Biology subjects

Simakov, O.

Publications and source records attributed to Simakov, O..

At least 19 recordsLinked to original sources

bioRxiv2026

Genome expansions and regulatory contact entanglement help preserve ancestral metazoan synteny

Chromosomes constitute deeply conserved evolutionary units in many metazoan genomes, with chromosomal fusions and fissions, accompanied by sub-chromosomal rearrangements, rewiring three dimensional genome architecture. How chromatin loops and compartments that define distal regulatory interactions within chromosomes impose functional constraints that affect this long-term evolutionary process (and vice-versa) is an emerging research topic. Genome expansions, especially through transposable element (TE) activity, test these constraints by increasing the genomic distances over which regulatory interactions must function and were thus suggested to be the drivers of chromosomal rearrangements. To study dynamics and stability of such distal interactions in the light of genome expansions, we focus on the cnidarian Hydra vulgaris, which, based on its simple and well-understood biology as well as one of the largest genomes among cnidarians, is particularly suited to test how chromatin loop and genome architecture respond to genome expansion. We investigate genome architecture using Micro-C, single-cell Hi-C (Dip-C), and DNA FISH, and perform comparative analysis using available genomic and epigenomic data. Contrary to prior expectations, our analysis of whole-genome data and particular loci (e.g., Wnt) suggests a scenario where genome expansion did not only result in chromatin loops often reaching several megabases in hydra, but also led to regulatory contact mixing and entanglement, introducing additional constraints to maintain ancestral genomic architecture. Generalizing these findings across hundreds of metazoan genomes, we show a new mechanistic role for genome expansion in yielding entangled long-range regulatory configurations that, in turn, decelerate chromosomal rearrangements, thus maintaining (and not breaking) ancestral regulatory states and synteny. Significance statementSome of the largest and most repetitive animal genomes retain a surprisingly high level of deeply conserved metazoan synteny. As repetitive regions are often associated with chromosomal rearrangements, it has been enigmatic why syntenic retention is so frequently observed. In this study, using hydra as a model system for both stem cell biology and an evolutionary history rich in transposable-element driven genome expansion, a multi-level conformational landscape dissection reveals a multitude of long-range regulatory states. We show that mixing of multiple such regulatory links accompanied by genomic expansion is associated with maintained ancestral synteny, thus pointing to the counter-intuitive role of genome expansions as "fossilization" agents across metazoan genomes.

evolutionary biology↗

bioRxiv2026

Histo-anatomical atlas and thermal tolerance of Garra rufa: A novel small teleost model adaptable to human body temperature

Garra rufa, commonly known as the doctor fish, is a small freshwater cyprinid notable for its exceptional tolerance to high temperatures, surviving even at around the human body temperature of 37 {degrees}C, and has emerging potential as a novel laboratory model for human cancer xenotransplantation and infectious disease research. To establish a foundation for its experimental use, we conducted comprehensive anatomical and histological analyses across major organ systems. The overall body organization and tissue architecture of G. rufa are broadly similar to those of zebrafish (Danio rerio), indicating a conserved cyprinid body plan. However, several organ systems in G. rufa exhibited species-specific differences compared with zebrafish, including a well-developed adhesive disc around the oral region, a long and coiled intestine, and a distinct dark pigmentation of the peritoneum. These species-specific traits may reflect ecological and behavioral adaptations of G. rufa, including benthic scraping in warm, flowing habitats. Physiological assays confirmed that G. rufa maintains high survival rates and normal swimming activity at 37 {degrees}C, whereas zebrafish exhibit significant mortality and reduced locomotion under the same conditions. Collectively, this work provides a comprehensive histo-anatomical atlas of G. rufa, highlighting its unique morphological specializations while establishing an essential reference for the development of this species as a novel experimental fish model.

zoology↗

bioRxiv2025

Genome reorganisation and expansion shape 3D genome architecture and define a distinct regulatory landscape in coleoid cephalopods

How genomic changes translate into organismal novelties is often confounded by the multi-layered nature of genome architecture and the long evolutionary timescales over which molecular changes accumulate. Coleoid cephalopods (squid, cuttlefish, and octopus) provide a unique system to study these processes due to a large-scale chromosomal rearrangement in the coleoid ancestor that resulted in highly modified karyotypes, followed by lineage-specific fusions, translocations, and repeat expansions. How these events have shaped gene regulatory patterns underlying the evolution of coleoid innovations, including their large and elaborately structured nervous systems, novel organs, and complex behaviours, remains poorly understood. To address this, we integrate Micro-C, RNA-seq, and ATAC-seq across multiple coleoid species, developmental stages, and tissues. We find that while topological compartments are broadly conserved, hundreds of chromatin loops are species- and context-specific, with distinct regulation signatures and dynamic expression profiles. CRISPR-Cas9 knockout of a putative regulatory sequence within a conserved region demonstrates the role of loops in neural development and the prevalence of long-range, inter-compartmental interactions. We propose that differential evolutionary constraints across the coleoid 3D genome allow macroevolutionary processes to shape genome topology in distinct ways, facilitating the emergence of novel regulatory entanglements and ultimately contributing to the evolution and maintenance of complex traits in coleoids.

evolutionary biology↗

bioRxiv2025

Chromosomal fusions and subsequent rearrangements shaped octopus genomes

Why some animal groups retain ancestral chromosomal complements while others change significantly is a fundamental question in evolutionary genomics. Few systems exist where accumulations of chromosomal changes can be studied in the context of morphological innovation. In coleoid cephalopods (octopus, squid, cuttlefish), an ancient coleoid chromosomal rearrangement event (ACCRE) has led to a substantial increase in the chromosome number and a new set of chromosomal homologies. Compared to typical molluscan or bilaterian genomes, ACCRE has enabled the origin of many novel regulatory regions in coleoid cephalopods. However, the discrepancies between extant octopodiform (octopus, [~]30 chromosomes) and decapodiform (squid and cuttlefish, [~]46 chromosomes) karyotypes and the direction of these evolutionary changes remain unexplained. Here we provide a draft genome assembly of the vampire squid Vampyroteuthis sp., the largest cephalopod genome sequenced to-date (over 10 gigabasepairs). Through syntenic comparisons, we infer that this basally branching octopodiform species shows partial retention of the chromosomal complement of Decapodiformes, indicating its more ancestral state and the derived nature of the octopod karyotype. Together with the analysis of a new chromosome-level assembly of the pelagic octopod Argonauta hians, we identified irreversible chromosomal fusion-with-mixing events followed by inter-chromosomal translocations in octopods. We show that this secondary reduction and mixing within octopod chromosomes has enabled the origin of a more entangled genomic configuration, shedding light onto the early evolutionary transitions within the clade. Our results offer broader insights into general patterns of chromosomal evolution following large-scale rearrangement events in animal genomes. Significance statementHow changes to the ancient animal synteny result in novel chromosomal homologies is difficult to dissect due to the lack of intermediate states. Here we report that the genome of Vampyroteuthis, one of the largest animal genomes sequenced to-date (over 11 gigabasepairs), despite its phylogenetic position within the octopodiform cephalopods, partially retains squid and cuttlefish chromosomal complement, reflecting an ancestral karyotypic state that existed at the time of divergence between these cephalopod lineages. Our findings reveal karyotype reductions through chromosomal fusions were followed by inter-chromosomal translocations in octopods, leading to a more specialized genomic and gene regulatory architecture. These data show how chromosomal fusions can act as drivers of further inter-chromosomal rearrangements in animal genomes.

genomics↗

bioRxiv2025

A Chromosome-Scale Genome of Nanomia septata Reveals Extensive Rearrangement But No Clear Driver of the Unique Colony-Level Organization of Siphonophores

Siphonophores (Cnidaria:Hydrozoa) are pelagic colonial marine invertebrates with many highly specialized bodies (zooids) within a single colony. Their unique biology and ecological importance have made them of particular interest. Recent work revealed siphonophore genomes to be larger than in most other cnidarians. To investigate siphonophores genome biology and develop resources for future studies, we sequenced the genome of a single Nanomia septata to chromosome scale. The haploid genome is 1.5GB across 8 chromosomes, a reduction relative to the 15 chromosomes seen in closely related hydrozoan genomes, and is highly rearranged, consistent with multiple mixing events. Genome expansion occurred through intergenic repeat expansion, with protein-coding genes shorter than in most cnidarians. We found no genomic features clearly associated with siphonophores exceptional colony-level complexity. Gene families that play critical roles in cnidarian development have not expanded, and gene proximity was not generally correlated to their expression across zooids, except in male gonophores. To contextualize these observations, we genome sequenced 20 additional Nanomia specimens across the globe and mapped them to our chromosome-scale reference. Population genomic analyses support three previously recognized species of Nanomia, and at least one additional undescribed species. Overlapping geographic distribution of some Nanomia species suggest reproductive isolation in sympatry. Phylogenetic analyses of genome size indicate Nanomia septata and Nanomia cara have similarly large genomes between 1.5-1.7GB, while Nanomia bijuga and an undescribed species show a secondary reduction to 0.7GB. These results highlight how genomic factors have shaped colony organization and genome diversity within Nanomia.

genomics↗

bioRxiv2025

Chromosome-scale genome assembly of the European common cuttlefish Sepia officinalis

Coleoid cephalopods, a subclass of mollusks that includes octopuses, cuttlefish and squid, exhibit sophisticated biological features such as dynamic and neurally driven camouflage behavior, inter-individual communication, single-lens camera-like eyes, the largest brains among invertebrates and a distinctive embryonic development. The common cuttlefish Sepia officinalis has served as a model organism in various research fields, spanning biophysics, neurobiology, behavior, evolution, ecology and biomechanics. More recently, it has become a model to investigate the neural mechanisms underlying cephalopod camouflage, using quantitative behavioral approaches alongside molecular techniques to characterize the identity, evolution and development of neuronal cell types. Despite significant interest in this animal, a high-quality, annotated genome of this species is still lacking. To address this, we sequenced and assembled a chromosome-scale genome for S. officinalis. Our assembly spans 5.68 billion base pairs and comprises 1n=47 repeat-rich chromosome scaffolds. This was unexpected because the haploid karyotypes of other decapods indicate 46 chromosomes. Detailed comparisons of our data to those from published decapod genome assemblies and to another recent genome assembly of S. officinalis (itself suggesting 1n=49 chromosomes) in fact revealed clear homologies between 46 scaffolds across all the datasets. The discrepancies between datasets are explained by highly repetitive regions, impairing proper read alignments. We conclude that the true karyotype of S. officinalis is probably 1n=46 chromosomes, a likely ancestral and if true, conserved decapod karyotype. Our results include a comprehensive gene annotation and full-length transcript prediction, which we used to characterize orthologous gene families across mollusks. We identified several large-scale expansions specific to cephalopods, with many genes specific to neural or non-neural tissues of adult S. officinalis. In summary, this genome should provide a valuable resource for future research on the evolution, brain organization, information processing, development and behavior in this important clade.

genomics↗

bioRxiv2025

Chromosome-level genome assembly of the doctor fish (Garra rufa)

Garra rufa, commonly known as doctor fish, is a small freshwater cyprinid fish recognized for its high-temperature tolerance. G. rufa is primarily known for its role in ichthyotherapy, in which it helps remove keratinized skin from human hands and feet. However, in recent years, its high-temperature tolerance has attracted attention owing to its potential use as a model for human disease research, including infectious diseases and cancer xenograft models. Despite this interest, the genomic basis underlying high-temperature tolerance remains largely unexplored, primarily because of the limited availability of genomic resources, which hinders its development as an experimental model. In the present study, a high-quality chromosome-level genome assembly of G. rufa was generated using a combination of PacBio HiFi long-read sequencing and Hi-C technology. We generated a chromosome-level genome assembly with 25 chromosomes, 1.38 Gb in total length, and scaffold N50 of 49.3 Mb. Approximately 59% of the genome comprises repetitive elements, with DNA and LTR elements being particularly abundant. In total, 27,352 protein-coding genes were annotated, of which 26,900 genes (98.3%) were functionally annotated. Benchmarking Universal Single-Copy Orthologs (BUSCO) benchmark for genome assembly and gene annotation demonstrated 94.5% and 94.7% of complete BUSCOs, respectively. We identified two heat shock transcription factor (HSF) and 239 heat shock protein (HSP)-related genes. Heat shock elements, which are HSF-binding motifs, were present within 3 kb upstream of 944 genes, with statistically significant enrichment of HSP-related genes in this set. Furthermore, molecular phylogenetic analysis and whole-genome comparisons revealed that G. rufa is evolutionarily closely related to species in the Labeoninae subfamily of the Cyprinidae family. This chromosome-level reference genome provides a valuable resource for future research aimed at elucidating the molecular mechanisms underlying high-temperature tolerance in G. rufa and establishing it as a model organism for human biomedical studies.

genomics↗

bioRxiv2024

Expansion of a single Helitron subfamily in Hydractinia symbiolongicarpus suggests a shared mechanism of cnidarian chromosomal extension

Helitrons are rolling-circle transposons that amplify through rolling-circle replication mechanism. Since Helitrons were relatively recently identified, their impact on genome evolution is still not fully understood. Here, we describe that a single Helitron subfamily specifically accumulates in the subtelomeric regions of Hydractinia symbiolongicarpus, a colonial hydrozoan cnidarian. Based on the sequence divergence, it is suggested that the Helitron subfamily underwent a burst of activity in the species recent history. Additionally, there is a IS3EU DNA element accumulation at the putative centromeric regions, as well as minisatellite sequences of approximately 200 bp in length extending from the telomere-side end of the Helitron towards the telomere. Phylogenetic analysis of Helitrons in the H. symbiolongicarpus genome suggests that the Helitrons underwent local propagation at the subtelomeric regions. The single Helitron subfamily, along with the consecutive minisatellite, accounts for 26.1% of the genome coverage (126 Mb of the 483 Mb genome), which collectively contribute to the genome size increase observed in H. symbiolongicarpus compared with other cnidarians. Homologous sequences of Helitron in H. symbiolongicarpus were identified in the genomes of other cnidarians, suggesting that Helitrons in hydractinia were present in at least the common ancestor of Cnidaria. Furthermore, in Nematostella vectensis, an anthozoan cnidarian, Helitrons were also accumulated at the subtelomeric regions. All these findings suggest that Helitrons constitute a common cnidarian mechanism of chromosomal extension through local amplification in subtelomeric regions, driving diverse genome expansions within the clade.

genomics↗

bioRxiv2024

Topological mixing and irreversibility in animal chromosome evolution

Abstract/Summary ParagraphAnimal chromosomes can persist with recognizable homology over hundreds of millions of years, in spite of homology-obfuscating processes such as chromosomal fusion and translocation. The frequency and pace of these major genome structural changes are unknown, and it remains unclear whether or how they impact long-term genome evolution. Here, we compare whole chromosomal sequences of 3,631 genomes from 2,291 species spanning all major animal clades and show that animal karyotypes evolve primarily via karyotype contraction, associated with increased rates of chromosomal fusion-with-mixing and dispersion that largely obey chromosomal algebra1, or karyotype expansion, which breaks up ancestral linkage groups and forms new chromosomal elements via non-algebraic changes. We show that chromosomal changes can be associated with major extinction events. Using a multi-scale encoding of pan-animal genome homology and a manifold representation of genomic changes, we find that genome evolution is not only driven by changes at the chromosomal level, but that subchromosomal mixing and irreversibility define clade-specific evolution. Using this evolutionary genome topology approach, we calculate extrema of irreversible genomic configurations and identify species that occupy intermediate manifold positions, providing evidence for distinct macro-evolutionary trajectories. We propose that investigation of mixed state accumulation around important gene loci (such as Hox) will be crucial in capturing and further study of clade-specific regulatory innovations.

evolutionary biology↗

bioRxiv2024

A genome resource for the marine annelid Platynereis dumerilii

The marine annelid Platynereis dumerilii is a model organism used in many research areas including evolution and development, neurobiology, ecology and regeneration. Here we present the genomes of P. dumerilii (laboratory culture reference and a single individual assembly) and of the closely related P. massiliensis and P. megalops (single individual assembly) to facilitate comparative genomic approaches and help explore Platynereis biology. We used long-read sequencing technology and chromosomal-conformation capture along with extensive transcriptomic resources to obtain and annotate a draft genome assembly of [~]1.47 Gbp for P. dumerilii, of which more than half represent repeat elements. We predict around 29,000 protein-coding genes, with relatively large intron sizes, over 38,000 non-coding genes, and 105 miRNA loci. We further explore the high genetic variation ([~]3% heterozygosity) within the Platynereis species complex. Gene ontology reveals the most variable loci to be associated with pigmentation, development and immunity. The current work sets the stage for further development of Platynereis genomic resources.

genomics↗

bioRxiv2024

Acceleration of genome rearrangement in clitellate annelids

Comparisons of multiple metazoan genomes have revealed the existence of ancestral linkage groups (ALGs), genomic scaffolds sharing sets of orthologous genes that have been inherited from ancestral animals for hundreds of millions of years (Simakov et al. 2022; Schultz et al. 2023) These ALGs have persisted across major animal taxa including Cnidaria, Deuterostomia, Ecdysozoa and Spiralia. Notwithstanding this general trend of chromosome-scale conservation, ALGs have been obliterated by extensive genome rearrangements in certain groups, most notably including Clitellata (oligochaetes and leeches), a group of easily overlooked invertebrates that is of tremendous ecological, agricultural and economic importance (Charles 2019; Barrett 2016). To further investigate these rearrangements, we have undertaken a comparison of 12 clitellate genomes (including four newly sequenced species) and 11 outgroup representatives. We show that these rearrangements began at the base of the Clitellata (rather than progressing gradually throughout polychaete annelids), that the inter-chromosomal rearrangements continue in several clitellate lineages and that these events have substantially shaped the evolution of the otherwise highly conserved Hox cluster.

evolutionary biology↗

bioRxiv2024

The dynamic genomes of Hydra and the anciently active repeat complement of animal chromosomes

Many animal genomes are characterized by highly conserved chromosomal homologies that pre-date the ancient origin of this clade. Despite such conservation, the evolutionary forces behind the retention, expansion, and contraction of chromosomal elements, and the resulting macro-evolutionary implications, are unknown. Here we present a comprehensive stem-cell resolved genomic and transcriptomic study of the fresh-water cnidarian Hydra, an animal characterized by its high regenerative capacity, the ability to propagate clonally, and an apparent lack of aging. Using single-haplotype telomere-to-telomere genome assemblies of two recently diverged hydra strains, we show how the macro-evolutionary history of chromosomal elements is shaped by both old and recent transposable element (TE) expansions. Unique features of hydra biology allowed us to compare the individual genomes of hydras three stem cell lineages. We show that distinct TE families are active at both transcriptional and genomic levels via non-random insertions in the genomes of each of these lineages. In transcriptomes, over 14,000 transcripts were composed of nearly complete TE sequences, and further classification into families, subfamilies, and individual loci reveals cell type-specific TE expression. The active TEs include elements that differentially contribute to changes in the genome size as well as persistent structural variants around loci associated with cell proliferation. Our study reveals 14 active TE families that primarily act in this role and are predominantly composed of DNA elements. Evolutionary analysis revealed that these families constitute a highly conserved TE core in eukaryotic and metazoan genomes. Our results suggest an ancient role for these core TEs as self-renewing genomic components that persist beyond ancient chromosomal homologies.

genomics↗

bioRxiv2023

The genome of the colonial hydroid Hydractinia reveals their stem cells use a toolkit of genes shared with all animals

Hydractinia is a colonial marine hydroid that exhibits remarkable biological properties, including the capacity to regenerate its entire body throughout its lifetime, a process made possible by its adult migratory stem cells, known as i-cells. Here, we provide an in-depth characterization of the genomic structure and gene content of two Hydractinia species, H. symbiolongicarpus and H. echinata, placing them in a comparative evolutionary framework with other cnidarian genomes. We also generated and annotated a single-cell transcriptomic atlas for adult male H. symbiolongicarpus and identified cell type markers for all major cell types, including key i-cell markers. Orthology analyses based on the markers revealed that Hydractinias i-cells are highly enriched in genes that are widely shared amongst animals, a striking finding given that Hydractinia has a higher proportion of phylum-specific genes than any of the other 41 animals in our orthology analysis. These results indicate that Hydractinias stem cells and early progenitor cells may use a toolkit shared with all animals, making it a promising model organism for future exploration of stem cell biology and regenerative medicine. The genomic and transcriptomic resources for Hydractinia presented here will enable further studies of their regenerative capacity, colonial morphology, and ability to distinguish self from non-self.

genomics↗

bioRxiv2023

An ancient split of germline and somatic stem cell lineages in Hydra

In many animals, germ cell segregation occurs during early embryogenesis to protect the genome, but its origin in basal metazoans is controversial. Here, we show in the freshwater polyp Hydra by clonal analysis and transgenic animals that interstitial stem cells comprise two separate stem cell populations, i.e., germline and multipotent somatic stem cells. We isolated genetically labelled stem cells for a global transcriptome study and discovered a broad set of germline-specific/enriched genes including Prdm9, Pax5, Dmrt1. In an alternative splicing analysis, we identified many genes with germline-specific isoforms; among them, male-specific isoforms of Dmrt1 and Snf5. The somatic interstitial stem cell lineage was characterized by numerous neuronal control genes like Neurog. But all stem cells in Hydra also share a core of stemness genes that has its roots in unicellular eukaryotes. This suggests an evolutionary scenario in which, at the emergence of animal multicellularity, there was an early split into a stable germline and different somatic stem cell lineages.

developmental biology↗

bioRxiv2023

A chromosome-level reference genome for the common octopus, Octopus vulgaris (Cuvier, 1797)

Cephalopods are emerging animal models and include iconic species for studying the link between genomic innovations and physiological and behavioral complexities. Coleoid cephalopods possess the largest nervous system among invertebrates, both for cell counts and brain-to-body ratio. Octopus vulgaris has been at the center of a long-standing tradition of research into diverse aspects of cephalopod biology, including behavioral and neural plasticity, learning and memory recall, regeneration, and sophisticated cognition. However, no chromosome-scale genome assembly is available for O. vulgaris to aid in functional studies. To fill this gap, we sequenced and assembled a chromosome-scale genome of the common octopus, O. vulgaris. The final assembly spans 2.8 billion basepairs, 99.34% of which are in 30 chromosome-scale scaffolds. Hi-C heatmaps support a karyotype of 1n=30 chromosomes. Comparisons with other octopus species genomes show a conserved octopus karyotype, and a pattern of local genome rearrangements between species. This new chromosome-scale genome of O. vulgaris will further facilitate research in all aspects of cephalopod biology, including various forms of plasticity and the neural machinery underlying sophisticated cognition, as well as an understanding of cephalopod evolution.

genomics↗

bioRxiv2023

The hagfish genome and the evolution of vertebrates

As the only surviving lineages of jawless fishes, hagfishes and lampreys provide a critical window into early vertebrate evolution. Here, we investigate the complex history, timing, and functional role of genome-wide duplications in vertebrates in the light of a chromosome-scale genome of the brown hagfish Eptatretus atami. Using robust chromosome-scale (paralogon-based) phylogenetic methods, we confirm the monophyly of cyclostomes, document an auto-tetraploidization (1RV) that predated the origin of crown group vertebrates [~]517 Mya, and establish the timing of subsequent independent duplications in the gnathostome and cyclostome lineages. Some 1RV gene duplications can be linked to key vertebrate innovations, suggesting that this early genomewide event contributed to the emergence of pan-vertebrate features such as neural crest. The hagfish karyotype is derived by numerous fusions relative to the ancestral cyclostome arrangement preserved by lampreys. These genomic changes were accompanied by the loss of genes essential for organ systems (eyes, osteoclast) that are absent in hagfish, accounting in part for the simplification of the hagfish body plan; other gene family expansions account for hagfishes capacity to produce slime. Finally, we characterise programmed DNA elimination in somatic cells of hagfish, identifying protein-coding and repetitive elements that are deleted during development. As in lampreys, the elimination of these genes provides a mechanism for resolving genetic conflict between soma and germline by repressing germline/pluripotency functions. Reconstruction of the early genomic history of vertebrates provides a framework for further exploration of vertebrate novelties.

genomics↗

bioRxiv2023

Using a handful of transcriptomes to detect sex-linked markers in a lizard with homomorphic sex chromosomes

To understand the biology of a species it is often crucial to be able to differentiate males and females. Many species lack distinguishable sexually dimorphic traits, but in those that possess sex chromosomes, molecular sexing offers a good alternative. Designing molecular sexing assays is typically achieved through the comparison of male and female genomic sequences, often from reduced-representation sequencing. However, in many non-model species sex chromosomes are poorly differentiated, and identifying sex-limited sequences and developing PCR-based sexing assays is challenging without additional genomic resources. Here we highlight a simple procedure for detection of sex-linked markers based on transcriptomes that circumvents limitations of other approaches. We apply it to the spotted snow skink Carinascincus ocellatus, a lizard with homomorphic XY chromosomes that also experiences environmentally-induced sex reversal. With transcriptomes from 3 males and 3 females alone, we identify thousands of putative Y-linked sequences. We confirm linkage through alignment of assembled transcripts to a distantly related genome, and readily design PCR primers to sex C. ocellatus and related species. In addition to providing an important molecular sexing tool for these species, this approach also facilitated valuable comparisons of sex determining systems on a large taxonomic scale.

genetics↗

bioRxiv2022

New Hydra Genomes Reveal Conserved Principles of Hydrozoan Transcriptional Regulation

The epithelial and interstitial stem cells of the freshwater polyp Hydra are the best characterized stem cell systems in any cnidarian, providing valuable insight into cell type evolution and the origin of stemness in animals. However, little is known about the transcriptional regulatory mechanisms that determine how these stem cells are maintained and how they give rise to their diverse differentiated progeny. To address such questions, a thorough understanding of transcriptional regulation in Hydra is needed. To this end, we generated extensive new resources for characterizing transcriptional regulation in Hydra, including new genome assemblies for Hydra oligactis and the AEP strain of Hydra vulgaris, an updated whole-animal single-cell RNA-seq atlas, and genome-wide maps of chromatin interactions, chromatin accessibility, sequence conservation, and histone modifications. These data revealed the existence of large chromatin interaction domains in the Hydra genome that likely influence transcriptional regulation in a manner distinct from topologically associating domains in bilaterians. We also uncovered the transcriptomic profiles of two previously molecularly uncharacterized cell types, isorhiza-containing nematocytes and somatic gonad ectoderm. We identified novel candidate regulators of cell-type-specific transcription, several of which have likely been conserved at least since the divergence of Hydra and the jellyfish Clytia hemisphaerica over 200 million years ago. The resources generated in this study, which collectively represent the most comprehensive characterization of transcriptional regulation in a cnidarian to date, are accessible through a newly created genome portal, available at research.nhgri.nih.gov/HydraAEP/.

developmental biology↗