Genome Biology and Evolution

BackgroundNotothenioids are a well characterised species flock endemic to the Antarctic and an important model group for the study of genome adaptation to extreme cold. We used a new reference assembly and clade-wide comparative genomic analysis to investigate cryonotothenioid evolution and the appearance of novel functionalities linked to cold adaptation. ResultsA new phased assembly of a model notothenioid, Harpagifer antarcticus, demonstrated low levels of haplotypic variability across the genome. Nevertheless, numerous insertions from multiple LINE-L2 clades were found, suggesting ongoing transposition with potential contribution to speciation. Contrary to expectations the afgp locus was highly similar between haplotypes, except for large length allelic variants of afgp genes. Analysis suggests a model for the afgp locus expansion in H. antarcticus through segmental tandem duplications involving two pairs of afgp genes at time. Syntenic reconstruction of genomes from across the clade demonstrates conserved macrosyntenic relationships and group specific chromosomal fusions of notothenioids. Quantification of genome gain and transposition rates during cryonotothenioid diversification showed a first ancestral slow genome expansion concurrent with historic temperature drops. This was followed by lineage-specific massive peaks of genomic gain and transposition activity. Finally, we identified a set of genes that underwent ancestral diversifying selection and acquired novel conserved non-coding elements during the cryonotothenioid emergence. These were related to antioxidants and proteostasis, which may have facilitated the notothenioid Antarctic radiation. ConclusionDiversifying selection and genomic gain linked to transposon activity are primary contributors to lineage-specific evolutionary dynamics through the clade which facilitated adaptation to life in the cold.

Genomic repeats, particularly simple sequence repeats, influence genome stability and gene regulation. While many genomic traits exhibit phylogenetic signal and pulsed evolution, repeat elements have rarely been examined in a comparative framework, and their evolutionary relationships with other genome features remain poorly understood. We contrasted the trait evolution of genomic repeats with non-repeat traits across diverse actinobacterial orders, testing for phylogenetic signal, evolutionary mode, and pulsed dynamics using time-calibrated, 16S rRNA, and whole-genome sequence (WGS) trees. Non-repeat traits consistently exhibited signs of punctuated evolution, with larger pulses in species-rich orders such as Mycobacteriales and Actinomycetales; repeats, by contrast, were evolutionarily labile, lacking phylogenetic signal and largely decoupled from other genomic traits. Bifidobacteriales was the sole exception, with repeats exhibiting phylogenetic signal only under the WGS tree. The WGS tree also recovered a stronger signal for genome-level traits, highlighting its utility in comparative analyses. Genome size evolution in Actinomycetota appears driven primarily by protein-coding gene expansion rather than repeat accumulation.

The haplochromine cichlid fishes of Lake Malawi form one of the most dramatic examples of recent rapid radiation in vertebrates. Here we describe nine new diploid telomere-to-telomere (T2T) genome sequences generated using ultra-long ONT reads, which include 78 ungapped chromosomes. We provide accurate annotations of transposable elements and tandem repeats, identify rDNA cluster regions and putative centromeres, and confirm previously reported large chromosomal inversions. The putative centromeres are primarily composed of satellite tandem arrays of previously reported 237 bp repeats, but notably on most chromosomes these are organised in a novel structure in which four blocks of satellites in alternating orientation are separated by an inverted pair of ~15 kb sequences we term 'centroids', which have similarity to a non-autonomous DNA transposable element and containing potential CENP-B binding boxes. The methylation dip region indicating the likely active centromere always lies between the centroids, whose separation is almost always around 200 kb (interquartile range 151-221kb). A structurally equivalent but non-homologous organisation is seen in the distantly related Etroplus cichlid genera from South Asia. By comparing these structures across chromosomes and species, we suggest how they may have evolved, and potentially how they could contribute to the rampant sympatric speciation seen in these species, based on meiotic drive and chromosome missegregation.

Ciliates are a diverse group of single-celled eukaryotes that can exhibit a wide range of genetic diversity within morphologically indistinguishable species. However, they are still not well studied as their mechanisms of speciation and the extent of diversification remain unknown. Mitochondrial genomes offer an effective framework for resolving species relationships and evolutionary changes. Here, we analyzed a globally sampled dataset of Paramecium to understand the evolution of mitochondrial genomes in ciliates. Phylogenetic analysis of linear mitochondrial genomes shows the presence of cryptic diversity beyond the P. aurelia complex, with P. bursaria lineage appearing as a deeply diverging out-group. Protein-coding genes are largely conserved, with limited rearrangements, and some ciliate-specific genes appear to be missing in P. bursaria. Population genetic analysis show little to no evidence of recombination along with substantial differences in effective population size across species. Patterns of molecular evolution also indicate purifying selection as the predominant force, the strength of which is at least as strong as in the nucleus and consistent with mitochondrial effective population sizes that are similar or larger than those of the nucleus. Across the functional groups, the electron transport chain and ribosomal genes are highly constrained, while ciliate-specific ymf genes show reduced efficacy of selection compared to the others. These findings offer a basis for connecting mitochondrial variation to evolutionary divergence, functional constraint, and speciation in microbial eukaryotes.

Population size is a key factor underlying the mode and tempo of evolution, particularly as it relates to the strength of selection and drift. While the mechanisms underlying the interactions between population size and selection have been studied in population genetics for over a century, empirical knowledge of these dynamics has been limited to species with small-to-moderate historical population sizes. This gap in knowledge highlights the need for empirical studies in systems with historically large population sizes and elevated diversity. The Pacific acorn barnacle (Balanus glandula) presents an exceptional model to study evolution in extremely large populations, exhibiting census sizes often exceeding the tens of thousands of individuals per meter squared. We present one of the first large-scale genomic analyses in this system, generating a new chromosome-level genome assembly for this species. This assembly reveals a highly polymorphic genome with over 3% heterozygosity. At a population level, B. glandula exhibits extreme levels of polymorphism, with nucleotide diversity surpassing 5% genome-wide in just a small collection of individuals. Across the genome, nucleotide diversity predictably decreases at functional elements, including both coding and non-coding sequences, likely reflecting strong purifying selection along the genome. At the same time, McDonald-Kreitman tests reveal that the majority of non-synonymous substitutions between barnacle species were driven by positive selection, consistent with the expected increase in the efficacy of selection in large populations. These remarkable levels of diversity set B. glandula as a unique model for the study of evolution at extreme demographic scales and highlights the importance of testing evolutionary theory across a wide variety of empirical systems.

The phylogenetic position of Nanohaloarchaea has been debated, these nanosized archaea being alternatively proposed as sister group to Haloarchaea, members of the DPANN-Archaea, or sister group to Methanocellales. Screening a set of universal proteins, we identified four insertions located at critical locations in three ribosomal proteins and one RNA polymerase subunit that support the branching of Nanohaloarchaea as sister group to Aenigmarchaea within DPANN cluster II (sensu Dombrowski et al., 2020). Insertion analyses and phylogeny of the monomeric primase specific to DPANN-Archaea confirm the existence of a robust clade grouping Undinarchaea, Naiadarchaea and DPANN cluster II, that we propose to call Nanostetteria. Our insertion analysis also supports including Altiarchaea within DPANN-Archaea and suggest a new clades that has not been recovered in phylogenetic analyses, one grouping DPANN-Archaea with Stygia (Hadarchaea and relative) and an even large one grouping these lineages with Acherontia (Thermococci and relatives). The insertion defining this larger clade, present in the ribosomal protein uS7, is also present at the same position in Thaumarchaea, Korarchaea and a subgroup of Asgardarchaea. Whereas the insertion in Thaumarchaea is certainly due to an independent event, we discuss alternative hypotheses that can explain those present in Korarchaea and Asgardarchaea. Finally, we noticed several cases of MAGs misannotations, indicating that insertion analysis can be useful to identify protein with misleading affiliations. The existence of insertions in otherwise highly conserved universal proteins involved in translation or transcription could partly explain the high rate of protein evolution in some archaeal lineage, especially in DPANN-Archaea.

Microbial eukaryotes often exhibit large effective population sizes and broad dispersal, yet the extent of population structure and the forces shaping it remain poorly understood. While biogeographic structure is often attributed to limits on dispersal, the role of natural selection in maintaining differentiation has received less attention. We investigated population structure and adaptive evolution in the cosmopolitan soil alga Chlamydomonas reinhardtii. In addition to the 35 available North American genome sequences we have sequenced 38 new isolates from Ontario (Canada). Population genetic structure analyses demonstrate that these new isolates from Ontario represent a second well-sampled genetically distinct cluster, and that this structure persists despite the presence of recent migrants. Using this data set we were able to conduct genome-wide scans for selective sweeps across the species and within each population. Our results conservatively identify 151 species-wide sweeps and 325 population-specific signals, showing that positive selection is widespread and common. The continued presence of the two distinct genetic clusters as well as loci under differential selection, provide evidence that local adaptation persists despite ongoing gene flow. Together, our results demonstrate that selection plays a central role in reinforcing geographic structure in this highly dispersive microbe.

Ciliates are one of the most ecologically diverse and morphologically intricate unicellular organisms. Despite their evolutionary significance and their prominence in cell-biological research, the population-genetic processes governing their diversification have received remarkably little attention. A fundamental unresolved problem is the existence of geographic isolation among free-living protists and its consequences for species richness. We addressed this issue in the model ciliate Paramecium by sequencing genomes of hundreds of isolates collected worldwide, capturing multiple morphological and cryptic species, with multiple populations each. Contrary to previous reports, we found evidence of geographic differentiation in the majority of species. In a few cases, geographic structure became evident when deeply diverging clades in a species were treated separately. This suggests that the biogeographical patterns of Paramecium have been shaped by periods of genetic isolation leading to speciation, with rare events of global dispersal realized over its long evolutionary history. Despite being largely isolated, populations were remarkably similar in their effective population size, recombination rate, and efficacy of natural selection. Across species, selection appears to be least effective in Paramecium aurelia lineages, and most effective in P. bursaria, presumably due to differences in their breeding characteristics. Despite differences among species in the population-genetic environment, patterns of variation across the genome remained consistent. Selective constraints on a core set of genes seemed to have gradually diverged across the species phylogeny. Genes with multiple copies retained from whole-genome duplication events in P. aurelia were found to be under relatively relaxed purifying selection. Moving forward, this dataset will serve to test hypotheses on the ecological and cellular complexity of Paramecium and beyond.

BackgroundThe black soldier fly (Hermetia illucens) is an emerging model for bioconversion and industrial rearing. Its genome is highly repetitive, yet the contribution of transposable elements (TEs) to population divergence and demographic processes. The sampled populations represent a gradient of demographic histories, including wild and near-wild North American populations, and domesticated European strains with shared industrial origins. Difference in TE composition may influence genome structure, regulatory variation, and evolutionary responses to captive environments. ResultsA comparative analysis of the repetitive landscape was done for four H. illucens genomes, one of which is a wild-caught specimen. Total repeat content was high across all assemblies (67.6% to 70.8%) and dominated by LINE elements. Class-level TE diversity was nearly identical among genomes, but multiple DNA transposon families showed distinct lineage-specific differences. Large families including Maverick and Academ were generally depleted relative to the wild sample. Divergence profiles revealed patterns consistent with recent turnover in several families. Family level turnover, rather than class level change, accounted for the most difference among the genomes. TE-associated structural variants (TESVs) were also not uniformly distributed. Most chromosomes showed mid-chromosome enrichment, and a pronounced TESV peak on chromosome 5 overlapped a histone rich region containing many unclassified repeats. Use of a repeat library derived from multiple genomes increased the number of detected TESVs and improved classification within complex regions, demonstrating that multi-genome libraries enhance annotation accuracy compared to single reference-based models. ConclusionsMultiple DNA transposon families show evidence of recent or lineage-specific amplification in H. illucens, suggesting that TE amplification contributes to genome variation during demography-associated TE turnover. The multi-genome-based library improved TE detection and classification, providing a proof of concept that even a small lineage-inclusive repeat library enhances annotation accuracy and capture TE diversity missed by single-reference approaches. Together, these findings demonstrate that TE family turnover plays a significant role in shaping genome architecture and adaptation in this species.

Transposable elements (TE) jump from one genomic locus to another. Since increase in their copy number is a metabolic burden for the host, TE are considered as genomic parasites. Although host-TE co-existence is regarded as an evolutionary arms race, the hypothesis is not extensively tested especially using evolutionary genomics. We provide a hypothesis testing framework to understand the distribution of TE in genic regions of the host genome, variation in the regulation of TE by host, and effect of these two factors on host-TE co-evolutionary dynamics. We test our hypothesis by understanding the distributions of potentially active TEs in the genome of 78 teleost fishes, representing major families and orders within the clade. Our analysis reveals coevolutionary arms race predicted by the Red Queen dynamics.

Most cyanobacterial genomes are rich in the GCGATCGC octamer, also known as Highly Iterated Palindrome 1 (HIP1). Despite its description over three decades ago, the biological function of this highly abundant sequence is only beginning to be elucidated. HIP1 is recognized by two DNA methylases, DmtA and DmtC, and is characterized by its evolutionary conservation and a quasi-periodic distribution within genomes. However, whether the phylogenetic distribution of HIP1 correlates with the presence of functional categories of protein families remains unknown. Here we investigated whether certain protein families share a phylogenetic distribution with this abundant palindromic sequence across cyanobacterial genomes. Our analysis revealed a strong phylogenetic correlation between several proteins of the Type IV secretion system (T4SS) and the abundance of HIP1. This finding aligns with recent discoveries demonstrating that HIP1 enhances DNA transformation in a methylation-dependent manner in two distinct cyanobacterial species. Consequently, we hypothesize that HIP1 function as a conserved adaptation for horizontal gene transfer (HGT) at the phylum level, potentially by serving as a DNA-uptake recognition sequence in cyanobacteria. Significance statementScientists have long been baffled by the HIP1 sequence, a short, highly common, repetitive DNA pattern found across almost all cyanobacterial genomes. Our study used a whole-genome evolutionary approach and found that the presence of this repetitive pattern is tightly linked to the presence of a cells external DNA uptake system. This tight co-evolutionary relationship suggests that HIP1 isnt just random genomic feature, but a conserved evolutionary adaptation used by the entire cyanobacterial phylum to specifically enhance their ability to acquire new genes from one another.

Population genetic theory predicts that a species demographic history shapes patterns of genome-wide variation. However, conservation genomic studies have disproportionately focused on small or declining species, where low genetic diversity and inbreeding are major concerns, while highly abundant species have attracted comparatively less attention. Here, we investigate the crabeater seal (Lobodon carcinophaga) which, despite being one of the most numerous large mammals on Earth, remains largely uncharacterised in terms of its genomic diversity and demographic history. We assembled a high-quality crabeater seal reference genome from a combination of Illumina and PacBio HiFi reads, generating a 2.44 Gb assembly spanning 138 scaffolds with high completeness. To evaluate genomic diversity in a comparative context, we whole-genome resequenced 20 crabeater seals alongside 20 individuals each of three Antarctic phocids spanning a population size gradient: the Weddell seal (Leptopnychotes weddellii), leopard seal (Hydrurga leptonyx) and southern elephant seal (Mirounga leonina). Crabeater seals carried 61.5 million SNPs compared to 1216 million in the other species and exhibited markedly higher nucleotide diversity and negligible genomic inbreeding. We observed an excess of rare alleles, with nearly half of all variants segregating at frequencies below 5%. Demographic reconstruction revealed persistently large effective population sizes over the past million years and sustained population expansion, paralleling inferred increases in Antarctic krill associated with sea-ice expansion during the late Pleistocene. This study provides a new genomic resource and sheds new light on the evolutionary dynamics of the worlds most abundant pinniped.

Laboratory cultivation subjects model organisms to selective pressure and genetic drift that can result in the accumulation of many genomic and phenotypic differences over time. The nematode Caenorhabditis elegans has been used for research since the 1970s, and studies comparing the N2 Bristol and CB4856 Hawaiian isolates provided foundational knowledge about metazoan genome evolution. Most comparative genomics studies have used these isolates because their long-term geographical isolation promoted a high degree of genomic divergence within the species. Further, there is growing evidence of phenotypic differences between laboratory lineages of each wild type isolate after repeated independent lab cultivation of these strains. To examine the genomic divergence between different laboratory lineages the Bristol and Hawaiian backgrounds, we first generated de novo genome assemblies of two Bristol and two Hawaiian lineages from Illumina and PacBio sequencing reads. Following genome assembly, we quantified Single Nucleotide Polymorphisms (SNPs), short insertion/deletions (indels), and genomic structural variants (SVs). Between laboratory lineages of the Bristol isolate, we identified 25,432 SNPs, 5,202 indels, and 441 SVs. When aligning laboratory lineages of the Hawaiian isolate, we identified 4,518 SNPs, 1,188 indels, and 387 SVs. For both sets of comparisons, we find that SNPs and indels are broadly enriched in introns and depleted from coding sequences. In contrast to SNPs and indels, we find that genomic SVs are enriched in intergenic sequences. Taken together, our analyses reveal the accumulation of genomic divergence between lineages of Bristol and Hawaiian C. elegans from independent lab cultivation, and how these variants may underpin emergent phenotypic differences observed in the two most popularly used C. elegans wild type isolates. Author SummaryLaboratory model organisms, like natural populations, are subject to evolutionary pressures and genomic changes during prolonged laboratory cultivation. In this study we comprehensively quantify SNPs, indels, and SVs between independent lab cultivations of the C. elegans lineages of the Bristol and Hawaiian isolates.

The coffee bean weevil, Araecerus fasciculatus (Coleoptera, Curculionoidea, Anthribidae), is a cosmopolitan pest of over 100 stored agricultural commodities, with particular economic impact on coffee (Coffea arabica). Although two chromosome-level anthribid genomes have recently been released as part of the Darwin Tree of Life (DToL) project (Booth et al. 2024; Crowley et al. 2025), no functionally annotated genome has been available for the family. Here we present a draft genome assembly for A. fasciculatus, generated from PacBio HiFi long reads and processed through a three tiered metagenomic filtering pipeline to remove host plant (C. arabica) and microbial contamination. The final assembly spans 475 Mb across 3,617 scaffolds (N50 = 170 kb) with 88.5% BUSCO completeness (insecta_odb10) and only 3.1% duplication. Gene prediction with BRAKER2 identified 22,384 protein-coding genes, of which 11,783 received functional annotations through SwissProt similarity. Notably, we identified 92 cytochrome P450 (CYP) genes, including tandem gene clusters on two scaffolds (4 genes on ptg000464l, 5 genes on ptg001867l), suggestive of lineage-specific expansion through tandem duplication. Homology searches against Drosophila melanogaster caffeine-metabolizing P450s (CYP12D1, CYP6d5, CYP6a8) recovered strong matches (e-values 9.7 x 10-110 to 5.4 x 10-101, 33-38% identity). In stark contrast, comprehensive BLAST searches for bacterial caffeine N-demethylase genes (ndmA/B/C/D), which mediate caffeine degradation via horizontal gene transfer in the coffee berry borer Hypothenemus hampei (Scolytinae), returned zero hits across the A. fasciculatus genome, predicted proteome, and associated bacterial scaffolds. AlphaFold2 structure prediction of four top Araecerus P450 candidates produced high-confidence models (pLDDT 84.5-93.9, pTM 0.735-0.930) with conserved P450 catalytic motifs. Foldseek structural homology searches confirmed that all four candidates adopt cytochrome P450 folds (top hits: human CYP3A4, CYP3A7, CYP11A1; TM-scores 0.90-0.92; probability 1.000), with zero hits to bacterial Rieske-fold enzymes. Molecular docking of caffeine against these structures yielded binding affinities of -5.41 to -5.80 kcal/mol for the Araecerus candidates, comparable to or exceeding the -5.55 kcal/mol obtained for the experimentally validated Drosophila CYP6a8 and substantially stronger than the -3.70 kcal/mol for the bacterial NdmA structural outgroup (PDB: 6ICP). Phylogenetic analysis revealed that all four candidates have clear orthologs in two non-seed-feeding DToL anthribids (Pseudeuparius sepicola and Platystomos albinus), demonstrating that these P450 genes predate the dietary transition to caffeine-containing seeds. The Araecerus candidates predominantly belong to the CYP6 family (clan 3), whereas the primary Drosophila caffeine P450 CYP12D1 belongs to the mitochondrial clan, confirming convergent recruitment of different P450 subfamilies for caffeine metabolism. These results support the hypothesis that A. fasciculatus employs an insect-encoded, P450-mediated caffeine detoxification pathway fundamentally distinct from the bacterial horizontal gene transfer mechanism documented in Scolytinae. This represents convergent evolution of caffeine resistance via independent molecular strategies within Curculionoidea, and provides the first functionally annotated genomic resource for comparative studies across the Anthribidae.

Recent studies have characterised the mutational profile across multiple mammalian species, highlighting substantial differences across lineages. However, none of these studies investigated whether mutation profiles and geography are significantly correlated. In this study, we present a multi-genome alignment spanning several Capra taxa, reconstruct the ancestral genome of Capra hircus and use it to characterize the mutational profiles across multiple Capra species by using the 1000 genomes VarGoats dataset. Results confirmed that the scale of differences among Capra species largely reflects their phylogenetic relationships, in particular with the Bezoar being genetically closer to domestic goats than to other wild species. Subsequently, we correlated the mutational profile and the geographical origin of the different individuals. In particular, ACG>ATG changes have the strongest correlation with longitude (r = -0.79, P-value = 3.02*10-204), while TCA>TGA are strongly correlated with latitude (r = -0.51, P-value = 4.30*10-63). We highlight how sequential dinucleotide mutations (SDMs) place cosmopolitan breeds closer to the sampling location, rather than the country of origin, showing how the recent relocation of cosmopolitan breeds to new continents is reshaping the genome of these animals. Finally, we used the mutational profile to predict the coordinate of origin of each animal in the dataset. In conclusion, we show the important role that geography had in shaping the genomes of domestic goats.

Many flowering plant species have adopted an aquatic lifestyle, contrasting with their terrestrial ancestors. Adapting to an aquatic environment required numerous evolutionary changes, including gene expansion and contraction. One of the most striking contractions has been observed in the genomes of seagrasses, where the ACO and ACS genes, involved in ethylene biosynthesis, are very few in number or even completely absent. To confirm this adaptation, we identified traces of gene loss in the genomes of four seagrass species, in the form of pseudogenes. Surprisingly, no gene loss was found in the species that had completely lost the function of ethylene synthesis, likely indicating an ancient loss of these genes. Conversely, several pseudogenes were found in the species where the ACO and ACS genes are contracting, indicating a recent and potentially ongoing process. We used the same approach on Utricularia gibba, a submerged freshwater plant, and also found a reduced number of ACO and ACS genes. In contrast, two terrestrial species closely related to seagrasses and U. gibba found a higher number of ACO and ACS genes, with no definitive evidence of gene loss. These results confirm that the loss of ethylene biosynthesis function in seagrasses is indeed linked to gene loss and suggests that it is an adaptation to a submerged rather than a marine lifestyle.

Recent studies have reported consistent inter-population differences in GC content at polymorphic sites in multiple species, including humans. Specifically, populations that experienced recent bottlenecks exhibit lower average GC content (GC%) at common polymorphic sites compared to non-bottlenecked groups--an observation previously interpreted as indication of rapid evolution of base composition. In this study, we investigate the evolutionary and technical factors driving these patterns across humans, mice, maize, and silkworm. We find that GC% at polymorphic sites is highly sensitive to the allele frequency threshold applied. Relaxing this threshold reduces inter-population differences to negligible levels in humans and significantly attenuates similar signals in other species. We further observe substantial GC% variation across allele frequency bins, a pattern driven by the differential abundance of different mutation types. We demonstrate that these observations are collectively driven by an interaction between demographic history and a universal excess of strong-to-weak mutations relative to weak-to-strong mutations, which is counteracted by GC-biased gene conversion (gBGC) over long evolutionary timescales. Forward-in-time simulations with realistic parameters recapitulate observed patterns of GC% variation across both populations and allele frequency bins. Overall, our findings reveal that the base composition at polymorphic sites is strongly shaped by the interaction between demographic history, mutation bias, and gBGC, and does not represent stable, genome-wide trends. Consequently, inter-population differences in GC content--especially at common variants--should not be interpreted as evidence of ongoing divergence in base composition or shifts in mutation patterns.

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.

BackgroundPrimates constitute one of the most phylogenetically and ecologically diverse Eutherian mammalian orders, with a central role in advancing our knowledge of human evolution, speciation processes and conservation biology. While thousands of whole-genome sequences have been generated across a multitude of primate taxa, discrepancies in data processing - particularly the lack of ploidy-aware variant calling in sex-linked regions - have limited the utility of existing datasets for large-scale comparative analyses. ResultsHere, we utilized publicly available short-read sequencing data of non-human primates, recently published primate genome assemblies and a ploidy-aware variant calling procedure to generate a genome-scale nucleotide diversity panel comprising 3,240 individuals from 269 species and 71 genera. To further facilitate cross-species comparisons, we generated a multiple-genome alignment of primate assemblies used for variant calling. ConclusionThis curated resource of non-human primate diversity provides a foundation for future research in primate evolutionary biology, speciation, and sex chromosome evolution (https://pure.au.dk/portal/en/datasets/primate-diversity-panel/).

Centromeres ensure accurate chromosome segregation and are typically confined to a single, localised region in monocentric chromosomes. In contrast, holocentric chromosomes exhibit kinetochore activity distributed along the chromosome length. Although holocentricity is widespread in Cyperaceae, the composition and organisation of these centromeres, as well as their evolutionary diversification, remain poorly understood. Here, we investigated centromere organisation in representatives of the subfamilies Mapanioideae (Hypolytrum schraderianum Nees) and Cyperoideae (Cladium mariscus (L.) Pohl) by combining genome assemblies, repeatome characterisation (RepeatExplorer), fluorescence in situ hybridisation (FISH), and immunolocalisation. Comparative synteny analyses incorporating the genomes of Rhynchospora breviuscula (n = 5) and Carex littledalei (n = 29) identified conserved blocks, eventually expanding almost whole chromosomes of H. schraderianum (n = 30) and Cl. mariscus (n = 39), despite divergent chromosome numbers and deep evolutionary distances within Cyperaceae. Mobile elements showed very low abundances and were uniformly dispersed, with Ty1/Copia Angela being the most abundant in both species. In Cl. mariscus, holocentromeres showed an extended distribution of centromere- and kinetochore-associated proteins along the chromosomes, largely colocalised with two satellite DNA repeats that form dispersed clusters. In contrast, H. schraderianum also displayed kinetochore signals along chromatids, but the most abundant satellite DNA family was enriched in distal and interstitial chromosomal regions rather than interspersed along the chromatids. Together, these results reveal different genomic architectures underlying holocentric organisation in phylogenetically distinct Cyperaceae lineages, suggesting that holocentromeres in this family have diversified with variation in centromere organisation in regard to its association with repetitive DNA.