes and life histories. The Black-veined White butterfly (Aporia crataegi) was extirpated from Britain in the 1920s. Here, we sequenced historical DNA from 17 specimens collected between 1854 and 1924 to reconstruct demography and compare levels of genomic erosion between extirpated British and extant European mainland populations. We contrast these results using modern samples of the Common Blue butterfly (Polyommatus icarus); a species with relatively stable demographic trends in Great Britain. We provide evidence for bottlenecks in both these species around the period of post-glacial colonization of the British Isles. Our results reveal different demographic histories and Ne for both species, consistent with their fates in Britain, likely driven by differences in life history, ecology and genome size. Despite a difference, by an order of magnitude, in historical effective population sizes (Ne), reduction in genome-wide heterozygosity in A. crataegi was comparable to that in P. icarus. Symptomatic of A. crataegi's disappearance were marked increases in runs-of-homozygosity (RoH), potentially indicative of recent inbreeding, and accumulation of putatively mildly and weakly deleterious variants. Our results provide a rare glimpse of genomic erosion in a regionally extinct insect and support the potential use of genomic erosion metrics in identifying invertebrate populations or species in decline.

Genomic evidence for the widespread presence of GH45 cellulases among soil invertebrates

Lignocellulose is a major component of vascular plant biomass. Its decomposition is crucial for the terrestrial carbon cycle. Microorganisms are considered primary decomposers, but evidence increases that some invertebrates may also decompose lignocellulose. We investigated the taxonomic distribution and evolutionary origins of GH45 hydrolases, important enzymes for the decomposition of cellulose and hemicellulose, in a collection of soil invertebrate genomes. We found that these genes are common in springtails and oribatid mites. Phylogenetic analysis revealed that cellulase genes were acquired early in the evolutionary history of these groups. Domain architectures and predicted 3D enzyme structures indicate that these cellulases are functional. Patterns of presence and absence of these genes across different lineages prompt further investigation into their evolutionary and ecological benefits. The ubiquity of cellulase genes suggests that soil invertebrates may play a role in lignocellulose decomposition, independently or in synergy with microorganisms. Understanding the ecological and evolutionary implications might be crucial for understanding soil food webs and the carbon cycle.

Genetic Stock Identification Reveals Mismatches Between Management Areas and Population Genetic Structure in a Migratory Pelagic Fish

Sustainable fisheries management is important for the continued harvest of the world's marine resources, especially as they are increasingly challenged by a range of climatic and anthropogenic factors. One of the pillars of sustainable fisheries management is the accurate identification of the biological units, i.e., populations. Here, we developed and implemented a genetic baseline for Atlantic herring harvested in the Norwegian offshore fisheries to investigate the validity of the current management boundaries. This was achieved by genotyping > 15,000 herring from the northern European seas, including samples of all the known populations in the region, with a panel of population-informative SNPs mined from existing genomic resources. The final genetic baseline consisted of ~1000 herring from 12 genetically distinct populations. We thereafter used the baseline to investigate mixed catches from the North and Norwegian Seas, revealing that each management area consisted of multiple populations, as previously suspected. However, substantial numbers (up to 50% or more within a sample) of herring were found outside of their expected management areas, e.g., North Sea autumn-spawning herring north of 62° N (average = 19.2%), Norwegian spring-spawning herring south of 62° N (average = 13.5%), and western Baltic spring-spawning herring outside their assumed distribution area in the North Sea (average = 20.0%). Based upon these extensive observations, we conclude that the assessment and management areas currently in place for herring in this region need adjustments to reflect the populations present. Furthermore, we suggest that for migratory species, such as herring, a paradigm shift from using static geographic stock boundaries towards spatial dynamic boundaries is needed to meet the requirements of future sustainable management regimes.

A comparison of genomic diversity and demographic history of the North Atlantic and Southwest Atlantic southern right whales

Right whales (genus Eubalaena) were among the first, and most extensively pursued, targets of commercial whaling. However, understanding the impacts of this persecution requires knowledge of the demographic histories of these species prior to exploitation. We used deep whole genome sequencing (~40×) of 12 North Atlantic (E. glacialis) and 10 Southwest Atlantic southern (E. australis) right whales to quantify contemporary levels of genetic diversity and infer their demographic histories over time. Using coalescent- and identity-by-descent-based modelling to estimate ancestral effective population sizes from genomic data, we demonstrate that North Atlantic right whales have lived with smaller effective population sizes (Ne) than southern right whales in the Southwest Atlantic since their divergence and describe the decline in both populations around the time of whaling. North Atlantic right whales exhibit reduced genetic diversity and longer runs of homozygosity leading to higher inbreeding coefficients compared to the sampled population of southern right whales. This study represents the first comprehensive assessment of genome-wide diversity of right whales in the western Atlantic and underscores the benefits of high coverage, genome-wide datasets to help resolve long-standing questions about how historical changes in effective population size over different time scales shape contemporary diversity estimates. This knowledge is crucial to improve our understanding of the right whales' history and inform our approaches to address contemporary conservation issues. Understanding and quantifying the cumulative impact of long-term small Ne, low levels of diversity and recent inbreeding on North Atlantic right whale recovery will be important next steps.

Multi-omics analyzes of Rosa gigantea illuminate tea scent biosynthesis and release mechanisms

Rose is an important ornamental crop cultivated globally for perfume production. However, our understanding of the mechanisms underlying scent production and molecular breeding for fragrance is hindered by the lack of a reference genome for tea roses. We present the first complete telomere-to-telomere (T2T) genome of Rosa gigantea, with high quality (QV > 60), including detailed characterization of the structural features of repetitive regions. The expansion of genes associated with phenylpropanoid biosynthesis may account for the unique tea scent. We uncover the release rhythm of aromatic volatile organic compounds and their gene regulatory networks through comparative genomics and time-ordered gene co-expression networks. Analyzes of eugenol homologs demonstrate how plants attract pollinators using specialized phenylpropanoids in specific tissues. This study highlights the conservation and utilization of genetic diversity from wild endangered species through multi-omics approaches, providing a scientific foundation for enhancing rose fragrance via de novo domestication.

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

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.

Contextualising samples: supporting reference genomes of European biodiversity through sample and associated metadata collection

The European Reference Genome Atlas (ERGA) consortium aims to generate a reference genome catalogue for all of Europe's eukaryotic biodiversity. The biological material underlying this mission, the specimens and their derived samples, are provided through ERGA's pan-European network. To demonstrate the community's capability and capacity to realise ERGA's ambitious mission, the ERGA Pilot project was initiated. In support of the ERGA Pilot effort to generate reference genomes for European biodiversity, the ERGA Sampling and Sample Processing committee (SSP) was formed by volunteer experts from ERGA's member base. SSP aims to aid participating researchers through (i) establishing standards for and collecting of sample/specimen metadata; (ii) prioritisation of species for genome sequencing; and (iii) development of taxon-specific collection guidelines including logistics support. SSP serves as the entry point for sample providers to the ERGA genomic resource production infrastructure and guarantees that ERGA's high-quality standards are upheld throughout sample collection and processing. With the volume of researchers, projects, consortia, and organisations with interests in genomics resources expanding, this manuscript shares important experiences and lessons learned during the development of standardised operational procedures and sample provider support. The manuscript details our experiences in incorporating the FAIR and CARE principles, species prioritisation, and workflow development, which could be useful to individuals as well as other initiatives.

High-speed whole-genome sequencing of a Whippet: Rapid chromosome-level assembly and annotation of an extremely fast dog's genome

The time required for genome sequencing and de novo assembly depends on the interaction between laboratory work, sequencing capacity, and the bioinformatics workflow, often constrained by external sequencing services. Bringing together academic biodiversity institutes and a medical diagnostics company with extensive sequencing capabilities, we aimed at generating a high-quality mammalian de novo genome in minimal time. We present the first chromosome-level genome assembly of the Whippet, using PacBio long-read high-fidelity sequencing and reference-guided scaffolding. The final assembly has a contig N50 of 55 Mbp and a scaffold N50 of 65.7 Mbp. The total assembly length is 2.47 Gbp, of which 2.43 Gpb were scaffolded into 39 chromosome-length scaffolds. Annotation using mammalian genomes and transcriptome data yielded 28,383 transcripts, 90.9% complete BUSCO genes, and identified 36.5% repeat content. Sequencing, assembling, and scaffolding the chromosome-level genome of the Whippet took less than a week, adding another high-quality reference genome to the available sequences of domestic dog breeds.

KegAlign: Optimizing pairwise alignments with diagonal partitioning

Our ability to generate sequencing data and assemble it into high quality complete genomes has rapidly advanced in recent years. These data promise to advance our understanding of organismal biology and answer longstanding evolutionary questions. Multiple genome alignment is a key tool in this quest. It is also the area which is lagging: today we can generate genomes faster than we can construct and update multiple alignments containing them. The bottleneck is in considerable computational time required to generate accurate pairwise alignments between divergent genomes, an unavoidable precursor to multiple alignments. This step is typically performed with lastZ, a very sensitive and yet equally slow tool. Here we describe an optimized GPU-enabled pairwise aligner KegAlign. It incorporates a new parallelization strategy, diagonal partitioning, with the latest features of modern GPUs. With KegAlign a typical human/mouse alignment can be computed in under 6 hours on a machine containing a single NVidia A100 GPU and 80 CPU cores without the need for any pre-partitioning of input sequences: a ~150× improvement over lastZ. While other pairwise aligners can complete this task in a fraction of that time, none achieves the sensitivity of KegAlign's main alignment engine, lastZ, and thus may not be suitable for comparing divergent genomes. In addition to providing the source code and a Conda package for KegAlign we also provide a Galaxy workflow that can be readily used by anyone.

The genetic basis of the kākāpō structural color polymorphism suggests balancing selection by an extinct apex predator

The information contained in population genomic data can tell us much about the past ecology and evolution of species. We leveraged detailed phenotypic and genomic data of nearly all living kākāpō to understand the evolution of its feather color polymorphism. The kākāpō is an endangered and culturally significant parrot endemic to Aotearoa New Zealand, and the green and olive feather colorations are present at similar frequencies in the population. The presence of such a neatly balanced color polymorphism is remarkable because the entire population currently numbers less than 250 birds, which means it has been exposed to severe genetic drift. We dissected the color phenotype, demonstrating that the two colors differ in their light reflectance patterns due to differential feather structure. We used quantitative genomics methods to identify two genetic variants whose epistatic interaction can fully explain the species' color phenotype. Our genomic forward simulations show that balancing selection might have been pivotal to establish the polymorphism in the ancestrally large population, and to maintain it during population declines that involved a severe bottleneck. We hypothesize that an extinct apex predator was the likely agent of balancing selection, making the color polymorphism in the kākāpō a "ghost of selection past."

The Catalan initiative for the Earth BioGenome Project: contributing local data to global biodiversity genomics

The Catalan Initiative for the Earth BioGenome Project (CBP) is an EBP-affiliated project network aimed at sequencing the genome of the >40 000 eukaryotic species estimated to live in the Catalan-speaking territories (Catalan Linguistic Area, CLA). These territories represent a biodiversity hotspot. While covering less than 1% of Europe, they are home to about one fourth of all known European eukaryotic species. These include a high proportion of endemisms, many of which are threatened. This trend is likely to get worse as the effects of global change are expected to be particularly severe across the Mediterranean Basin, particularly in freshwater ecosystems and mountain areas. Following the EBP model, the CBP is a networked organization that has been able to engage many scientific and non-scientific partners. In the pilot phase, the genomes of 52 species are being sequenced. As a case study in biodiversity conservation, we highlight the genome of the Balearic shearwater Puffinus mauretanicus, sequenced under the CBP umbrella.

Proposals for consideration at IMC12 to modify provisions related solely to fungi in Chapter F of the International Code of Nomenclature for algae, fungi, and plants

Seven proposals or sets of proposals to modify the provisions of Chapter F of the International Code of Nomenclature for algae, fungi, and plants (ICNafp) have been received. These proposals are formally presented together here. The topics addressed relate to: fungi whose morph-names have the same epithet; the listing of synonyms under entries for protected names in the Code Appendices; the processes of protection and rejection; the use of DNA sequences as nomenclatural types; the use of genomes as nomenclatural types; and the designation of fungi known only from DNA sequences. In addition, a suggestion is included to update the mention of the World Directory of Culture Collections in Article 40.7 Note 4. A Synopsis of the formal proposals will be provided in early July 2024, and the mycological community will be invited to provide a guiding vote on the proposals with a closing date of 2 August 2024. Final decisions on the proposals will be made following debate at the Fungal Nomenclature Session of IMC12 in August 2024.

Forest genomics in the Caucasus through the lens of its dominant tree species - Fagus orientalis

The last glacial period is known to have greatly influenced the demographic history of temperate forest trees, with important range contractions and post-glacial expansions that led to the formation of multiple genetic lineages and secondary contact zones in the Northern Hemisphere. These dynamics have been extensively studied for European and North American species but are still poorly understood in other temperate regions of rich biodiversity such as the Caucasus. Our study helps filling that gap by deciphering the genomic landscapes of F. orientalis across the South Caucasus. The use of genome-wide data confirmed a past demographic history strongly influenced by the Last Glacial Maximum, revealing two disjunct glacial refugia in the Colchis and Hyrcanian regions. The resulting patterns of genetic diversity, load and differentiation are not always concordant across the region, with genetic load pinpointing the location of the glacial refugia more efficiently than genetic diversity alone. The Hyrcanian forests show depleted genetic diversity and substantial isolation, even if long-distance gene flow is still present with the main centre of diversity in the Greater Caucasus. Finally, we characterize a strong heterogeneity of genetic diversity and differentiation along the species chromosomes, with noticeably a first chromosome showing low diversity and weak differentiation.

Diving into broad-scale and high-resolution population genomics to decipher drivers of structure and climatic vulnerability in a marine invertebrate

Species with widespread distributions play a crucial role in our understanding of climate change impacts on population structure. In marine species, population structure is often governed by both high connectivity potential and selection across strong environmental gradients. Despite the complexity of factors influencing marine populations, studying species with broad distribution can provide valuable insights into the relative importance of these factors and the consequences of climate-induced alterations across environmental gradients. We used the northern shrimp Pandalus borealis and its wide latitudinal distribution to identify current drivers of population structure and predict the species' vulnerability to climate change. A total of 1514 individuals sampled across 24° latitude were genotyped at high geographic (54 stations) and genetic (14,331 SNPs) resolutions to assess genetic variation and environmental correlations. Four populations were identified in addition to finer substructure associated with local adaptation. Geographic patterns of neutral population structure reflected predominant oceanographic currents, while a significant proportion of the genetic variation was associated with gradients in salinity and temperature. Adaptive landscapes generated using climate projections suggest a larger genomic offset in the southern extent of the P. borealis range, where shrimp had the largest adaptive standing genetic variation. Our genomic results combined with recent observations point to further deterioration in southern regions and an impending vulnerable status in the regions at higher latitudes for P. borealis. They also provide rare insights into the drivers of population structure and climatic vulnerability of a widespread meroplanktonic species, which is crucial to understanding future challenges associated with invertebrates essential to ecosystem functioning.

Environmental and anthropogenic factors mediating the functional connectivity of the mesquite lizard along the eastern Trans-Mexican Volcanic Belt

Functional connectivity, the extent to which a landscape facilitates or impedes the dispersal of individuals across the landscape, is a key factor for the survival of species. Anthropogenic activities, such as urbanization, agriculture and roads, negatively impact functional connectivity of most species, particularly low-vagility species like lizards. Here, we examine how a landscape modified by anthropogenic activities affects the functional connectivity, at both broad and fine scales, of a widely distributed generalist lizard Sceloporus grammicus in the eastern Trans-Mexican Volcanic Belt, Mexico. We estimated for the first time the species' genetic structure, gene flow and functional connectivity in agricultural and forest zones using genomic data, a comprehensive landscape characterization and novel methods including gravity models. Our results showed not only marked genetic differentiation across the study region but also that functional connectivity is maintained for tens of kilometres despite S. grammicus low vagility. Specifically, we found that substrate and air temperature facilitated connectivity over broad and fine scales, respectively, while agricultural cover, relative humidity and slope were important for connectivity and gene flow. Contrastingly, forest cover and roads favoured (broad-scale) and limited (fine-scale) connectivity, likely associated with movement facilitated by small forest patches and with thermoregulation. Altogether, these results support that S. grammicus alternates its thermoregulatory behaviour depending on the distance travelled and the habitat environmental conditions, and that it can disperse through relatively modified landscapes, mainly using agricultural zones. The information obtained is crucial to understanding the response of lizards to current anthropogenic pressures and their potential to adapt.

Plant pangenomes for crop improvement, biodiversity and evolution

Plant genome sequences catalogue genes and the genetic elements that regulate their expression. Such inventories further research aims as diverse as mapping the molecular basis of trait diversity in domesticated plants or inquiries into the origin of evolutionary innovations in flowering plants millions of years ago. The transformative technological progress of DNA sequencing in the past two decades has enabled researchers to sequence ever more genomes with greater ease. Pangenomes - complete sequences of multiple individuals of a species or higher taxonomic unit - have now entered the geneticists' toolkit. The genomes of crop plants and their wild relatives are being studied with translational applications in breeding in mind. But pangenomes are applicable also in ecological and evolutionary studies, as they help classify and monitor biodiversity across the tree of life, deepen our understanding of how plant species diverged and show how plants adapt to changing environments or new selection pressures exerted by human beings.

Reference genome for the Mojave poppy bee (Perdita meconis), a specialist pollinator of conservation concern

The Mojave poppy bee, Perdita meconis Griswold (Hymenoptera: Anthophila: Andrenidae), is a species of conservation concern that is restricted to the eastern Mojave Desert of North America. It is a specialist pollinator of two poppy genera, Arctomecon and Argemone (Papaveraceae), and is being considered for listing under the US Endangered Species Act along with one of its pollinator hosts, the Las Vegas bearpoppy (Arctomecon californica). Here, we present a near chromosome-level genome of the Mojave poppy bee to provide a genomic resource that will aid conservation efforts and future research. We isolated DNA from a single, small (<7 mm), male specimen collected using non-ideal preservation methods and then performed whole-genome sequencing using PacBio HiFi technology. After quality and contaminant filtering, the final draft genome assembly is 327 Mb, with an N50 length of 17.5 Mb. Annotated repetitive elements compose 37.3% of the genome, although a large proportion (24.87%) of those are unclassified repeats. Additionally, we annotated 18,245 protein-coding genes and 19,433 transcripts. This genome represents one of only a few genomes from the large bee family Andrenidae and one of only a few genomes for pollinator specialists. We highlight both the potential of this genome as a resource for future research, and how high-quality genomes generated from small, non-ideal (in terms of preservation) specimens could facilitate biodiversity genomics.

Annotation and visualization of parasite, fungi and arthropod genomes with Companion

As sequencing genomes has become increasingly popular, the need for annotation of the resulting assemblies is growing. Structural and functional annotation is still challenging as it includes finding the correct gene sequences, annotating other elements such as RNA and being able to submit those data to databases to share it with the community. Compared to de novo assembly where contiguous chromosomes are a sign of high quality, it is difficult to visualize and assess the quality of annotation. We developed the Companion web server to allow non-experts to annotate their genome using a reference-based method, enabling them to assess the output before submitting to public databases. In this update paper, we describe how we have included novel methods for gene finding and made the Companion server more efficient for annotation of genomes of up to 1 Gb in size. The reference set was increased to include genomes of interest for human and animal health from the fungi and arthropod kingdoms. We show that Companion outperforms existing comparable tools where closely related references are available.

Variant calling in polyploids for population and quantitative genetics

Advancements in genome assembly and sequencing technology have made whole genome sequence (WGS) data and reference genomes accessible to study polyploid species. Compared to popular reduced-representation sequencing approaches, the genome-wide coverage and greater marker density provided by WGS data can greatly improve our understanding of polyploid species and polyploid biology. However, biological features that make polyploid species interesting also pose challenges in read mapping, variant identification, and genotype estimation. Accounting for characteristics in variant calling like allelic dosage uncertainty, homology between subgenomes, and variance in chromosome inheritance mode can reduce errors. Here, I discuss the challenges of variant calling in polyploid WGS data and discuss where potential solutions can be integrated into a standard variant calling pipeline.

Genomic insights into the conservation status of the Idle Crayfish Austropotamobius bihariensis Pârvulescu, 2019: low genetic diversity in the endemic crayfish species of the Apuseni Mountains

BACKGROUND

Biodiversity in freshwater ecosystems is declining due to an increased anthropogenic footprint. Freshwater crayfish are keystone species in freshwater ecosystems and play a crucial role in shaping the structure and function of their habitats. The Idle Crayfish Austropotamobius bihariensis is a native European species with a narrow distribution range, endemic to the Apuseni Mountains (Romania). Although its area is small, the populations are anthropogenically fragmented. In this context, the assessment of its conservation status is timely.

RESULTS

Using a reduced representation sequencing approach, we identified 4875 genomic SNPs from individuals belonging to 13 populations across the species distribution range. Subsequent population genomic analyses highlighted low heterozygosity levels, low number of private alleles and small effective population size. Our structuring analyses revealed that the genomic similarity of the populations is conserved within the river basins.

CONCLUSION

Genomic SNPs represented excellent tools to gain insights into intraspecific genomic diversity and population structure of the Idle Crayfish. Our study highlighted that the analysed populations are at risk due to their limited genetic diversity, which makes them extremely vulnerable to environmental alterations. Thus, our results emphasize the need for conservation measures and can be used as a baseline to establish species management programs.

A data-driven genome annotation approach for cassava

Genome annotation files play a critical role in dictating the quality of downstream analyses by providing essential predictions for gene positions and structures. These files are pivotal in decoding the complex information encoded within DNA sequences. Here, we generated experimental data resolving RNA 5'- and 3'-ends as well as full-length RNAs for cassava TME12 sticklings in ambient temperature and cold. We used these data to generate genome annotation files using the TranscriptomeReconstructoR (TR) tool. A careful comparison to high-quality genome annotations suggests that our new TR genome annotations identified additional genes, resolved the transcript boundaries more accurately and identified additional RNA isoforms. We enhanced existing cassava genome annotation files with the information from TR that maintained the different transcript models as RNA isoforms. The resultant merged annotation was subsequently utilized for comprehensive analysis. To examine the effects of genome annotation files on gene expression studies, we compared the detection of differentially expressed genes during cold using the same RNA-seq data but alternative genome annotation files. We found that our merged genome annotation that included cold-specific TR gene models identified about twice as many cold-induced genes. These data indicate that environmentally induced genes may be missing in off-the-shelf genome annotation files. In conclusion, TR offers the opportunity to enhance crop genome annotations with implications for the discovery of differentially expressed candidate genes during plant-environment interactions.

An epigenetic toolbox for conservation biologists

Ongoing climatic shifts and increasing anthropogenic pressures demand an efficient delineation of conservation units and accurate predictions of populations' resilience and adaptive potential. Molecular tools involving DNA sequencing are nowadays routinely used for these purposes. Yet, most of the existing tools focusing on sequence-level information have shortcomings in detecting signals of short-term ecological relevance. Epigenetic modifications carry valuable information to better link individuals, populations, and species to their environment. Here, we discuss a series of epigenetic monitoring tools that can be directly applied to various conservation contexts, complementing already existing molecular monitoring frameworks. Focusing on DNA sequence-based methods (e.g. DNA methylation, for which the applications are readily available), we demonstrate how (a) the identification of epi-biomarkers associated with age or infection can facilitate the determination of an individual's health status in wild populations; (b) whole epigenome analyses can identify signatures of selection linked to environmental conditions and facilitate estimating the adaptive potential of populations; and (c) epi-eDNA (epigenetic environmental DNA), an epigenetic-based conservation tool, presents a non-invasive sampling method to monitor biological information beyond the mere presence of individuals. Overall, our framework refines conservation strategies, ensuring a comprehensive understanding of species' adaptive potential and persistence on ecologically relevant timescales.

The dilemma of underestimating freshwater biodiversity: morphological and molecular approaches

BACKGROUND

Anthropogenic impacts on freshwater habitats are causing a recent biodiversity decline far greater than that documented for most terrestrial ecosystems. However, knowledge and description of freshwater biodiversity is still limited, especially targeting all size classes to uncover the distribution of biodiversity between different trophic levels. We assessed the biodiversity of the Lower Rhine and associated water bodies in the river's flood plain including the river's main channel, oxbows and gravel-pit lakes, spanning from the level of protists up to the level of larger invertebrate predators and herbivores organized in size classes (nano-, micro, meio- and macrofauna). Morphological diversity was determined by morphotypes, while the molecular diversity (amplicon sequencing variants, ASVs) was assessed through eDNA samples with metabarcoding targeting the V9 region of the 18S rDNA.

RESULTS

Considering all four investigated size classes, the percentage of shared taxa between both approaches eDNA (ASVs with 80-100% sequence similarity to reference sequences) and morphology (morphotypes), was always below 15% (5.4 ± 3.9%). Even with a more stringent filtering of ASVs (98-100% similarity), the overlap of taxa could only reach up to 43% (18.3 ± 12%). We observed low taxonomic resolution of reference sequences from freshwater organisms in public databases for all size classes, especially for nano-, micro-, and meiofauna, furthermore lacking metainformation if species occur in freshwater, marine or terrestrial ecosystems.

CONCLUSIONS

In our study, we provide a combination of morphotype detection and metabarcoding that particularly reveals the diversity in the smaller size classes and furthermore highlights the lack of genetic resources in reference databases for this diversity. Especially for protists (nano- and microfauna), a combination of molecular and morphological approaches is needed to gain the highest possible community resolution. The assessment of freshwater biodiversity needs to account for its sub-structuring in different ecological size classes and across compartments in order to reveal the ecological dimension of diversity and its distribution.