Evolution of the ancestral mammalian karyotype and syntenic regions

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(40)

Published: Sept. 26, 2022

Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded 26 chromosome-scale genome assemblies representing 23/26 mammal orders, we computationally reconstructed ancestral karyotypes syntenic relationships at 16 nodes along phylogeny. Three different reference genomes (human, sloth, cattle) phylogenetically distinct superorders were used assess bias in expand number clades with genomes. The ancestor likely had 19 pairs autosomes, nine smallest chromosomes shared common all amniotes (three still conserved extant mammals), demonstrating a striking conservation synteny for ∼320 My vertebrate evolution. numbers types classified transitions between karyotype, descendent ancestors, species. For example, 94 inversions, fissions, 14 fusions occurred over 53 differentiated therian from eutherian ancestor. highest breakpoint rate was observed ancestors (3.9 breakpoints/My). Reconstructed found have evolutionary histories reflected their rates rearrangements. distributions genes, repetitive elements, topologically associating domains, actively transcribed regions multispecies homologous blocks indicate purifying selection acted millions years maintain developmentally important genes regulatory landscapes gene-dense chromosomes.

Language: Английский

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Topological structures and syntenic conservation in sea anemone genomes

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Dec. 13, 2023

Abstract There is currently little information about the evolution of gene clusters, genome architectures and karyotypes in early branching animals. Slowly evolving anthozoan cnidarians can be particularly informative these features. Here we report chromosome-level assemblies two related anthozoans, sea anemones Nematostella vectensis Scolanthus callimorphus . We find a robust set 15 chromosomes with clear one-to-one correspondence between species. Both genomes show chromosomal conservation, allowing us to reconstruct ancestral cnidarian metazoan blocks, consisting at least 19 16 linkage groups, respectively. that, contrast Bilateria, Hox NK clusters investigated are largely disintegrated, despite presence staggered hox/gbx expression This loss microsynteny conservation may facilitated by shorter distances cis-regulatory sequences their cognate transcriptional start sites. no evidence for topologically associated domains, suggesting fundamental differences long-range regulation compared vertebrates. These data suggest that large sets genes have been retained groups some extant lineages; yet, higher order 3D architecture evolved only after cnidarian-bilaterian split.

Language: Английский

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Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2020, Volume and Issue: unknown

Published: Oct. 30, 2020

Abstract Draft genome sequences of non-bilaterian species have provided important insights into the evolution metazoan gene repertoire. However, there is little information about clusters, architectures and karyotypes during animal evolution. In this regard, slowly evolving anthozoan Cnidaria, sister group Bilateria, are particularly informative. Here we report chromosome-level assemblies two related cnidarians, sea anemones Nematostella vectensis Scolanthus callimorphus . We find a robust set 15 chromosomes with clear one-to-one correspondence between species. Both anemone genomes show remarkable chromosomal conservation other several bilaterians sponge Ephydatia muelleri , allowing us to reconstruct ancestral cnidarian blocks, consisting at least 19 16 linkage groups, respectively. that, in contrast Hox NK clusters investigated cnidarians largely disintegrated, despite presence staggered hox/gbx expression This loss microsynteny may be facilitated by shorter distances cis-regulatory their cognate transcriptional start sites. line no evidence for topologically associated domains, suggesting fundamental differences long-range regulation compared vertebrates. These data suggest that large sets genes been retained groups some extant lineages, yet, higher order 3D architecture evolved only after cnidarian-bilaterian split.

Language: Английский

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MyoD1 localization at the nuclear periphery is mediated by association of WFS1 with active enhancers

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: March 17, 2025

Abstract Spatial organization of the mammalian genome influences gene expression and cell identity. While association genes with nuclear periphery is commonly linked to transcriptional repression, also active, expressed can localize at periphery. The transcriptionally active MyoD1 gene, a master regulator myogenesis, exhibits peripheral localization in proliferating myoblasts, yet underlying mechanisms remain elusive. Here, we generate reporter line demonstrate that locus independent involved heterochromatin anchoring. Instead, identify envelope transmembrane protein WFS1 tethers primarily associates distal enhancer elements upstream , subset enhancers genome-wide, which are enriched histone marks myogenic genes. Overall, our data mechanism tethering regulatory

Language: Английский

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The application of irreversible genomic states to define and trace ancient cell type homologies

EvoDevo, Journal Year: 2025, Volume and Issue: 16(1)

Published: May 3, 2025

Homology, or relationship among characters by common descent, has been notoriously difficult to assess for many morphological features, and cell types in particular. The ontogenetic origin of traits means that the only physically inherited information is encoded genomes. However, complexity underlying gene regulatory network often miniscule changes can impact expression, make it practically impossible postulate a clear demarcation line what molecular signature should "define" homologous type between two deeply branching animals. In this Hypothesis article, we propose use recently characterized irreversible genomic states, occur after chromosomal sub-chromosomal mixing genes elements, dissect signatures each into reversible configurations. While such states will be non-functional, some may permanently expression given type. Our proposal evolutionarily irreversible, thus synapomorphic, functional constitute criterion timing deep evolutionary homologies. aims close gap clearly defined homology individual their at phenotypic level through identification linked states.

Language: Английский

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Topological mixing and irreversibility in animal chromosome evolution

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 30, 2024

Abstract/Summary Paragraph Animal chromosomes can persist with recognizable homology over hundreds of millions years, in spite homology-obfuscating processes such as chromosomal fusion and translocation. The frequency pace these major genome structural changes are unknown, it remains unclear whether or how they impact long-term evolution. Here, we compare whole sequences 3,631 genomes from 2,291 species spanning all animal clades show that karyotypes evolve primarily via karyotype contraction, associated increased rates fusion-with-mixing dispersion largely obey algebra 1 , expansion, which breaks up ancestral linkage groups forms new elements non-algebraic changes. We be extinction events. Using a multi-scale encoding pan-animal manifold representation genomic changes, find evolution is not only driven by at the level, but subchromosomal mixing irreversibility define clade-specific this ‘evolutionary topology’ approach, calculate extrema irreversible configurations identify occupy intermediate positions, providing evidence for distinct macro-evolutionary trajectories. propose investigation mixed state accumulation around important gene loci (such Hox) will crucial capturing further study regulatory innovations.

Language: Английский

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Genetic adaptations of marine invertebrates to hydrothermal vent habitats

Trends in Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 1, 2024

Language: Английский

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Emerging questions on the mechanisms and dynamics of 3D genome evolution in spiralians

Briefings in Functional Genomics, Journal Year: 2023, Volume and Issue: 22(6), P. 533 - 542

Published: Oct. 9, 2023

Abstract Information on how 3D genome topology emerged in animal evolution, stable it is during development, its role the evolution of phenotypic novelties and exactly affects gene expression highly debated. So far, data to address these questions are lacking with exception a few key model species. Several regulatory mechanisms have been proposed, including scenarios where has little no impact expression, vice versa. The ancient diverse clade spiralians may provide crucial testing ground for such mechanisms. Sprialians followed distinct evolutionary trajectories, some clades experiencing expansions and/or large-scale rearrangements, others undergoing contraction, substantially impacting their size organisation. These changes associated many innovations this clade. In review, we describe emerging data, along functional tools, allow discuss predicted outcomes.

Language: Английский

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Three-dimensional Digital Reconstruction and Application of AR_MR Technology in Medicine

Automation and Machine Learning, Journal Year: 2023, Volume and Issue: 4(2)

Published: Jan. 1, 2023

With the rapid development of modern medical technology, training imaging professionals is changing with each passing day, and science technology are developing rapidly, especially 3D digital reconstruction AR_MR applied to clinic education. continuous transformation mode, it most important problem for discuss how can better meet convenience characteristics connotation early diagnosis treatment. Aiming at discussion this paper applies many technologies directions in medicine. Combining practical application exploration, study systematically analyzes medicine, which proves operability, feasibility sustainable technology. It provides a new idea perspective virtual integration reality

Language: Английский

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