Genome Biology and Evolution

Centromeres are comprised of long stretches of repetitive DNA that evolve rapidly in organisms across the tree of life. Consistent selfish centromere evolution can also have cascading effects - driving rapid evolution in interacting kinetochore proteins - possibly to maintain centromere-kinetochore compatibility. Effects of selfishly evolving centromeres on interacting proteins are most heavily studied in the inner kinetochore and assembly proteins including the constitutive centromere-associated network proteins CENP-A and CENP-C with some exploration of the extended effects to other kinetochore-associated protein complexes. While rapid evolution of the centromere has been broadly studied in many organisms, studies assessing positive selection in centromere-associated kinetochore proteins have largely focused on Drosophila. Here, we tested the hypothesis that signatures of positive selection would be present in outer kinetochore and condensin genes in diverse animal groups. We selected two protein complexes -the Condensin I complex and the Mis12 Complex - to test for positive selection in parasitic wasps, two groups of ray-finned fishes (including the amazon molly an asexual diploid exempt from centromere drive), and two groups of primates. We did not find selection using any test in any protein in the amazon molly but did find sporadic positive selection in proteins in both complexes across all groups.

Eukaryotic genomes are ubiquitously occupied by mobile genetic elements termed transposons, which are silenced via a specialized class of small RNA called piRNA. The small RNA is produced from the transposons themselves when they occupy specialized regions of the genome termed piRNA clusters. The formation of these specialized regions, or their evolution over time, is not well understood. Recent work has suggested that they are extremely variable even within a single species such as Drosophila melanogaster. We were interested in taking a comparative approach to piRNA cluster evolution to ask the question - what processes are unique to D. melanogaster and which are shared? Shared phenomena are more likely to be fundamental aspects of piRNA formation and evolution compared to those that are more labile. Using five high-quality long-read genome assemblies and five genotype-specific piRNA libraries, we approach this question from a population genetics standpoint. We annotate piRNA clusters, transposons, and structural variants in each of these five genomes. We found extensive variation in piRNA clusters across strains, with smaller piRNA clusters more likely to be limited to a single genotype. By and large, our results are consistent with a model of piRNA cluster evolution in which piRNA clusters are rapidly formed and lost, with a small subset increasing in frequency and length over time. However, we find that the TEs which nucleate the formation of small piRNA clusters are entirely distinct in D. simulans compared to D. melanogaster, and likely reflect its invasion history rather than any inherent property of the transposon to nucleate clusters. Therefore, while large common clusters can act as traps as has been posited for piRNA clusters, there are also numerous small clusters that are born and lost rapidly within a species.

BackgroundAlthough strict maternal transmission of mitochondria is a general feature of animals and humans for ensuring homogeneity in mitochondrial DNA (mtDNA) across generations, exceptions were reported in the recent past. For example, some extremely rare but spectacular cases of heteroplasmy and paternal transmission in humans have questioned the universal evolutionary principle. Hence, as an alternative, the Mega-NUMT concept was coined to explain this discovery and was thereafter partly proven to exist. This concept expands on the quite common transfer of mtDNA fragments to the nucleus (NUMTs) by considering the existence of multicopy mitochondrial nuclear insertions. Mega-NUMT reports are currently restricted to a few cases in animals, including humans. However, even in humans, their detailed genomic organization, natural prevalence, and potential biological functions remain unclear. Methodology/Principal FindingsHere, we discovered that up to 60 full-sized mitochondrial genomes are integrated into the nuclear genome of the neotropical fruit fly Drosophila paulistorum using long-read sequencing and confirmed their presence by in situ hybridization. The copies are organized in one cluster on chromosome 3, which we, due to its similarity with the Mega-NUMT concept, designated the "Dpau Mega-NUMT". Contrary to the rarity in humans, this Mega-NUMT is found at high prevalence (40%) in both long-term laboratory lines and natural D. paulistorum populations of different semispecies. Additionally, the mitochondrial copies in the Mega-NUMT cluster are phylogenetically separated from the current mitotypes of D. paulistorum. Together, these observations suggest long-term maintenance of the Mega-NUMT in nature. Hence, we propose that the Dpau Mega-NUMT may have been transferred to the nuclear genome before D. paulistorum semispecies radiation and maintained at relatively high prevalence in nature by balancing selection due to yet undetermined functions. Conclusions/SignificanceTo our knowledge, this is the first verified existence and detailed dissection of a Mega-NUMT outside cats and humans. We show that Mega-NUMTs can be persistent in nature, even at high prevalence, potentially due to balancing selection. Our findings strengthen the importance of high-quality long-read sequencing technologies for deciphering complex repeat-rich genomic regions to deepen our understanding of the dynamics of genome evolution within genomic "dark matter".

Horizontal gene transfer (HGT) is one of the fundamental processes in the evolution of prokaryotic genomes, while its importance in eukaryotes is still debated. Some of the hallmark eukaryotic organelles, such as mitochondria and chloroplasts, are of an ancient endosymbiotic origin. The process of acquiring (and losing) new endosymbionts is dynamic and still ongoing in many lineages. Endosymbiotic gene transfer (EGT) between symbionts and their hosts has been considered as one of the major sources of overall HGTs in eukaryotes. Thanks to recent advances in genomics and microscopy, more and more endosymbionts are discovered in protists offering suitable models for the study of EGT and its impact on the host. Recently, the presence of holosporacean and chlamydiacean symbionts in the novel strains of marine euglenozoan flagellates of genus Rhynchopus has been discovered. Here, we present an analysis of the genomes and transcriptomes of five Rhynchopus strains and examine the extent of EGT/HGT and the role of endosymbiosis in shaping the nuclear genome of symbiont-bearing hosts. Our results have shown that there is no evidence of a recent EGT from either Holosporales or Chlamydiales symbionts. The absence of such transfers suggests that EGT or at least a stable retention of EGT genes is not a requisite for a successful endosymbiosis. Furthermore, our results show striking differences between patterns of detected HGTs among the Rhynchopus lineages pointing to a dynamic and largely neutral evolution of horizontally-acquired genes.

The process of evolutionary change remains poorly understood. By analyzing genomic data from 12 populations in Lenskis long-term evolution experiment (LTEE) over 60,000 generations, we identified a clear sequence in gene adaptation: growth-related genes evolved early, while survival-related genes evolved later. Early-evolving genes exhibited higher rates of both nonsynonymous and synonymous substitutions. We also observed a general decline in gene evolutionary rates across LTEE populations, with additional data highlighting the role of fitness gains in determining evolutionary rates. These findings suggest that, in a relatively stable environment, the fitness gains from beneficial mutations decrease as adaptation progresses. This diminishing return on fitness gains may represent a key evolutionary rule, potentially contributing to evolutionary stasis and the prevalence of neutral evolution.

Cytochrome P450 (CYP) genes form a large and functionally diverse superfamily of heme-thiolate monooxygenases that catalyse the oxidation of endogenous and exogenous compounds. Within this superfamily, CYP4 enzymes primarily act on fatty acids, substrates central to energy metabolism. Sustained flight and long-distance migration in birds rely on efficient use of fatty acids, making CYP4 a pertinent system for examining how lipid-associated functions may vary across avian lineages. Across Aves, species occupy diverse ecological niches and display substantial variation in metabolic demands. Here, we characterised CYP4 evolution across birds using 363 avian whole genomes, which cover over 90% of bird families, to investigate how gene variation relates to differences in ecological traits and metabolic strategies. Using this extensive genomic dataset, we identified 4 CYP4 subfamilies and analysed their patterns of sequence evolution. The analyses revealed conserved elements of the avian CYP4 repertoire alongside lineage-specific variation. Several amino-acid positions under positive selection were located within substrate recognition sites (SRS), regions that influence substrate binding and catalytic properties. Changes at these positions may reflect shifts in enzymatic function associated with differences in ecological or physiological traits among species. Overall, the results highlight SRS-associated variation within CYP4 that may reflect adaptive responses to environmental change. These findings advance understanding of how lipid-associated metabolic pathways have been shaped during avian diversification and provide insight into the evolutionary history of a CYP family linked to metabolic adaptation in birds.

The extraordinary complexity of the brain depends in part on the vast diversity of mRNA isoforms it expresses, often in a cell-type specific manner. In a recent study, we found that intronic transposable elements (TEs) are spliced into neural transcripts and diversify the splice isoform repertoire of neurons and glia (Treiber and Waddell, 2020). A recent paper by Azad et al. revisits these findings using their TIDAL analysis pipeline applied to our published data (Azad et al., 2024). Their analysis did not find any of the splicing reads we reported, and although they used RT-PCR to test seven of the 264 TE-gene pairs we had previously reported, they failed to validate TE-gene splicing in any of them. Here, we conduct a quantitative analysis of TE exonisation and show that intronic TE insertions are frequently recruited as alternative exons, with exon usage ranging from rare events to near-complete inclusion in transcripts. We implement this analysis in an improved version of our TEChim software, and present clear support for TE-gene splicing at the seven loci tested by Azad et al. We also identify methodological issues in the experimental and computational design of the Azad et al. study that likely explain their failure to detect TE-gene chimeras, while demonstrating that TE-gene splicing can be detected by RT-PCR under appropriate experimental conditions. Together, our data demonstrates that TE splice isoforms are not rare artefacts but measurable and biologically relevant features of the Drosophila brain transcriptome that may contribute to the molecular complexity and functional adaptability of the brain.

Successful establishment of long-term, obligate endosymbiotic relationships requires integration of hosts and endosymbionts across multiple levels. For example, highly integrated, host-beneficial endosymbionts typically have extremely reduced genomes and metabolisms. However, we do not yet fully understand the specific mechanisms that drive this integration or if there is a specific order in which these changes must occur. To investigate the early stages of endosymbiont genome reduction, we greatly expanded available whole genome data for the nitrogen-fixing endosymbionts (spheroid bodies, SBs) of diatoms in the family Rhopalodiaceae. We used these data to reconstruct SB evolutionary history and to characterize SB core metabolic capacity. We found two key genes missing from all SB genomes, mltA and dnaA, which could provide points of host control over SB cell division. Although most of the SB core genome is experiencing moderately strong purifying selection, we identified 54 genes under positive selection. Eighteen of these are peripheral proteins or involved in cell wall and cell membrane metabolism and could be involved in direct interactions with the host. Unexpectedly, we also found three nif genes under positive selection that are core to the central nitrogen-fixing enzyme. Overall, our results provide early insights into how SBs and their hosts interact, showing that SBs are still in the early stages of endosymbiont genome reduction, but they differ in key ways from current models, including the early loss of all mobile elements.

Population genetic theory predicts that natural selection will be more efficient in large than small populations because genetic drift reduces the efficiency of selection in small populations. Small populations adapting to new environments can also be expected to evolve higher recombination rates to facilitate adaptation as well as to dissociate and purge harmful mutations. We tested these hypotheses (1) by investigating differences in the strength of association between nucleotide diversity ({pi}) and recombination rate across the genomes of nine-spined sticklebacks (Pungitius pungitius) from four small freshwater (mean Ne {approx} 2 578) and four large marine (mean Ne = 86 742) populations, as well as (2) by comparing recombination rates between small and large populations using population specific linkage maps. We found the predicted positive correlation of{pi} with recombination rate from all but the smallest freshwater populations, suggesting prevalent linked selection even after accounting for variation in GC/CpG content, and gene density. Mean recombination rates did not differ between freshwater and marine populations, except that the smallest Ne freshwater population exhibited significantly elevated recombination rate. GWAS analyses suggested a polygenic basis for recombination rates. These results suggest an important role for linked selection in reducing{pi} in low recombination regions especially in large populations. Moreover, as predicted by theory, at least one of the small freshwater populations appears to have evolved a higher recombination rate than its marine ancestors.

Structural variants (SVs) are important components of genetic architecture, expanding beyond traditionally used single nucleotide polymorphisms (SNPs). Though growing, our understanding of the evolutionary forces maintaining SVs in natural populations is limited. Inversions in particular can facilitate local adaptation in populations with high gene flow, including many marine species. The purple sea urchin (Strongylocentrotus purpuratus) spans a broad latitudinal range with diverse environmental conditions and is known for its high genetic diversity, making it an ideal system for studying inversion polymorphism, as well as being a crucial foundation species for marine ecosystems. We used low-coverage whole genome sequence data from 140 individuals from seven populations to identify structural variants using a range of methods including local PCA. We integrated Bayesian selection scans to test for local adaptation in putative inversions. We identified nine loci of interest as putative inversions, three of which overlap with areas of the genome associated with local adaptation scans. Additionally, we find functional enrichment within these regions associated with biomineralisation and development. Our results are the first instance of identifying putative inversions in the purple sea urchin and add to the genomic repertoire of model species. This study offers a valuable resource for future research and reinforces the growing evidence that chromosomal inversions represent a fundamental component of standing genetic variation in natural populations, with important implications for the study of local adaptation. Significance statementChromosomal inversions are an important part of the repertoire of standing genetic variation in wild populations and can facilitate adaptation despite strong gene flow. The purple sea urchin, a widely studied marine species, exhibits high gene flow, large population sizes, and extensive genetic diversity across diverse environmental conditions, making it an ideal model for evolutionary genomics. We identified nine putative inversions, three with signatures of selection, adding echinoderms to the growing list of phyla with putatively adaptive inversions. These findings provide new insights into structural variation in a highly dispersive marine species and highlight potential evolutionary mechanisms maintaining these polymorphisms.

Hydra is a freshwater cnidarian genus that provides a unique comparative model for aging research, contrasting the immortal H. vulgaris with the aging-inducible H. oligactis. Here, we report a high-quality, chromosome-level genome assembly of H. vulgaris strain AEP.JNIG. Our assembly is comparable in quality to existing resources, facilitating the analysis of genomic diversity across laboratory strains. Epigenomic profiling revealed that gene-body hypermethylation correlates with transcriptional stability and the suppression of spurious transcription in evolutionary conserved genes, suggesting an epigenetic mechanism for genomic integrity. Furthermore, comparative genomics demonstrated that while Hydra conserves fundamental Hallmarks of Aging pathways, the immortal H. vulgaris paradoxically lacks canonical anti-aging genes (e.g., Klotho, NAMPT) found in the aging-inducible H. oligactis. Instead, H. vulgaris exhibits a distinct metabolic signature related to mitochondrial energy production and NTP synthesis. Collectively, our comparative genomics results suggest multiple potential mechanisms associated with the H. vulgaris immortality and the aging traits of H. oligactis, providing novel targets for future functional studies. Significance statementWhy do some organisms age while others appear not to? The freshwater animal Hydra provides a unique opportunity to investigate this question, as closely related species display contrasting aging phenotypes. We generated a high-quality genome assembly for a new strain of a non-aging species and conducted comparative analyses with related strains and an aging species. Even closely related strains can accumulate substantial genetic divergence over time, and stable DNA modification patterns were associated with consistent gene activity, suggesting a mechanism that may help maintain cellular balance. Surprisingly, several well-known longevity genes are present in the aging species but absent in the non-aging one. This suggests that extended lifespan may not simply depend on possessing more "anti-aging" genes, but instead may reflect differences in how core biological processes are organized. Our study provides new insights into the genetic basis of aging and highlights Hydra as a powerful model for understanding longevity.

A longstanding goal in human genetics is to prioritize noncoding loci that, when disrupted, lead to developmental disorders and other Mendelian traits. In pursuit of this goal, multiple metrics have been developed to distinguish neutrally evolving sequences from those subjected to purifying selection. These metrics are commonly evaluated genome-wide, e.g., by computing a precision-recall curve on windows tiling the entire noncoding genome. Here, we identify parts of the noncoding genome where these metrics significantly underperform relative to their genome-wide performance due to "bias" in the underlying models of neutral genetic variation and/or a low "signal-to-noise ratio" in the genetic data. The most extreme effects are found for Gnocchi (Chen et al. 2024), the performance of which declines as GC content increases. We suggest annotating constraint scores of noncoding genomic intervals with robust measures of the bias of the corresponding model, allowing users to gauge confidence in those scores.

Octopuses are phenotypically distinctive organisms, and recent genomic work raises questions about the contributions of transposable elements (TE) to their genomic architecture. We leveraged a robust repeat annotation pipeline, in combination with manual and automated curatorial techniques, to produce a more comprehensive repeat annotation of Octopus vulgaris. This revealed that [~]66% of the genome are repeats, in contrast to previous estimates of 43-50%. Whereas previous studies of TE expansion in Octopus bimaculoides identified two bursts of activity, 25 and 56 MYA, our re-annotation revealed four such expansions at 18, 25, 33, and 56 MYA. We further identified a landscape of TE hot- and cold spots. This much refined TE timescape and landscape will serve as a useful basis for understanding TE contributions to O. vulgaris evolution, and also for identifying factors contributing to variation in the TE community across genomic space and evolutionary time.

Chromosomes can undergo large-scale rearrangements such as fissions and fusions. Occasional rearrangements can be common, especially in organisms with holocentric chromosomes such as butterflies. However, high rates of fissions and fusions have only been observed in a few taxonomic groups. One such group is the Palearctic Leptidea butterflies, where fissions and fusions have resulted in considerable inter- and intraspecific variation in chromosome numbers. The large number of rearrangements in Leptidea, provides a rare opportunity to study the mutational determinants of chromosomal rearrangements within a statistical framework. Using nine chromosome-level genome assemblies and 138 whole-genome re-sequenced individuals, we mapped evolutionary breakpoint regions and quantified the association between annotation features and rearrangements. Evolutionary breakpoint regions were significantly depleted in protein-coding genes and the majority resided in repetitive regions. However, rearrangements were only weakly associated with transposable elements. Instead, the strongest sequence predictors were large clusters of satellite DNA, ribosomal DNA and segmental duplications, with differing patterns among rearrangement types. Copy-number variation was observed in evolutionary breakpoint regions and lineages dominated by fissions or fusions were associated respectively with genome expansion and reduction. The results give novel insights into the mechanistic basis of interchromosomal rearrangements.

Genomic rearrangements are fundamental drivers of biodiversity, yet dynamics of structural evolution following polyploidization remain poorly understood. Genus Xenopus provides a valuable tool to study these phenomena. Utilizing the diploid X. tropicalis as a reference, we employed cytogenetic and genomic mapping to track the structural evolution of the allotetraploids X. borealis and X. laevis across a 50-million-year timeline. Based on chromosome morphometrics and C-banding patterns, we characterized the X. borealis pseudotetraploid karyotype (2n = 4x = 36), localizing the nucleolus organizer region (NOR) to chromosome 5L, U1 and U2 small nuclear DNAs to 1S and 8L, and 5S rDNA to nearly all chromosomes. Our analysis revealed 17 genomic rearrangements distributed within three temporal strata: ancestral (50-35 Mya), intermediate (35-15 Mya), and recent (< 15 Mya). Although we categorized chromosome 9/10 fusion as an ancestral rearrangement, the 2/9 translocation previously identified in X. mellotropicalis was absent in both studied allotetraploids. Furthermore, we tested for sex-specific structural polymorphism on the X. borealis W chromosome. Despite a large region of recombination suppression between the W and Z, no inversions were detected, indicating persistent sex chromosome homomorphism. Results are consistent with the expectation that tandem repeats such as NORs follow an asymmetric trajectory driven by a jumping mechanism and biased deletion, whereas small nuclear DNA loci are governed by copy number reduction-expansion dynamics. These findings indicate that structural rearrangements in Xenopus were not limited to punctuated bursts immediately following whole-genome duplication; rather, they accumulated over a prolonged evolutionary history, affecting the entire polyploid complement.

Accurate estimation of population demographic history is central to population genetics yet remains challenging due to the sensitivity of inference methods to the number of individuals and the demographic scenario assumed in inference. The site-frequency spectrum (SFS) of neutral variants, a widely used summary statistic of genetic variation, is particularly sensitive to demographic processes, but studies have shown that qualitative results from demographic inference, i.e., population expansion vs. contraction, can depend strongly on the number of individuals in the dataset. Here, we analyzed two simulated datasets and one empirical dataset characterized by an ancient population bottleneck followed by a recent population expansion. Fitting a two-epoch demographic model across a range of sample sizes, we found that inference shifted from signals of ancient population contraction at small sample sizes to signals of recent population expansion at large sample sizes. Other summary statistics, including Tajimas D and the proportion of singletons, also changed with sample size. We found that these changes of inferred evolutionary signals under a two-epoch model can be explained by the epoch which contributes the highest mean proportion of coalescent branch lengths. Our results highlight that demographic inference depends critically on the number of individuals analyzed and suggest that analyzing datasets at multiple sample sizes can reveal complementary aspects of population history.

A widespread observation in molecular evolution is that X-linked genes adapt faster than autosomal genes--a pattern known as "faster-X" adaptation. Yet the classical explanation for faster-X adaptation--that partially recessive beneficial mutations experience more efficient selection in hemizygous males--conflicts with theories of dominance, which predict that beneficial mutations should be partially dominant for fitness. Recently, a new theory for faster-X adaptation that does not invoke partial recessivity of beneficial mutations has been proposed, in which mutations with large phenotypic effects experience more positive selection on the X. Here, we tested this theory by estimating rates of adaptation of nonsynonymous mutations in three lineages with a well-documented faster-X: Drosophila melanogaster, Mus musculus, and Homo sapiens. We used three proxies for the phenotypic effects of mutations: amino-acid dissimilarity, sequence conservation, and gene age. As expected, all proxies for scaled phenotypic effects correlated negatively with measures of the efficiency of purifying selection and with adaptive substitution rates on both chromosome types. However, we found no evidence that faster-X adaptation was enriched among large-effect mutations, as predicted by the new theory. We discuss why this could be the case, including challenges in measuring scaled phenotypic effects, in modelling faster-X adaptation, and in estimating rates of adaptation using McDonald-Kreitman tests. Overall, our results highlight that faster-X adaptation is a major unsolved puzzle in evolutionary genetics.

Small marsupials in the family Dasyuridae are a key component of Australias arid and semi-arid fauna, whose high species richness is proposed to reflect an opportunity-driven adaptive radiation. Despite growing interest in this group from both ecological and evolutionary perspectives, genomic data for most species is non-existent, or limited to a few marker loci. Here, we generated a chromosome-level reference genome and a de novo mitochondrial genome for the desert-dwelling Wongai ningaui (Ningaui ridei). The nuclear genome assembly is highly contiguous, with a scaffold N50 of 594.484 MB and high BUSCO gene recovery (93.84%). Additionally, we produced a draft assembly for the related, semi-arid slender-tailed dunnart (Sminthopsis murina). We then used these assemblies to explore the demographic histories of these species. We find evidence for contrasting patterns of population growth during the late Pleistocene and early Holocene, corresponding with differences in local climate, potentially consistent with differences in optimal habitat. The new genomic resources and demographic findings presented here provide a foundation for future studies on adaptive specialisation in this group of Australian marsupials. Significance StatementDasyurid marsupials are the primary carnivorous and insectivorous mammals in Australia. This diverse family includes species such as the endangered Tasmanian devil (Sarcophilus harrisii) and quolls (Genus Dasyurus), as well as an emerging laboratory model species, the fat-tailed dunnart (Sminthopsis crassicaudata). Despite the species richness within dasyurids, most species remain under-studied. This is particularly true of arid and semi-arid zone species, who are often small in size, live in remote habitats and are cryptic by nature. By creating genome assemblies for two dasyurid species, this study provides resources to support a variety of phylogenetic, population genetic and evolutionary developmental lines of research. Importantly, the studys finding that arid and semi-arid dasyurids show distinct trajectories of demographic change in response to historical climatic shifts may point to local adaptations with implications for the resilience of these species to ongoing and future climate change.

Genetic variation plays a central role in enabling organisms to adapt to ever-changing environments. Transposable elements (TEs) are key drivers of genetic variation and adaptation, partly due to their ability to respond to environmental changes, such as thermal variability, through transcriptional activation, potentially leading to insertion events. The new copies will eventually accumulate mutations, increasing the TE diversity in the genome. In this study, we investigated how the TE diversity varies across environments, contrasted by their average temperature and their thermal variability profile, using polychaete annelids as a model system. These primarily benthic organisms occupy a wide range of habitats, from polar waters to hydrothermal vents and temperate shores. TE diversity varied substantially among polychaete species, with significantly lower diversity observed in species inhabiting unstable habitats, such as those associated with hydrothermal vents. This link between TE diversity and environment was statistically consistent across the different TE orders, except for DIRS-like elements in Errantia polychaetes, that display a surprisingly high diversity. Our results suggest that TE diversity may be selected to balance the level of TE activation, linked to thermal variability, to maintain a sustainable mutation rate at the whole genome level. In unstable environments, high TE diversity may not be sustainable due to the accumulation of deleterious mutations, caused by a higher rate of stress-induced transposition compared to other habitats. These findings highlight the influence of environmental conditions on the long-term dynamics governing TE-host interactions and underscore the role of TEs in evolution.

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 in the high intertidal zone, 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 relatively 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 sequence 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 individuals of this population and members of the T. angulatus complex. The haplotypes that we assembled (qhTigAngs1.1.hap1 & qhTigAngs1.1.hap2) are placed into 12 major scaffolds (N50 18-19 Mbp, L50 6-7), equivalent to the number of chromosomes in other Tigriopus species. BUSCO and k-mer analyses of each haplotype and BUSCO analyses of gene models are relatively complete (95-99%) with respect to gene and k-mer content. Analyses of mitochondrial data also suggest that the Chilean population of Tigriopus we sampled 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.