A chromosome-scale epigenetic map of theHydragenome reveals conserved regulators of cell state

Genome Research, Journal Year: 2023, Volume and Issue: 33(2), P. 283 - 298

Published: Jan. 13, 2023

The epithelial and interstitial stem cells of the freshwater polyp

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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PIWI proteins and piRNAs: key regulators of stem cell biology

Frontiers in Cell and Developmental Biology, Journal Year: 2025, Volume and Issue: 13

Published: Feb. 6, 2025

In this mini review, we discussed the functional roles of PIWI proteins and their associated small RNAs, piRNAs, in regulating gene expression within stem cell biology. Guided by these transcriptionally post-transcriptionally repress transposons using mechanisms such as ping-pong amplification cycle phasing to protect germline genomes. Initially identified Drosophila melanogaster, piRNA pathway regulate self-renewal differentiation via cell-autonomous non-cell-autonomous mechanisms. Precisely, GSCs, piRNAs modulating chromatin states directly influencing mRNA translation. For instance, protein Aubergine loaded with promotes represses translation certain mRNAs balance differentiation. Thus, exhibits dual regulatory stability translation, highlighting its context-dependent functions. Moreover, are essential somatic cells support regenerative capacity highly species, planarians. Similarly, intestinal cells, Piwi regulates metabolic pathways genome integrity, impacting longevity gut homeostasis. case, appear absent gut, suggesting piRNA-independent Together, demonstrate evolutionary conservation regulation, integrating TE silencing regulation at levels lineages. Beyond canonical roles, emerging evidence reveal broader significance maintaining properties organismal health under physiological pathological conditions.

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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The genome of the venomous snail Lautoconus ventricosus sheds light on the origin of conotoxin diversity

GigaScience, Journal Year: 2021, Volume and Issue: 10(5)

Published: May 1, 2021

Abstract Background Venoms are deadly weapons to subdue prey or deter predators that have evolved independently in many animal lineages. The genomes of venomous animals essential understand the evolutionary mechanisms involved origin and diversification venoms. Results Here, we report chromosome-level genome Mediterranean cone snail, Lautoconus ventricosus (Caenogastropoda: Conidae). total size assembly is 3.59 Gb; it has high contiguity (N50 = 93.53 Mb) 86.6 Mb assembled into 35 largest scaffolds pseudochromosomes. On basis venom gland transcriptomes, annotated 262 complete genes encoding conotoxin precursors, hormones, other venom-related proteins. These were scattered different pseudochromosomes located within repetitive regions. precursors normally structured 3 exons, which did not necessarily coincide with structural domains corresponding Additionally, found evidence L. for a past whole-genome duplication event by means conserved gene synteny Pomacea canaliculata genome, only one available at chromosome level Caenogastropoda. was further confirmed presence duplicated hox cluster. Key gastropod biology including those proteins related development, shell formation, sex genome. Conclusions new high-quality should become reference assembling analyzing will contribute future genomic studies among animals.

Language: Английский

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Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine

Cell Genomics, Journal Year: 2023, Volume and Issue: 3(8), P. 100348 - 100348

Published: June 25, 2023

The annotation of microRNAs depends on the availability transcriptomics data and expert knowledge. This has led to a gap between novel genomes high-quality microRNA complements. Using >16,000 from manually curated gene database MirGeneDB, we generated trained covariance models for all conserved families. These are available in our tool MirMachine, which annotates within genomes. We successfully applied MirMachine range animal species, including those with large genome duplications extinct where small RNA sequencing is hard achieve. further describe score expected that can be used assess completeness assemblies. closes long-persisting field by facilitating automated pipelines deeper studies into evolution regulation, even organisms.

Language: Английский

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The genome of the colonial hydroidHydractiniareveals that their stem cells use a toolkit of evolutionarily shared genes with all animals

Genome Research, Journal Year: 2024, Volume and Issue: unknown

Published: March 20, 2024

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

Language: Английский

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Homeotic Genes: Clustering, Modularity, and Diversity

Frontiers in Cell and Developmental Biology, Journal Year: 2021, Volume and Issue: 9

Published: Aug. 11, 2021

Hox genes code for transcription factors and are evolutionarily conserved. They regulate a plethora of downstream targets to define the anterior-posterior (AP) body axis developing bilaterian embryo. Early work suggested possible role clustering ordering their expression in spatially restricted manner along AP axis. However, recent availability many genome assemblies different organisms uncovered several examples that defy this constraint. With advancements genomics, current review discusses arrangement various organisms. Further, we revisit discovery regulation Drosophila melanogaster . We also arthropods vertebrates, with significant focus on crustacean Parahyale hawaiensis It is noteworthy subtle changes levels gene can contribute development novel features an organism. We, therefore, delve into distinct these during primary formation, segment identity, extra-embryonic roles such as formation hair follicles or misregulation leading cancer. Toward end each section, emphasize possibilities experiments involving organisms, owing field genomics CRISPR-based engineering. Overall, present holistic view functioning animal world.

Language: Английский

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Genome of the ramshorn snail Biomphalaria straminea-an obligate intermediate host of schistosomiasis.

PubMed, Journal Year: 2022, Volume and Issue: 11

Published: Feb. 15, 2022

Schistosomiasis, or bilharzia, is a parasitic disease caused by trematode flatworms of the genus Schistosoma. Infection Schistosoma mansoni in humans results when cercariae emerge into water from freshwater snails Biomphalaria and seek out penetrate human skin. The snail straminea native to South America now also present Central China, represents potential vector host for spreading schistosomiasis. To date, genomic information restricted neotropical species glabrata. This limits understanding biology management other schistosomiasis vectors, such as B. straminea.Using combination Illumina short-read, 10X Genomics linked-read, Hi-C sequencing data, our 1.005 Gb genome assembly high contiguity, with scaffold N50 25.3 Mb. Transcriptomes adults were obtained. Developmental homeobox genes, hormonal stress-response genes identified, repeat content was annotated (40.68% content). Comparisons mollusc genomes (including Gastropoda, Bivalvia, Cephalopoda) revealed syntenic conservation, patterns gene linkage indicative evolutionary changes clusters, expansion heat shock protein presence sesquiterpenoid cholesterol metabolic pathway Gastropoda. In addition, hormone treatment together RT-qPCR assay reveal responsive system straminea, illustrating that this renowned insect lophotrochozoan lineage.This study provides first offers an unprecedented opportunity address variety phenomena related vectors schistosomiasis, well genomics questions molluscs more widely.

Language: Английский

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Differential microRNA expression, microRNA arm switching, and microRNA:long noncoding RNA interaction in response to salinity stress in soybean

BMC Genomics, Journal Year: 2022, Volume and Issue: 23(1)

Published: Jan. 20, 2022

Abstract Background Soybean is a major legume crop with high nutritional and environmental values suitable for sustainable agriculture. Noncoding RNAs (ncRNAs), including microRNAs (miRNAs) long noncoding (lncRNAs), are important regulators of gene functions in eukaryotes. However, the interactions between these two types ncRNAs context plant physiology, especially response to salinity stress, poorly understood. Results Here, we challenged cultivated soybean accession (C08) wild one (W05) salt treatment obtained their small RNA transcriptomes at six time points from both root leaf tissues. In addition thoroughly analyzing differentially expressed miRNAs, also documented first case miRNA arm-switching (miR166m), swapping dominant arm expression, different Two arms miR166m target genes related stress (chloroplastic beta-amylase 1 targeted by miR166m-5p calcium-dependent protein kinase miR166m-3p), suggesting play roles stress. Furthermore, pairs miRNA:lncRNA interacting partners (miR166i-5p lncRNA Gmax_MSTRG.35921.1; miR394a-3p Gmax_MSTRG.18616.1) were discovered reaction Conclusions This study demonstrates how ncRNA involves responses switching interactions. The behaviors revealed this will shed new light on molecular regulatory mechanisms plants, hence provide potential strategies improvement.

Language: Английский

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