The olfactory receptor (OR) gene represent a significant multigene family in vertebrates, forming the core molecular basis of olfactory perception and playing a crucial role in the environmental adaptation of species. High-altitude ecosystems represent extreme habitats characterized by specific abiotic stresses, including low oxygen levels, low temperatures, and intense ultraviolet radiation. These environments also exhibit low aquatic biodiversity and a limited variety of odor molecules, factors that have influenced the adaptive evolution of the sensory systems in endemic species. However, the genetic mechanisms underlying olfactory adaptation in high-altitude freshwater fish remained inadequately understood. In this study, we performed comparative genomics analyses to reveal the evolutionary processes underlying the adaptive and functional evolution of OR genes in S. younghusbandi, a cyprinid fish endemic to the Qinghai-Xizang Plateau. The results indicated that, compared to their low-altitude relatives, S. younghusbandi possessed a significantly smaller number of OR genes, with only 98 genes, which revealed the contraction of the gene family. Phylogenetic analysis revealed that the OR genes of cyprinid fish could be categorized into two major lineages: type I and type II. The η and δ families, which perceive water-soluble odors, in S. younghusbandi underwent significant and specific expansion, while the ε family was completely absent. This pattern reflected adaptive changes in olfactory recognition to accommodate the simplified odor spectrum of high-altitude water bodies. Chromosomal localization analysis demonstrated that OR genes were clustered, and collinearity analysis confirmed the presence of conserved genomic fragments among species. Selection pressure analysis revealed that the Ka/Ks values of all homologous gene pairs were less than 1, indicating that the OR genes of S. younghusbandi underwent strong purifying selection as a group to preserve core olfactory function. A few genes exhibited relaxed selection characteristics, which may have facilitated the fine-tuning of adaptability to high-altitude environments. In conclusion, this study elucidated the evolutionary dynamics and adaptive characteristics of the OR gene in S. younghusbandi, offering a new perspective on the molecular mechanisms underlying olfactory adaptation at high altitudes and enriching the research on sensory evolution in vertebrates.
We present a reference-quality genome assembly for the desert night lizard (Xantusia vigilis). The night lizards (Xantusiidae) are a family of small-bodied lizards found in North America (Xantusia), Central America (Lepidophyma), and Cuba (Cricosaura). The night lizard family has an independent evolutionary history of at least 80 million years from its sister taxa within Scincoidea. The Xantusiids have several unique ecological, behavioral and evolutionary characteristics. For instance, the family contains the only squamate species that form diploid, unisexual, parthenogenic lineages. In addition, most night lizards are viviparous and form stable kin groups that are maintained over multiple years, an unusual life history strategy among lizards. Combining PacBio long-read sequencing, Hi-C, and RNAseq data we developed a reference-quality genome for the desert night lizard, X. vigilis. We assembled a complete mitochondrion and ~ 2.2 Gb nuclear genome, with 20 scaffolds that correlate in size to the X. vigilis karyotype. In addition, we found that X. vigilis chromosome 1 aligns with gene content of both of macrochromosome 1 and microchromosome 9 from a genome assembly of a species in the sister family Cordylidae (Hemicordylus capensis).
The Agamidae (agamids, also known as dragon lizards or dragons) is a species-rich squamate family adapted to all non-polar continents except the Americas. Flying dragons (Draco) belong to this family and are widespread across South and Southeast Asia. To date, no nuclear genome assemblies of flying dragons have been published, limiting our understanding of the genetic underpinnings of their unique adaptive gliding trait and population dynamics. We report a high-quality chromosome-level assembly of Draco maculatus (the spotted flying dragon) with a size of 1.73Gb, a scaffold N50 of 255.50 Mb, and 18,805 annotated protein-coding genes. The assembly (99.88% of assembled sequence) was anchored to 17 pseudochromosomes (6 macro-11 micro), consistent with the reported karyotype of Draco species in cytogenetic studies. We also provide transcriptomic data from the patagium, skin, and four internal tissues.
Contemporary sugarcane cultivars originate from interspecific hybridization between Saccharum officinarum and Saccharum spontaneum, resulting in highly complex polyploid genomes. Dissecting chromosomal inheritance and structural variation is critical for accelerating molecular breeding in sugarcane. Here, we applied chromosome-specific painting using ten probes, together with S. spontaneum-specific probes, to resolve chromosomal composition and translocation patterns in the cultivar CT89-103 and its derived hybrids. High-resolution physical map was constructed in sugarcane cultivar CT89-103 that harbors 111 chromosomes, with 7-12 copies of each chromosome (1-10), and exhibits 13 distinct chromosomal translocation types. Its genome comprises 7.14% S. spontaneum-derived chromosomes and 24.11% interspecific recombinant chromosomes. The hybrids contain 108-116 chromosomes, with 5-15 copies of chromosomes 1-10 converging toward ~12 copies, and show similar genomic composition (8.20% S. spontaneum and 23.88% recombinant chromosomes). These findings demonstrate that S. spontaneum chromosomal segments and parental translocations are largely transmitted through n + n inheritance. Notably, extensive structural variation was observed, with 35 translocation types predominating in the hybrids. Altogether, this study provides a high-resolution view of chromosomal inheritance and structural variation in sugarcane, offering a cytogenetic framework for sugarcane hybridization.
The goitered gazelle, Gazella subgutturosa, is a conservation priority globally, one of the important ungulates in the arid and semiarid ecosystem. We produced Illumina short reads, PacBio HiFi long reads and Hi-C sequencing data of a road-killed male individual of this species to assemble whole genome at the chromosome level. Consequently, the assembly is a 3.13 Gb in size, consisting of 16 pseudochromosomes (14 autosomes + X chromosome + partial Y chromosome), with a scaffold N50 length of 186.56Mb. The quality value and Benchmarking Universal Single-Copy Ortholog score were 47.6 and 99.3%, respectively, indicating that our genomes sequence is of high quality and completeness. A total of 20,896 protein-coding genes were predicted in the genome, with an average gene length of 38,012 bp and an average coding sequence length of 1,291 bp. Comparison with other Bovidae genome revealed that each of the pseudochromosome of G. subgutturosa corresponds to two chromosomes of Bovidae species, suggesting multiple whole chromosome fusions. Notably, the X chromosome corresponds to a fusion of the Bos taurus X chromosome and BTA5, consistent with a known X-autosomal translocation in the tribe Antilopini. However, the underlying molecular mechanism of this chromosome fusion has yet to be elucidated in future studies. In summary, the whole genome generated provides a high-quality reference for conservation genomics and genome evolution studies of Gazella species, especially of G. subgutturosa.
Use of ephemeral habitats may lead to high vagility and an increase in gene flow and panmixia across a species' range. Range expansions associated with habitat alterations may also spur connectivity among previously isolated habitats and reduce genetic diversity at the colonization front. A century and a half of historical and modern single nucleotide polymorphism (SNP) data for Bachman's Sparrow (Peucaea aestivalis) demonstrate that panmixia is characteristic of this ephemeral habitat specialist, not a byproduct of a recent range expansion or retraction. Furthermore, high vagility has apparently dampened expected genetic signatures at the colonization front where no consistent signal of lower genetic diversity was observed in the extralimital region compared to other regions during expansion or retraction. Overall, our data support an emerging pattern of limited genetic structure for a species associated with ephemeral habitats, for which high vagility may have evolved to help individuals locate transient habitat across large spatial scales. Nevertheless, extensive habitat loss and fragmentation in recent decades have begun to influence genetic variation in P. aestivalis with small but significant increases in genetic structure. If this exceptionally vagile ephemeral habitat specialist is unable to reach remaining isolated habitat fragments, it is likely that barriers to its dispersal are limiting gene flow in other species, even those thought to be capable of traversing long distances.
Advances in genetic tools such as next and third generation sequencing, paired with a focus on representative clades, provide insight into how processes including adaptation, admixture, and genome structure shape the evolution and maintenance of species. However, our understanding of the genomics of speciation is dominated by systems where ecological adaptations are thought to cause initial barriers to gene exchange. In contrast to other model systems, the 38 species of the genus Laupala constitute a very rapid radiation, where evolution of reproductive barriers and speciation is thought to be driven by sexual selection. Here, with novel PacBio HiFi reads and RNA- and Iso-Seq data, we provide a highly contiguous, chromosome-level genome and markedly improved annotation of the endemic Hawaiian cricket, Laupala kohalensis Otte, 1994. Our new resources advance previous efforts, placing 99% of 47 scaffolds on 7 autosomes and 1 sex chromosome in the 1.67 Gb assembly, with a 98.8% BUSCO score (insecta_db10), N50 of ~268 Mb, and L50 of 3. Using a custom repeat library, we estimate the genome to have 46.09% repeat content, and the new annotation includes an increased estimate of 17,670 genes, which coincides with that known from other Orthopterans. Notably, we find a large nuclear DNA segment of mitochondrial origin on chromosome 7. This new resource provides a powerful tool to identify and compare genomic causes of phenotypic diversification in a system characterized by strong signatures of sexual differentiation, representing an underappreciated but potentially widespread cause of speciation.
We present the first chromosome-level reference genome for Lepidurus arcticus (Pallas, 1793), a freshwater crustacean with circumpolar distribution. L. arcticus belongs to the small order of freshwater Notostracan crustaceans that are representatives of the ancient group Branchiopoda. This group has a remarkable morphological stability and is frequently labelled "living fossils". Its ancient origin, streamlined genome and reproductive flexibility makes this a very interesting candidate for genomic studies. The pseudo-haplotype-resolved assemblies, hap1 and hap2, span 81.2 megabases (Mb) and 81.8 Mb, respectively, and were each scaffolded into six chromosomes. Both hap1 and hap2 showed high completeness, with identical BUSCO completeness scores of 98.3%. Scaffold N50 lengths were 13.4 Mb for hap1 and 13.9 Mb for hap2, and k-mer completeness estimated from PacBio HiFi reads was 95.79% and 96.18%, respectively. The pseudo-haplotypes showed very low estimated genome-wide heterozygosity of 0.133%. Gene annotation identified 10,901 protein-coding genes in hap1 and 10,910 in hap2. Repetitive elements comprised approximately 24-25% of each assembly, with long terminal repeat retrotransposons representing the most abundant transposable element class at approximately 8-9%. Comparison with the near chromosome-level genome of Lepidurus packardi revealed substantial intrachromosomal rearrangements, despite similar chromosome numbers and chromosome sizes. Differences in transposable element content between L. arcticus and L. packardi were primarily driven by retrotransposons, particularly LTR and LINE elements. This reference genome provides a valuable resource for future population genomic studies and for investigating evolutionary stasis at the genome level.
The hypothesis that mountain uplift creates riverine barriers to alpine plant gene flow is widely accepted in biogeography, yet how these barriers drive species genetic differentiation remains poorly understood. Here, we tested this hypothesis using Allium macranthum (section Bromatorrhiza), a diploid-tetraploid alpine herb endemic to southwest China with a core distribution in the Jinsha-Yalong River basin. We genotyped 280 individuals from 22 range-wide populations (including sympatric cytotypes) using nuclear ITS and two chloroplast (cpDNA) fragments (trnL-F and rps16). Population karyotypic characteristics were investigated, and population genetic structure, differentiation and divergence time were estimated, with biogeographical history investigated. Our results reveal striking asymmetric genetic diversity, with biparentally inherited ITS showed far higher haplotype diversity (Hd = 0.95) than cpDNA markers (trnL-F: Hd = 0.54; rps16: Hd = 0.48). Meanwhile, significant population differentiation were revealed, with three deeply divergent phylogenetic clades detected, which corresponding to different geographic regions: the internal Hengduan Mountains between the Jinsha and Yalong Rivers (I), the external Hengduan Mountains (E), and Qinling Mountains (Q). Karyotypic analyses demonstrated that A. macranthumis characterized by pronounced polyploidy (coexisting diploid and tetraploid forms), and the tetraploid populations exhibited a significantly high level of karyotype asymmetry.Divergent time estimation showed that the intraspecific differentiation of A. macranthum was approximate at 6.72-1.91 Ma, coinciding with the intense uplift of the HMR and formation of the Jinsha-Yalong drainage system. Our findings suggest that Early Pleistocene mountain building might promote river incision, expediting the differentiation of A. macranthum, while riverine barriers, ploidy variation, and reproductive shifts may have synergistically shaped the observed asymmetric differentiation.
ABSTRACT Tigriopus copepods are found in splash pools on all seven continents from the equator to Arctic and Antarctic regions. Given their geographic distribution, frequent exposure to extreme environmental conditions, and strong signatures of local adaptation, these copepods have become models for exploring patterns of adaptation to stressful environments. However, most studies focus on a small subset of Tigriopus species, and there are few genome resources representing the diversity of Tigriopus species and populations. Here, we combine long-read, Pacific Biosciences HiFi data with short-read, Illumina HiC and RNA-seq data to assemble and annotate a genome representing a Tigriopus population from the coast of central Chile. Based on the level of divergence that we observed in mitochondrial genes, we also performed a comparison of morphological characteristics between this population and members of the T. angulatus complex. The assembly that we generated (qhTigAngs1.1.pri) includes 12 major scaffolds (N50 19Mbp, L50 7), equivalent to the number of chromosomes in other Tigriopus species. BUSCO and k-mer analyses of the assembly and BUSCO analyses of gene models are relatively complete (89-99%) with respect to gene or k-mer content. The level of divergence that we observed, morphological differences we recorded, and the spatial distance of this population from the type locality suggest that this Chilean population of Tigriopus may represent a novel species that we call Tigriopus aff. angulatus . These genomic resources will help us understand the diversity and structure of Tigriopus species and populations as well as facilitate future comparisons of adaptation across parallel environmental gradients.
The rice stink bug (Oebalus pugnax; RSB) is a major agricultural pest that poses significant threats to rice production throughout the United States. Yet, despite its economic significance, almost nothing is known about genome structure, function, and evolution in this species. Here, we sequenced, assembled, and annotated the first high-quality reference genome for RSB and conducted comparative analyses with related hemipteran genomes to understand its historical evolutionary context. The assembly spans 826.62 Mb across 211 contigs, with an N50 of 17.25 Mb, the largest contig of 67.15 Mb, and a BUSCO representation of 99.30% completeness. Hi-C-based scaffolding supported six putative chromosome-scale scaffolds. Genome-wide repeats comprised 47.55% of the genome, consisting largely of interspersed elements, including DNA transposons, LINEs, and LTRs, with evidence of recent expansions. Our annotation identified 13,175 putative genes, with predicted functions for 97.87% of them. We further uncovered candidate genes and enzyme families involved in detoxification and insecticide resistance, including cytochrome P450s, UDP-glycosyltransferases, and glycoside hydrolases. Comparative analyses revealed rapid expansion and contraction of gene families associated with feeding, host specialization, and insecticide resistance. Together, these resources provide a new framework for future investigations into genome structure, function, and evolution in this ecologically and economically important insect clade.
Local extirpations and extreme bottlenecks can deplete genetic variation and obscure population dynamics, especially in highly mobile species. The gray whale (Eschrichtius robustus) undertakes some of the longest known migrations among mammals, and two stocks (eastern and western gray whales) were historically recognized in the Pacific. Commercial whaling depleted both stocks, and while the Eastern North Pacific (ENP) stock has rebounded, the western stock was feared extirpated. In the post-whaling era, the origin of a small summer aggregation near Sakhalin Island, Russia (which we refer to as the Western North Pacific (WNP) stock) is unclear; this group may include descendants from the original western stock, founders from the eastern stock, or some combination of the two. To clarify the genetic affinities of WNP gray whales, we analyzed whole genome resequencing data for 71 individuals sampled from both geographic regions. Surprisingly, WNP whales are more genetically varied than ENP whales according to principal components and admixture analyses. We present evidence that this structure reflects mixed ancestry in the WNP, where some contemporary whales retain ancestry from the feared-extirpated western population, detectable as "ghost" introgression, while others are of eastern ancestry. Genomic signals based on both single nucleotide polymorphisms and on copy number variants indicate that despite mixed ancestry, the influx of recent eastern gene flow has largely homogenized genomic diversity across the Pacific. These findings highlight the ability of whole-genome data to help resolve questions of extirpation and to clarify complex gene flow dynamics in highly mobile species.
Small and isolated populations often have low levels of standing genetic variation, which limits their capacity to evolutionarily adapt to climate change. In freshwater ecosystems, habitat fragmentation caused by instream barriers and water regulation is a prominent global issue impacting on connectivity among populations. We investigated genomic vulnerability to climate change in a small-bodied and poorly dispersing species, the southern pygmy perch, in Australia's Murray-Darling Basin (MDB). We used a genome-wide dataset for 467 individuals from 30 sites covering the range of the species in the MDB. This included temporal sampling of a population in the Lower Lakes region, prior to its extirpation during the Millennium Drought and after its re-establishment through a captive breeding and reintroduction program. Southern pygmy perch exhibited high levels of population structure, with 11 distinct genetic clusters mainly delineated by river catchments. Genetic diversity was low, especially in small and isolated headwater populations. Genomic vulnerability, assessed via a genomic offset approach, correlated positively with elevation, being generally higher in upland and lower in lowland populations. We suggest that elevation could potentially serve as a proxy for climate change vulnerability in dendritic freshwater systems, particularly for species with limited dispersal capacity. The signal of low genomic vulnerability for the Lower Lakes population was consistent both before and after ex situ captive breeding and reintroduction. This highlights the importance of downstream populations as sinks of diversity. It also shows that integrating genetic management into captive breeding programs can help maintain climatic adaptive potential in threatened populations.
The transverse lady beetle Coccinella transversoguttata Faldermann, 1835 is an ecologically important aphid predator and a declining native biocontrol agent in parts of its range. To provide a genomic resource for evolutionary, ecological, and applied research, we generated a chromosome-level genome assembly using PacBio HiFi long reads, Illumina whole-genome short reads, Hi-C chromatin conformation capture, and full-length transcriptome sequencing. The final assembly spans 376.3 Mb and comprises 58 scaffolds ≥1 kb, of which 363.4 Mb (96.6%) was anchored onto 10 chromosome-scale pseudomolecules. Assembly contiguity was high (contig N50 = 41.6 Mb; scaffold N50 = 41.6 Mb), and completeness was supported by 98.4% complete arthropod BUSCOs. Repetitive sequences constituted 58.2% of the genome, and 13,808 protein-coding genes were annotated with strong transcriptomic and homology-based support. Comparative analysis with a recently published conspecific genome revealed strong chromosome-scale collinearity but notable differences in total assembly size, repeat content, and local structural variation, suggesting either population-level genomic divergence or methodological differences in repeat resolution. Cross-species synteny with Coccinella septempunctata Linnaeus, 1758 further demonstrated substantial conservation of chromosome architecture across the genus. This resource provides a high-quality reference genome with broad utility for comparative genomics, predator ecology, biological control, and genome evolution studies in Coccinellidae.
The threespine stickleback represents a model system for studying parallel evolution, due to the repeated phenotypic adaptation of ancestral marine/anadromous populations to freshwater. Consequently, the genomic architecture underpinning these phenotypic traits has been extensively studied, and an increasing number of genomic resources are available. These include high quality chromosomal reference genome assemblies for Pacific marine and freshwater sticklebacks. However, these reference genomes may bias mapping of short-read data from Atlantic stickleback, and do not fully resolve some repeat-rich regions. Here, we present a chromosome-level reference genome (fGasAcu404) generated from an Atlantic anadromous stickleback using PacBio HiFi and Hi-C data. The assembly improves representation of repeat-rich regions, including on chromosome VII, where the Pitx1 locus and upstream PelA enhancer (Quantitative Trait Loci underpinning repeated loss of the pelvic girdle and spines) are located. Syntenic comparisons and mapping of short reads from well-studied spined and spineless stickleback indicate these loci are incorporated into the new assembly. We evaluate the utility of this reference for paleogenomic analyses by mapping ancient (>10,000 years BP) Norwegian stickleback DNA and assessing inversion karyotypes. We find marginal mapping gains and the ability to robustly infer homozygous ancestral karyotypes at three inversions in two ancient genomes which have predominantly marine-adaptive ancestry. However, karyotype is more ambiguous in an ancient genome with predominantly freshwater ancestry, reflecting the need for further genomic resources for this system. This new reference represents an important step towards the construction of a pangenome that better encompasses genetic variation among ancient and contemporary threespine stickleback populations across their range.
The spotted turtle (Clemmys guttata) is the sole extant member of the genus Clemmys and can be found in shallow wetlands across eastern North America. In recent decades, habitat alterations and poaching have reduced spotted turtle populations by more than 50% range-wide, resulting in federal protection in Canada and state-level protection within the United States. Here, we provide an annotated, chromosome-level assembly of C. guttata derived from long- and ultra-long read data as an addition to the conservation genomics resources for the species. The assembly comprises 2,286,936,868 base pairs, 98.5% of which are assembled in 25 contigs, consistent with published karyotypic data (n = 25) and including 16 gapless, telomere-to-telomere chromosome sequences. BUSCO scores indicate a highly complete assembly (99.4%). Annotation of the genome yielded 21,335 protein-coding genes with a BUSCO completeness score of 98.4%. Comparisons with a separate assembly derived from long-read and Hi-C data show that substituting ultra-long for Hi-C sequencing can improve telomere assembly and reduce structural errors in this taxon at the cost of reduced haplotype phasing, though primary assemblies are highly syntenic overall. PSMC analyses of both assemblies independently revealed a long, essentially identical history of population declines in spotted turtles. Coupled with range-wide genomic sampling, these resources will provide critical data to understand genetic structure, patterns of local adaptation, and demographic history in this species and help stem further declines.
The paired appendages of vertebrates are a pivotal developmental innovation, of which the pelvic fins of teleosts are evolutionarily homologous to the hind limbs of tetrapods. The small snakehead (Channa asiatica), an important freshwater fish with significant commercial value, lacks the pelvic fins while some other fish species in the same genus have. To determine the genetic changes underlying the pelvic fin loss in the small snakehead, we assembled the chromosome-level genome of the species based on PacBio HiFi and Hi-C sequencing technology and performed comparative genomics analyses. The final genome assembly of the small snakehead has a total length of 714.57 Mb with 23 chromosomes (contig N50 of 27.93 Mb and scaffold N50 of 28.54 Mb), and 193.09 Mb (27.02%) interspersed repeats and 22,300 protein-coding genes were annotated. Phylogenetic and divergence analyses indicated that the small snakehead was the sister branch to the combination of the northern snakehead (C. argus) and the blotched snakehead (C. maculata) and diverged from the common ancestor approximately 24.7 Mya. Three small snakehead-specific missense mutations were identified in tbx4 gene whose loss could cause the pelvic fin loss. Significant chromosomal rearrangement and 214 small snakehead-specific structural variations (SSSVs) were detected between the small snakehead and other Channa species. Among these SSSVs, the deletion in pax7a was likely to play a role in the pelvic fin loss. Furthermore, the specific loss of conserved non-coding regulatory elements (CNEs) related to limb/fin development was detected in the small snakehead, which possibly led to the pelvic fin loss of the small snakehead. The present study generated the high-quality chromosome-scale reference genome of the small snakehead, which provided a valuable genomic resource for the follow-up studies, and our findings shed light on the important genetic clues regarding pelvic fin loss in the species.
The speckled dace, Rhinichtyhs osculus, is a cyprinoid fish species complex (family: Leuciscidae) with one of the widest native ranges of any freshwater fish in western North America. It occupies a variety of freshwater habitats and exhibits considerable morphological and genetic variation across its range. Several endemic taxa within the species complex are imperiled, four of which are protected under the US Endangered Species Act, with two more proposed for listing. Here, we present an annotated, scaffold-level assembly of the speckled dace genome as part of the California Conservation Genomics Project (CCGP). Consistent with the CCGP genome assembly strategy, we used Pacific Biosciences HiFi long reads and Omni-C data for our de novo genome assembly and performed genome annotations on NCBI Eukaryotic Genome Annotation Pipeline using novel, species-specific RNA-Seq reads generated from five tissue types. The assembly consists of 490 scaffolds totaling approximately 1.15 Gb, with a contig N50 of 10.9 Mb and a scaffold N50 of 44.5 Mb. A BUSCO score of 97.7% reflects the assembly's strong completeness. The genome of Rhinichthys osculus is estimated to consist of 25 chromosomes. This is the first scaffold-level genome assembly within the genus Rhinichthys. We annotated a total of 39,919 genes with a BUSCO completeness score of 98.3%. This reference genome will be a valuable resource for understanding the phylogeography and evolution of speckled dace and informing its conservation.
The golden eagle (Aquila chrysaetos) is an apex predator across its Holarctic range. Although chromosome-level reference genome assemblies are available for two of the six golden eagle subspecies (European and Japanese), current assemblies for the North American subspecies (A. c. canadensis) were generated using short-read sequencing technology, limiting completeness, contiguity, and accuracy. Here we present a chromosome-length de novo genome assembly for a male A. c. canadensis as part of the California Conservation Genomics Project. We used Pacific Biosciences HiFi reads and Omni-C chromatin-proximity sequencing to produce a high-quality assembly consistent with the standard California Conservation Genomics Project reference genome protocol. Our assembly spans 1.28 Gbp and comprises 316 scaffolds with a scaffold N50 of 47.3 Mbp, a contig N50 of 30.3 Mbp, and a benchmarking universal single-copy ortholog completeness score of 97.4%. This reference genome assembly offers a valuable resource for delineating genomic variation and assessing conservation needs in golden eagle populations across California and its North American range more broadly.
We describe a chromosome-level genome assembly from an individual male plant of the cloudberry (Rubus chamaemorus). The haplotype-resolved assemblies contain 1 pseudo-haplotype spanning 1,198 megabases and 1 pseudo-haplotype spanning 1161 megabases. Most of these 2 assemblies, 93.57% and 96.55% respectively, are each scaffolded into 28 pseudo-chromosomes. Both assemblies show high completeness, with the same Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score of 99.2%. Most BUSCO genes are duplicated in both pseudo-haplotypes, in line with the polyploid nature of the cloudberry genome. The assemblies contain 74,132 and 70,692 predicted protein-coding genes, respectively. Analysis of repetitive sequences classified ~60% of each haplotype as repeats. Comparative synteny with red raspberry (Rubus idaeus) reveals a 4:1 chromosome correspondence, supporting an octoploid origin. Across k-mer composition, synonymous divergence, and genome-wide gene-tree analyses, 1 set of 7 chromosomes is consistently distinct (β), while the remaining 21 (3 × 7) chromosomes form an α set with no resolvable internal subdivision. These results are consistent with a complex polyploid origin of the cloudberry genome, involving a combination of allopolyploid and autopolyploid processes. Significance statement Cloudberry cultivation has lagged due to limited genomic resources and an unresolved polyploid history. We present a haplotype-resolved, chromosome-scale assembly that resolves 4 homologs per ancestral chromosome into 28 pseudo-chromosomes per haplotype and shows a 4:1 correspondence with red raspberry (Rubus idaeus). Genome-wide analyses support an octoploid architecture with 1 distinct 7-chromosome set (β) and a remaining α-set of 21 chromosomes with no resolvable internal subdivision. This reference provides a foundation for future work on polyploid origin, trait discovery, and breeding.
