Biology subjects

Skage, M.

Publications and source records attributed to Skage, M..

14 recordsLinked to original sources

bioRxiv2026

A chromosome-level assembly of an aquatic passerine bird, the northern white-throated dipper, Cinclus cinclus cinclus (Linnaeus, 1758)

We present a chromosome-level genome assembly of a female Norwegian white-throated dipper (Cinclus cinclus cinclus) generated using Oxford Nanopore Technologies (ONT) long reads and Hi-C scaffolding. The assembly comprises two pseudo-haplotypes, hap1 (1186 Mb) and hap2 (1115 Mb), with 96.7% and 94.4% of sequences assigned to chromosome-scale scaffolds, respectively. Both pseudo-haplotypes contain 40 autosomes, with the Z and W sex chromosomes assigned to hap1. Compared with the PacBio HiFi-based C. c. gularis reference assembly bCinCin1.1.pri, which contains 38 autosomes, sequence represented as a single dot-chromosome (chr 36) is resolved into three distinct dot-chromosomes (chr 36, 39, and 40), a configuration supported by Hi-C contact patterns. BUSCO completeness was high for hap1 (99.2%) and hap2 (95.0%), with 19,003 and 17,746 predicted protein-coding genes, respectively. Compared with the HiFi-based C. c. gularis reference and HiFi-based assemblies generated from the same individual, the ONT-derived assemblies were substantially less fragmented and recovered more sequence from the smallest chromosomes. Synteny was otherwise largely conserved between subspecies. HiFi depletion increased strongly from macrochromosomes to micro- and dot-chromosomes, and HiFi-depleted regions were enriched for repeats and predicted non-B-DNA-associated features, particularly G-quadruplexes and direct repeats, whereas ONT coverage remained comparatively stable. These results show that conventional genome-wide assembly metrics can obscure substantial differences in the recovery of repeat-rich avian dot-chromosomes and highlight the value of chromosome-aware evaluation and ONT sequencing for recovering these regions.

genomics↗

bioRxiv2026

A chromosome-level reference genome of the largest cervid species - the European moose (Alces alces; Linnaeus, 1758)

We describe a chromosome-level, haplotype-resolved genome assembly from a male European moose (Alces alces alces). The assembly comprises two pseudo-haplotypes of 3,148 Mb and 3,112 Mb, with sex chromosomes in haplotype one, and 33 autosomes in each haplotype (68 in total). Assembly completeness is high (BUSCO 98.3% and 95.7%), with 21,496 and 20,498 annotated protein-coding genes for haplotypes one and two, respectively. This genome assembly is the most complete so far generated for European moose.

genomics↗

bioRxiv2026

A chromosome-level genome assembly of the Eurasian great grey owl, Strix nebulosa lapponica (Thunberg 1798)

We present a chromosome-level genome assembly of a female great grey owl (Strix nebulosa lapponica). The assembly comprises two pseudo-haplotypes of 1554 Mb and 1242 Mb, with 83.2% and 91.4% scaffolded into 40 autosomal chromosomes, in addition to the W and Z sex chromosomes both placed in hap1. Assembly completeness is high (BUSCO 99.2% and 94.8%), with 18,493 and 17,279 annotated protein-coding genes for hap1 and hap2, respectively. This genome establishes a reference for investigating genetic variation and chromosome evolution in great grey owls. Compared with the previous S. nebulosa assembly, this assembly includes both sex chromosomes, separates regions that were previously collapsed, and resolves 82 chromosomes total. While larger chromosomes show broadly conserved synteny across owl assemblies, the recovery of additional conserved microchromosome-associated genes suggests that ONT reads improved resolution of the smallest chromosomes relative to HiFi-based assemblies.

genomics↗

bioRxiv2026

A chromosome-level genome assembly of a "living fossil", the tadpole shrimp Lepidurus arcticus (Pallas, 1793)

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 (estimated to 0.11 Gb) and reproductive flexibility makes this a very interesting candidate for genomic studies. The haplotype-resolved assemblies are composed of two pseudo-haplotypes spanning 81.2 megabases (Mb) and 81.8 Mb, respectively, and each scaffolded into 6 chromosomes. Both haplotypes (hap) show high completeness and identical BUSCO scores of 98.3 for hap1 and hap2. The scaffold N50 length is 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 haplotypes display very low estimated genome-wide heterozygosity of 0.133%. The assembly contains 10901 (hap1) and 10910 (hap2) protein-coding genes. Repetitive elements comprised approximately 24-25% of each haplotype, 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.

genomics↗

bioRxiv2026

A haplotype-resolved bluethroat (Luscinia s. svecica) genome assembly uncovers the complex MHC region

We describe a chromosome-level, haplotype-resolved genome assembly from a female bluethroat (Luscinia s. svecica). The assembly comprises two pseudo-haplotypes of 1461 Mb and 1171 Mb, with 77.4% and 88.4% scaffolded into 40 autosomal chromosomes and the W and Z sex chromosomes (haplotype one). Assembly completeness is high (BUSCO 99.2% and 94.9%), with 22,462 and 18,769 annotated protein-coding genes for haplotypes one and two, respectively. The use of Oxford Nanopore Technologies sequencing enables resolution of genomic regions that are often fragmented in genome assemblies, including the hypervariable Major Histocompatibility Complex (MHC). We find that MHC loci include both the canonical organization of tandemly duplicated MHCII{beta} genes with a single MHCIIA, and a distinct arrangement in which MHCI and MHCII{beta} loci are interspersed in intermixed arrays, and that substantial structural differences between haplotypes are directly resolved in the assembly.

genomics↗

bioRxiv2025

Chromosomal fusions shaped the genome of the greater hornwrack bryozoan (Flustra foliacea) (Linnaeus, 1758)

The phylum Bryozoa is an understudied, yet commonly-occurring, globally distributed bilaterian metazoan organismal group. They have a colonial lifestyle and an evolutionary history that spans at least 480 million years but likely longer. Despite their contentious phylogenetic affinities among metazoans, disproportionately little genomic investigations have been performed thus far. Here, we describe the first chromosome-level genome assembly of an individual Flustra foliacea colony belonging to the order Cheilostomatida, collected in southern Norway. The haplotype-resolved assembly of F. foliacea contains two pseudo-haplotypes spanning 956 megabases and 880 megabases, respectively. Both assemblies are highly complete both in terms of scaffolding (>90% of sequences placed in 8 autosomal chromosomal pseudomolecules), and gene content (BUSCO completeness scores >90%). We also present gene and repeat annotations of the two assemblies. A comparison of our newly sequenced F. foliacea with five previously published bryozoan genomes supports the hypothesis that the group has undergone extensive genome rearrangements. This includes multiple chromosomal fusions in F. foliacea since their split with other cheilostome bryozoans. These fusions were enriched with long terminal repeat (LTR) retrotransposons, highlighting the complex interplay between genome organization and genomic repeats. Our study contributes to a deeper understanding of bryozoan genome evolution and the role of repeats in metazoan genome organization.

genomics↗

bioRxiv2025

The genome of the Glacier lanternfish shows loss of MHC I and II function and provides insight into evolution of lanternfish immune systems

Lanternfishes (Myctophidae) are one of the most abundant and species diverse orders inhabiting the mesopelagic zone. Exploitation of marine resources has recently attracted increased interest. It is therefore essential to improve our understanding of the meso- and deep pelagic ecosystems with respect to conservation and management strategies. Genomic resources are paramount to enable in-depth studies of population structuring and understanding the inherent genetic diversity, but also to enable studies of processes such as local adaptation and selection. Here we present a genome assembly of the Glacier lanternfish (Benthosema glaciale) generated with long-read PacBio and Hi-C contact map data. By comparing additional available genomes from the Myctophiformes order we explore their adaptive immune strategies. Our findings reveal that multiple lineages within this order have lost a significant proportion of genes related to adaptive immunity (Electrona, Protomyctophum and Benthosema). We find simultaneous loss of both classical MHC class I and class II function coinciding with reduction in genetic diversity with respect to immunoglobulin and T-cell receptors. In contrast, the sister branch represented by Gymnoscopelus and Nannobrachium appear to have maintained the standard configuration of the jawed vertebrate adaptive immune system apart from large gene expansions in MHC class II. Our results demonstrate that the Benthosema-belonging lineage (Myctophinae) has completely lost the core functions of the adaptive immune system. How, when and why this occurred warrants further investigations.

genomics↗

bioRxiv2025

Haplotype-resolved chromosome-level genome assemblies of four Diamesa species reveal the genetic basis of cold tolerance and high-altitude adaptations in arctic chironomids

Arctic and alpine insects face extreme environmental stressors, yet the genomic basis of their adaptation remains poorly understood. Here, we present the first haplotype-resolved, chromosome-level genomes for four species of Diamesa (Diptera: Chironomidae), a genus of cold-adapted midges inhabiting glacial and high-altitude freshwater ecosystems. Using PacBio HiFi sequencing and Hi-C scaffolding, we assembled high-quality genomes with chromosome-level resolution and high k-mer completeness. Phylogenomic analyses support Diamesinae as sister to other Chironomidae except Podonominae, and genomic comparisons provide evidence for introgression between the evolutionary distinct D. hyperborea and D. tonsa. Comparative genomic analyses across 20 Diptera species revealed significant gene family contractions in Diamesa associated with oxygen transport and metabolism, suggesting adaptations to high-altitude, low-oxygen environments. Conversely, expansions were detected in histone-related and Toll-like receptor gene families, likely enhancing chromatin remodeling and immune regulation under cold stress. A single gene family encoding glucose dehydrogenase was significantly expanded across all cold-adapted species studied, implicating its role in cryoprotectant synthesis and oxidative stress mitigation. Notably, Diamesa species exhibit the largest gene family contraction at any node, with minimal overlap in expansions with other cold-adapted Diptera, indicating lineage-specific adaptation. Our findings support the hypothesis that genome size condensation and selective gene family changes underpin survival in cold environments. These genome assemblies represent a valuable resource for investigating adaptation, speciation, and conservation in cold-specialist insects. Future work integrating gene expression and population genomics will further illuminate the evolutionary resilience of Diamesa in a warming world.

genomics↗

bioRxiv2025

Chromosome-level assembly of the octoploid cloudberry(Rubus chamaemorus)

We describe a chromosome-level genome assembly from an individual male plant of the cloudberry (Rubus chamaemorus). The haplotype-resolved assemblies contain one pseudo-haplotype spanning 1198 megabases and one pseudo-haplotype spanning 1161 megabases. Most of these two assemblies, 93.57% and 96.55% respectively, are each scaffolded into 28 pseudo-chromosomes. Both assemblies show high completeness, with the same 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. Ks distributions and k-mer clustering indicate a fairly recent polyploidization involving one divergent ({beta}) and three closely related () subgenomes. Low coverage targeted sequencing data mapped to our assembly link the {beta}-subgenome to a relative of R. pedatus or R. lasiococcus, while the -subgenomes might derive from a putative auto-allohexaploid within the main Rubus clade. In conclusion, these results indicate that the cloudberry genome arose through multiple hybridization events, including recurrent allopolyploidy and possibly autopolyploidy. Significance statementCloudberry cultivation has lagged due to unclear origin and genome structure. We present a haplotype-resolved, chromosome-scale assembly that resolves four homologs per ancestral chromosome into 28 pseudo-chromosomes per haplotype and shows a 4:1 correspondence with red raspberry (Rubus idaeus). Genomic analyses indicate a recent polyploidization in which three closely related subgenomes likely derive from a putative hexaploid within the main Rubus clade, associated with R. arcticus (Arctic raspberry), whereas the fourth, more divergent subgenome is linked to relatives of R. pedatus (strawberryleaf raspberry) and R. lasiococcus (dwarf bramble). These results clarify cloudberrys formation and provide a foundation for trait discovery and accelerated breeding.

genomics↗

bioRxiv2025

Chromosome-level genome assembly of Norwegian wild alpine reindeer (Rangifer tarandus tarandus)

We describe a chromosome-level genome assembly from a wild alpine reindeer individual (Rangifer tarandus tarandus) from the Rondane area in Southern Norway. The assembly is resolved into two pseudo-haplotypes: hap 1 spanning 3,081 megabases and hap 2 spanning 2,633 megabases. Contig N50 and scaffold N50 lengths are in the range of 31-41 Mb and 66-69 Mb, respectively. A large part of these two haplotypes (83.8% and 90.4%, respectively) are scaffolded into 34 autosomal chromosomal pseudomolecules, and in sex chromosomes X and Y for hap 1. The BUSCO completeness scores are 98.0% and 95.2%, respectively, and gene annotations of the assemblies identified 37,998 and 36,977 protein-coding genes. We also present an updated and improved genome assembly for Svalbard reindeer (Rangifer tarandus platyrhynchus) and a comparison with previously published genome assemblies of reindeer.

genomics↗

bioRxiv2024

Comparison of whole-genome assemblies of European river lamprey (Lampetra fluviatilis) and brook lamprey (Lampetra planeri)

We present haplotype-resolved whole-genome assemblies from one individual European river lamprey (Lampetra fluviatilis) and one individual brook lamprey (Lampetra planeri), usually regarded as sister species. The genome assembly of L. fluviatilis consists of pseudo-haplotype one, spanning 1073 Mb and pseudo-haplotype two, spanning 963 Mb. Likewise for the L. planeri specimen, the genome assembly spans 1049 Mb and 960 Mb for pseudo-haplotypes one and two, respectively. Both the L. fluviatilis pseudo-haplotypes have been scaffolded into 82 pseudo-chromosomes, with the same number for the L. planeri pseudo-haplotypes. All four pseudo-haplotype assemblies were annotated, identifying 21,479 and 16,973 genes in pseudo-haplotypes one and two for L. fluviatilis, and 24,961 and 21,668 genes in pseudo-haplotypes one and two for L. planeri. A comparison of the genomes of L. fluviatilis and L. planeri, alongside a separate chromosome level assembly of L. fluviatilis from the UK, indicates that they form a species complex, potentially representing distinct ecotypes. This is further supported by phylogenetic analyses of the three reference Lampetra genomes in addition to sea lamprey (Petromyzon marinus).

genomics↗

bioRxiv2024

Evolutionary new centromeres in the snowy owl genome putatively seeded from a transposable element

Comparative genomic studies in birds have revealed that bird genomes are relatively repeat-poor and stable in terms of karyotype, size, and gene synteny/collinearity compared to other vertebrates. One notable exception is the owls, with cytogenetic studies demonstrating large variations in karyotypes and the evolution of unusual centromeric satellite repeats in some species. However, there has so far not been an investigation into genome architecture and repeat landscape of owls. Here, we present a chromosome-level genome assembly for the snowy owl (Bubo scandiacus). We find that the repeat DNA content in the relatively large snowy owl genome (1.6 Gb) is among the highest reported for any bird genome to date (28.34% compared to an average of [~]10% in other birds). The bulk of the snowy owl genomic repeat landscape consists of centromeric satellite DNA, which appears to have originated from an endogenous retrovirus (ERV1). Using gene collinearity analyses we show that the position of these evolutionary new centromeres (ECNs) are not homologous with chicken centromeres, and are located in regions with collinearity breaks to other bird genomes due to chromosomal rearrangements. Our results support rapid transposable element-driven evolution of lineage-specific centromeres, which could have played a role in reproductive isolation and speciation of the snowy owl.

genomics↗

bioRxiv2023

A fast and inexpensive plate-based NGS library preparation method for insect genomics

Entomological sampling and storage conditions often prioritise efficiency, practicality and conservation of morphological characteristics, and may therefore be suboptimal for DNA preservation. This practice can impact downstream molecular applications, such as the generation of high-throughput genomic libraries, which often requires substantial DNA input amounts. Here, we investigate a fast and economical Tn5 transposase tagmentation-based library preparation method optimised for 96-well plates and low yield DNA extracts from insect legs stored under different conditions. Using a standardised input of 6ng DNA, library preparation costs were significantly reduced through the 6-fold dilution of a commercially available tagmentation enzyme. Costs were further suppressed by direct post-amplification pooling, skipping quality assessment of individual libraries. We find that reduced DNA yields associated with ethanol-based storage do not impede overall sequencing success. Furthermore, we find that the efficiency of tagmentation-based library preparation can be improved by thorough post-amplification bead clean-up which selects against both short and large DNA fragments. By lowering data generation costs, broadening the scope of whole genome studies to include low yield DNA extracts and increasing throughput, we expect this protocol to be of significant value for a range of applications in the field of insect genomics.

genomics↗

bioRxiv2018

Long-read sequence capture elucidates the evolution of the hemoglobin gene clusters in codfishes

Combining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. These approaches are not designed to capture intergenic regions needed to reconstruct genomic organization, including regulatory regions and gene synteny. Here, we demonstrate the power of combining targeted sequence capture with long-read sequencing technology for comparative genomic analyses of the hemoglobin (Hb) gene clusters across eight species separated by up to 70 million years. Guided by the reference genome assembly of the Atlantic cod (Gadus morhua) together with genome information from draft assemblies of selected codfishes, we designed probes covering the two Hb gene clusters. Use of custom-made barcodes combined with PacBio RSII sequencing led to highly continuous assemblies of the LA (~100kb) and MN (~200kb) clusters, which include syntenic regions of coding and intergenic sequences. Our results revealed an overall conserved genetic organization and synteny of the Hb genes within this lineage, yet with several, lineage-specific gene duplications. Moreover, for some of the species examined, we identified amino acid substitutions at two sites in the Hbb1 gene as well as length polymorphisms in its regulatory region, which has previously been linked to temperature adaptation in Atlantic cod populations. This study highlights the use of targeted long-read capture as a versatile approach for comparative genomic studies by generation of a cross-species genomic resource elucidating the evolutionary history of the Hb gene family across the highly divergent group of codfishes.

genomics↗