Genome Architecture Research Articles

Chromosome-scale genomes of the flightless caterpillar hunter beetles Calosoma tepidum and Calosoma wilkesii from British Columbia (Coleoptera: Carabidae).

The giant ground beetle genus Calosoma (Coleoptera, Carabidae) comprises ca. 120 species distributed worldwide. About half of the species in this genus are flightless due to a process of wing reduction likely resulting from the colonization of remote habitats such as oceanic islands, highlands and deserts. This clade is emerging as a new model to study the genomic basis of wing evolution in insects. In this framework, we present the de novo assemblies and annotations of two Calosoma species genomes from British Columbia, Calosoma tepidum and Calosoma wilkesii. Combining PacBio HiFi and Hi-C sequencing, we produce high-quality reference genomes for these two species. Our annotation using long-read RNAseq and existing Coleoptera protein evidence, identified a total of 21,976 genes for C. tepidum and 26,814 genes for C. wilkesii. Using synteny analyses, we provide an in-depth comparison of genomic architectures in these two species. We infer an overall pattern of chromosome-scale conservation between the two species, with only minor rearrangements within chromosomes. These new reference genomes represent a major step forward in the study of this group, providing high-quality references that open the door to different approaches such as comparative genomics or population scale resequencing to study the implications of flight evolution.

The genome of the cryopelagic Antarctic bald notothen, Trematomus borchgrevinki.

The Antarctic bald notothen, Trematomus borchgrevinki (family Nototheniidae) occupies a high latitude, ice-laden environment and represents an extreme example of cold-specialization among fishes. We present the first, high quality, chromosome-scale genome of a female T. borchgrevinki individual comprised of 23 putative chromosomes, the largest of which is 65 megabasepairs (Mbp) in length. The total length of the genome 935.13 Mbp, composed of 2,094 scaffolds, with a scaffold N50 of 42.67 Mbp. Annotation yielded 22,192 protein coding genes while 54.75% of the genome was occupied by repetitive elements; an analysis of repeats demonstrated that an expansion occurred in recent time. Conserved synteny analysis revealed that the genome architecture of T. borchgrevinki is largely maintained with other members of the notothenioid clade, although several significant translocations and inversions are present, including the fusion of orthologous chromosomes 8 and 11 into a single element. This genome will serve as a cold-specialized model for comparisons to other members of the notothenioid adaptive radiation.

The recombination landscape of the barn owl, from families to populations.

Homologous recombination is a meiotic process that generates diversity along the genome and interacts with all evolutionary forces. Despite its importance, studies of recombination landscapes are lacking due to methodological limitations and limited data. Frequently used approaches include linkage mapping based on familial data that provides sex-specific broad-scale estimates of realized recombination and inferences based on population LD that reveal a more fine scale resolution of the recombination landscape, albeit dependent on the effective population size and the selective forces acting on the population. In this study, we use a combination of these two methods to elucidate the recombination landscape for the Afro-European barn owl (Tyto alba). We find subtle differences in crossover placement between sexes that leads to differential effective shuffling of alleles. LD based estimates of recombination are concordant with family-based estimates and identify large variation in recombination rates within and among linkage groups. Larger chromosomes show variation in recombination rates, while smaller chromosomes have a universally high rate which shapes the diversity landscape. We find that recombination rates are correlated with gene content, genetic diversity and GC content. We find no conclusive differences in the recombination landscapes between populations. Overall, this comprehensive analysis enhances our understanding of recombination dynamics, genomic architecture, and sex-specific variation in the barn owl, contributing valuable insights to the broader field of avian genomics.

Can Transcriptomics Elucidate the Role of Regulation in Invasion Success?

When a species invades a novel environment, it must bridge the environment-phenotype mismatch in its new range to persist. Contemporary invasion biology research has focused on the role that trait variation and adaptation, and their underlying genomic factors, play in a species' adaptive potential, and thus facilitating invasion. Empirical studies have provided valuable insights into phenotypes that persist and arise in novel environments, coupled with 'omics tools that further the understanding of the contributions of genomic architecture in species establishment. Particularly, the use of transcriptomics to explore the role of plasticity in the initial stages of an invasion is growing. Here, we assess the role of various mechanisms relating to regulation and functional adaptation (often measured via the transcriptome) that support trait-specific plasticity in invasive species, allowing phenotypic variability without directly altering genomic diversity. First, we present a comprehensive review of the studies utilising transcriptomics in invasion biology. Second, we collate the evidence for and against the role of a range of regulatory processes in contributing to invasive species plasticity. Finally, we pose open questions in invasion biology where the use of transcriptome data may be valuable, as well as discuss the methodological limitations.

Novel toxin biosynthetic gene cluster in harmful algal bloom-causing Heteroscytonema crispum: Insights into the origins of paralytic shellfish toxins.

Caused by both eukaryotic dinoflagellates and prokaryotic cyanobacteria, harmful algal blooms (HABs) are events of severe ecological, economic, and public health consequence, and their incidence has become more common of late. Despite coordinated research efforts to identify and characterize the genomes of HAB-causing organisms, the genomic basis and evolutionary origins of paralytic shellfish toxins (PSTs) produced by HABs remain at best incomplete. The PST saxitoxin has an especially complex genomic architecture and enigmatic phylogenetic distribution, spanning dinoflagellates and multiple cyanobacterial genera. Using filtration and extraction techniques to target the desired cyanobacteria from non-axenic culture, coupled with a combination of short and long read sequencing, we generated a reference-quality hybrid genome assembly for Heteroscytonema crispum UTEX LB 1556, a freshwater, PST-producing cyanobacterium thought to have the largest known genome in its phylum. We report a complete, novel biosynthetic gene cluster for the PST saxitoxin. Leveraging this biosynthetic gene cluster, we find support for the hypothesis that PST production has appeared in divergent Cyanobacteria lineages through widespread and repeated horizontal gene transfer. This work demonstrates the utility of long-read sequencing and metagenomic assembly toward advancing our understanding of PST biosynthetic gene cluster diversity and suggests a mechanism for the origin of PST biosynthetic genes.

Genomic Architecture Underlying the Striking Colour Variation in the Presence of Gene Flow for the Guinan Toad-Headed Lizard.

How divergence occurs between closely related organisms in the absence of geographic barriers to gene flow stands as one of the long-standing questions in evolutionary biology. Previous studies suggested that the interplay between selection, gene flow and recombination strongly affected the process of divergence with gene flow. However, the extent to which these forces interact to drive divergence remains largely ambiguous. Guinan toad-headed lizards (Phrynocephalus guinanensis) in the Mugetan Desert exhibit striking colour differences from lizards outside the desert and provide an excellent model to address this question. Through extensive sampling and whole genome sequencing, we obtained genotypes for 191 samples from 14 populations inside and outside the desert. Despite the colour differences, continuous and asymmetric gene flow was detected across the desert border. More importantly, 273 highly diverged regions (HDRs) were identified between them, accounting only for 0.47% of the genome but widely distributed across 20 (out of the total 24) chromosomes. Strong signatures of selection were identified in HDRs, and local recombination rates were repressed. Furthermore, five HDRs exhibited significantly higher divergence, which contained key genes associated with crucial functions in animal coloration, including pteridine and melanocyte pigmentation. Genes related to retinal cells and steroid hormones were identified in other HDRs, which might have also contributed to the formation of colour variation in the presence of gene flow. This study provided novel insights into the understanding of the evolutionary mechanisms of genetic divergence in the presence of gene flow.

Sequence modeling and design from molecular to genome scale with Evo.

The genome is a sequence that encodes the DNA, RNA, and proteins that orchestrate an organism's function. We present Evo, a long-context genomic foundation model with a frontier architecture trained on millions of prokaryotic and phage genomes, and report scaling laws on DNA to complement observations in language and vision. Evo generalizes across DNA, RNA, and proteins, enabling zero-shot function prediction competitive with domain-specific language models and the generation of functional CRISPR-Cas and transposon systems, representing the first examples of protein-RNA and protein-DNA codesign with a language model. Evo also learns how small mutations affect whole-organism fitness and generates megabase-scale sequences with plausible genomic architecture. These prediction and generation capabilities span molecular to genomic scales of complexity, advancing our understanding and control of biology.

HIRA and dPCIF1 coordinately establish totipotent chromatin and control orderly ZGA in Drosophila embryos

Early embryos undergo profound changes in their genomic architecture to establish the totipotent state, enabling pioneer factors to access chromatin and drive zygotic genome activation (ZGA). However, the mechanisms by which the totipotent state is established and properly interpreted by pioneer factors to allow orderly ZGA remain unknown. Here, we identify the H3.3-specific chaperone HIRA as a factor involving establishing totipotent-state chromatin in Drosophila early embryos. Through cophase separation with HIRA, the pioneer factor GAGA factor (GAF) efficiently binds to H3.3-marked nucleosomes to activate major-wave zygotic genes. Importantly, dPCIF1, a chromatin-associated protein, antagonized the GAF-HIRA interaction by competitively binding to HIRA, thereby restricting GAF on earlier chromatin and avoiding premature ZGA. Hence, the coordinated action of HIRA and dPCIF1 ensures sequential ZGA from the minor to major wave in early embryos. This study provides insights into understanding how a totipotent state is established and properly controlled during ZGA.

Comprehensive pan-genome analysis of Mycobacterium marinum: insights into genomic diversity, evolution, and pathogenicity.

Mycobacteria is a diverse genus that includes both innocuous environmental species and serious pathogens like Mycobacterium tuberculosis, Mycobacterium leprae, and Mycobacterium ulcerans, the causative agents of tuberculosis, leprosy, and Buruli ulcer, respectively. This study focuses on Mycobacterium marinum, a closely related species known for its larger genome and ability to infect ectothermic species and cooler human extremities. Utilizing whole-genome sequencing, we conducted a comprehensive pan-genome analysis of 100M. marinum strains, exploring genetic diversity and its impact on pathogenesis and host specificity. Our findings highlight significant genomic diversity, with clear distinctions in core, dispensable, and unique genes among the isolates. Phylogenetic analysis revealed a broad distribution of genetic lineages, challenging previous classifications into distinct clusters. Additionally, we examined the synteny and diversity of the virulence factor CpnT, noting a wide range of C-terminal domain variations across strains, which points to potential adaptations in pathogenic mechanisms. This study enhances our understanding of M. marinum's genomic architecture and its evolutionary relationship with other mycobacterial pathogens, providing insights that could inform disease control strategies for M. tuberculosis and other mycobacteria.

Abstract 4137846: Smooth muscle expression of RNA editing enzyme ADAR1 controls vascular integrity and progression of atherosclerosis

Mapping the genomic architecture of complex disease has been predicated on the understanding that genetic variants influence disease risk through modifying gene expression. However, recent discoveries have revealed that a significant burden of disease heritability in common autoinflammatory disorders and coronary artery disease is mediated through genetic variation modifying post-transcriptional modification of RNA through adenosine-to-inosine (A-to-I) RNA editing. This common RNA modification is catalyzed by ADAR enzymes, where ADAR1 edits specific immunogenic double stranded RNA (dsRNA) to prevent activation of the double strand RNA (dsRNA) sensor MDA5 ( IFIH1 ) and stimulation of an interferon stimulated gene (ISG) response. Multiple lines of human genetic data indicate impaired RNA editing and increased dsRNA sensing to be an important mechanism of coronary artery disease (CAD) risk. Here, we provide a crucial link between observations in human genetics and mechanistic cell biology leading to progression of CAD. Through analysis of human atherosclerotic plaque, we implicate the vascular smooth muscle cell (SMC) to have a unique requirement for RNA editing, and that ISG induction occurs in SMC phenotypic modulation, implicating MDA5 activation. Through culture of human coronary artery SMCs, generation of a conditional SMC specific Adar1 deletion mouse model on a pro-atherosclerosis background, and with incorporation of single cell RNA sequencing cellular profiling, we further show that Adar1 controls SMC phenotypic state, is required to maintain vascular integrity, and controls progression of atherosclerosis and vascular calcification. Our data implicates MDA5 activation to occur in SMC phenotypic modulation and accelerates formation of chondromyocytes in a distinct cellular lineage trajectory — indicating a cell type and context specific requirement of RNA editing. Through this work, we describe a fundamental new mechanism of CAD, where RNA editing and sensing of dsRNA in a cell type and context specific mechanism mediates disease progression, bridging our understanding of human genetics and disease causality.

A mini-review of single-cell Hi-C embedding methods

Single-cell Hi-C (scHi-C) techniques have significantly advanced our understanding of the 3D genome organization, providing crucial insights into the spatial genome architecture within individual nuclei. Numerous computational and statistical methods have been developed to analyze scHi-C data, with embedding methods playing a key role. Embedding reduces the dimensionality of complex scHi-C contact maps, making it easier to extract biologically meaningful patterns. These methods not only enhance cell clustering based on chromatin structures but also facilitate visualization and other downstream analyses. Most scHi-C embedding methods incorporate strategies such as normalization and imputation to address the inherent sparsity of scHi-C data, thereby further improving data quality and interpretability. In this review, we systematically examine the existing methods designed for scHi-C embedding, outlining their methodologies and discussing their capabilities in handling normalization and imputation. Additionally, we present a comprehensive benchmarking analysis to compare both embedding techniques and their clustering performances. This review serves as a practical guide for researchers seeking to select suitable scHi-C embedding tools, ultimately contributing to the understanding of the 3D organization of the genome.

Rapid chromosome evolution and acquisition of thermosensitive stochastic sex determination in nematode androdioecious hermaphrodites

The factors contributing to evolution of androdioecy, the coexistence of hermaphrodites and males such as in Caenorhabditis elegans, remains poorly known. However, nematodes exhibit androdioecy in at last 13 genera with the predatory genus Pristionchus having seven independent transitions towards androdioecy. Nonetheless, associated genomic architecture and sex determination mechanisms are largely known from Caenorhabditis. Here, studying 47 Pristionchus species, we observed repeated chromosome evolution which abolished the ancestral XX/XO sex chromosome system. Two phylogenetically unrelated androdioecious Pristionchus species have no genomic differences between sexes and mating hermaphrodites with males resulted in hermaphroditic offspring only. We demonstrate that stochastic sex determination is influenced by temperature in P. mayeri and P. entomophagus, and CRISPR engineering indicated a conserved role of the transcription factor TRA-1 in P. mayeri. Chromosome-level genome assemblies and subsequent genomic analysis of related Pristionchus species revealed stochastic sex determination to be derived from XY sex chromosome systems through sex chromosome-autosome fusions. Thus, rapid karyotype evolution, sex chromosome evolution and evolvable sex determination mechanisms are general features of this genus, and represent a dynamic background against which androdioecy has evolved recurrently. Future studies might indicate that stochastic sex determination is more common than currently appreciated.

A virus associated with the zoonotic pathogen Plasmodium knowlesi causing human malaria is a member of a diverse and unclassified viral taxon

ABSTRACT The Apicomplexa are a phylum of single-celled eukaryotes that can infect humans and include the mosquito-borne parasite Plasmodium, the cause of malaria. Viruses that infect non-Plasmodium spp. disease-causing protozoa affect pathogen life cycle and disease outcomes. However, only one RNA virus (Matryoshka RNA virus 1) has been identified in Plasmodium, and none have been identified in zoonotic Plasmodium species. The rapid expansion of the known RNA virosphere via metagenomic sequencing suggests that this dearth is due to the divergent nature of RNA viruses that infect protozoa. We leveraged newly uncovered data sets to explore the virome of human-infecting Plasmodium species collected in Sabah, east (Borneo) Malaysia. From this, we identified a highly divergent RNA virus in two human-infecting P. knowlesi isolates that is related to the unclassified group ‘ormycoviruses’. By characterising 15 additional ormycoviruses identified in the transcriptomes of arthropods we show that this group of viruses exhibits a complex ecology as non-infecting passengers at the arthropod-mammal interface. With the addition of viral diversity discovered using the artificial intelligence-based analysis of metagenomic data, we also demonstrate that the ormycoviruses are part of a diverse and unclassified viral taxon. This is the first observation of an RNA virus in a zoonotic Plasmodium species. By linking small-scale experimental data to advances in large-scale virus discovery, we characterise the diversity and confirm the putative genomic architecture of an unclassified viral taxon. This approach can be used to further explore the virome of disease-causing the Apicomplexa and better understand how protozoa-infecting viruses may affect parasite fitness, pathobiology, and treatment outcomes.

Genomic architecture in social insects is more strongly associated with phylogeny than social behavior

Abstract The evolution of sociality in insects has been predicted to reduce effective population sizes, in turn leading to changes in genome architecture, including higher recombination rates, larger genomes, increased GC-biased gene conversion (gBGC), and greater intragenomic variation in GC content to maintain castes through differential methylation. As the number of sequenced insect genomes continues to grow, it remains an open question which, if any, of these genomic features are consistent across social insect genomes. A major challenge to determining such commonalities has been the lack of phylogenetically controlled analyses across independent origins of sociality. Of the 15 Hymenoptera species for which recombination rate was available, social species had higher rates of recombination. Next, we conducted a broader analysis of genome architecture by analyzing genome assemblies for 435 species of Hymenoptera and 8 species of Blattodea to test if GC content, genome size, distribution of CpG sites or codon bias repeatedly differed between social and nonsocial species. Overall, there was little support for predictable changes in genome architecture associated with sociality across Hymenoptera, after accounting for phylogenetic relationships. However, we found a significant negative relationship between sociality and GC content within the family Apidae and a significant negative relationship between sociality and genome size within the family Halictidae. In all, these results suggest that unique origins of social behavior may produce unique trends in genomic architecture. Our study highlights the need to examine genome architecture across independent origins of social behavior.

EXPRESSO: a multi-omics database to explore multi-layered 3D genomic organization.

The three-dimensional (3D) organization of the human genome plays a crucial role in gene regulation. EXPloration of Regulatory Epigenome with Spatial and Sequence Observations (EXPRESSO) is a novel multi-omics database for exploration and visualization of multi-layered 3D genomic features across 46 different human tissues. Integrating 1360 3D genomic datasets (Hi-C, HiChIP, ChIA-PET) and 842 1D genomic and transcriptomic datasets (ChIP-seq, ATAC-seq, RNA-seq) from the same biosample, EXPRESSO provides a comprehensive resource for studying the interplay between 3D genome architecture and transcription regulation. This database offers diverse 3D genomic feature types (compartments, contact matrix, contact domains, stripes as diagonal lines extending from a genomic locus in contact matrix, chromatin loops, etc.) and user-friendly interface for both data exploration and download. Other key features include REpresentational State Transfer application programming interfaces for programmatic access, advanced visualization tools for 3D genomic features and web-based applications that correlate 3D genomic features with gene expression and epigenomic modifications. By providing extensive datasets and tools, EXPRESSO aims to deepen our understanding of 3D genomic architecture and its implications for human health and disease, serving as a vital resource for the research community. EXPRESSO is freely available at https://expresso.sustech.edu.cn.

Evolution of Plant Genome Size and Composition.

The rapid development of sequencing technology has led to an explosion of plant genome data, opening up more opportunities for research in the field of comparative evolutionary analysis of plant genomes. In this review, we take changes in plant genome size and composition as a starting point and describe the effects of polyploidy, whole genome duplication and transposable elements changes on plant genome architecture and evolution, respectively. In addition, to address the lack of relevant information in some areas, we also collected and analyzed 234 representative plant genome data as a supplement. We aim to provide a global, up-to-date summary of information on plant genome architecture and evolution in this review.

Activation of γ-globin expression by a common variant disrupting IKAROS-binding motif in β-thalassemia

Programmed silencing of γ-globin genes in adult erythropoiesis is mediated by several chromatin remodeling complexes, which determine the stage-specific genome architecture in this region. Identification of cis- or trans-acting mutations contributing to the diverse extent of Hb F might illustrate the underlying mechanism of γ-β globin switching. Here, we recruit a cohort of 1142 β-thalassemia patients and dissect the natural variants in the whole β-globin gene cluster through a targeted next-generation sequencing panel. A previously unreported SNP rs7948668, predicted to disrupt the binding motif of IKAROS as a key component of chromatin remodeling complexes, is identified to be significantly associated with higher levels of Hb F and age at onset. Gene-editing on this SNP leads to elevation of Hb F in both HUDEP-2 and primary CD34+ cells while the extent of elevation is amplified in the context of β-thalassemia mutations, indicating epistasis effects of the SNP in the regulation of Hb F. Finally, we perform ChIP-qPCR and 4C assays to prove that this variant disrupts the binding motif of IKAROS, leading to enhanced competitiveness of HBG promoters to locus control regions. This study highlights the significance of common regulatory SNPs and provides potential targets for treating of β-hemoglobinopathy.

Decoding the genomic terrain: functional insights into 14 chemosensory proteins in whitefly Bemisia tabaci Asia II-1

Genome-wide analysis of Bemisia tabaci Asia II-1 unravelled for the first-time full-length sequences of 14 chemosensory proteins (CSPs), their exon-intron boundaries, insertion sites of retrotransposons, and clustering patterns on chromosomes. All the CSPs sans CSP6 have an N-terminal signal peptide. The presence of OS-D superfamily and PhBP domains in different CSPs suggests their roles in chemosensory signal transduction and pheromone binding. Motif analysis reveals the conservation and cohesiveness of CSPs in hemiptera. The phylogenetic analysis uncovers the evolutionary lineages of Hemipteran CSPs. RT-qPCR analysis showed spatial expression of CSPs in different body tissues of B. tabaci adults. In-silico docking analysis showed high-affinity binding of CSP 1 and 5 with two insecticides, imidacloprid and fipronil, with energy values ranging from − 5.8 to -9.3 kcal/mol, along with the details of interacting aminoacidic residues in the hydrophobic binding pockets of these two CSPs. Further functional validation was done through insecticide bioassays and RNAi. This study provides novel insights into the genomic architecture of CSPs in B. tabaci Asia II-1, and functional characterisation suggests that CSP1 and 5 genes may have indirect roles in insecticide resistance. It lays the foundation for further research on developing new control strategies for B. tabaci.

Transcriptomic Response of Rhizobium leguminosarum to Acidic Stress and Nutrient Limitation Is Versatile and Substantially Influenced by Extrachromosomal Gene Pool.

Multipartite genomes are thought to confer evolutionary advantages to bacteria by providing greater metabolic flexibility in fluctuating environments and enabling rapid adaptation to new ecological niches and stress conditions. This genome architecture is commonly found in plant symbionts, including nitrogen-fixing rhizobia, such as Rhizobium leguminosarum bv. trifolii TA1 (RtTA1), whose genome comprises a chromosome and four extrachromosomal replicons (ECRs). In this study, the transcriptomic responses of RtTA1 to partial nutrient limitation and low acidic pH were analyzed using high-throughput RNA sequencing. RtTA1 growth under these conditions resulted in the differential expression of 1035 to 1700 genes (DEGs), which were assigned to functional categories primarily related to amino acid and carbohydrate metabolism, ribosome and cell envelope biogenesis, signal transduction, and transcription. These results highlight the complexity of the bacterial response to stress. Notably, the distribution of DEGs among the replicons indicated that ECRs played a significant role in the stress response. The transcriptomic data align with the Rhizobium pangenome analysis, which revealed an over-representation of functional categories related to transport, metabolism, and regulatory functions on ECRs. These findings confirm that ECRs contribute substantially to the ability of rhizobia to adapt to challenging environmental conditions.

Global loss of promoter-enhancer connectivity and rebalancing of gene expression during early colorectal cancer carcinogenesis.

Although three-dimensional (3D) genome architecture is crucial for gene regulation, its role in disease remains elusive. We traced the evolution and malignant transformation of colorectal cancer (CRC) by generating high-resolution chromatin conformation maps of 33 colon samples spanning different stages of early neoplastic growth in persons with familial adenomatous polyposis (FAP). Our analysis revealed a substantial progressive loss of genome-wide cis-regulatory connectivity at early malignancy stages, correlating with nonlinear gene regulation effects. Genes with high promoter-enhancer (P-E) connectivity in unaffected mucosa were not linked to elevated baseline expression but tended to be upregulated in advanced stages. Inhibiting highly connected promoters preferentially represses gene expression in CRC cells compared to normal colonic epithelial cells. Our results suggest a two-phase model whereby neoplastic transformation reduces P-E connectivity from a redundant state to a rate-limiting one for transcriptional levels, highlighting the intricate interplay between 3D genome architecture and gene regulation during early CRC progression.