Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny

Zimmermann, Bob; Robb, Sofia; Genikhovich, Grigory; Fropf, Whitney J.; Weilguny, Lukas; He, Shuonan; Chen, Cheng-Yi; Lovegrove-Walsh, Jessica; Hill, Eric M.; Ragkousi, Katerina; Praher, Daniela; Fredman, David; Moran, Yehu; Gibson, Matthew C.; Technau, Ulrich

doi:10.1101/2020.10.30.359448

Cited by 56 publications

(79 citation statements)

References 172 publications

(160 reference statements)

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“…In contrast to the hundreds of published chromosome-scale genome assemblies from vertebrates and other bilterians, there are currently only three from nonbilaterian animals: the freshwater sponge Ephydatia ( Kenny et al 2020 ), the cnidarian Rhopilema ( Li et al 2020 ; Nong et al 2020 ), and the cnidarian Nematostella ( Zimmermann et al 2020 ). The disparity in the number of bilaterian versus nonbilaterian chromosome-scale assemblies can be partly explained by the difficulties of isolating nucleic acids from nonbilaterians ( Dawson et al 1998 ; Simister et al 2011 ).…”

Section: Introductionmentioning

confidence: 99%

A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis

Schultz

Francis

McBroome

et al. 2021

G3 Genes|Genomes|Genetics

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Here, we present a karyotype, a chromosome-scale genome assembly, and a genome annotation from the ctenophore Hormiphora californensis (Ctenophora: Cydippida: Pleurobrachiidae). The assembly spans 110 Mb in 44 scaffolds and 99.47% of the bases are contained in 13 scaffolds. Chromosome micrographs and Hi-C heatmaps support a karyotype of 13 diploid chromosomes. Hi-C data reveal three large heterozygous inversions on chromosome 1, and one heterozygous inversion shares the same gene order found in the genome of the ctenophore Pleurobrachia bachei. We find evidence that H. californensis and P. bachei share thirteen homologous chromosomes, and the same karyotype of 1n = 13. The manually curated PacBio Iso-Seq-based genome annotation reveals complex gene structures, including nested genes and trans-spliced leader sequences. This chromosome-scale assembly is a useful resource for ctenophore biology and will aid future studies of metazoan evolution and phylogenetics.

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Section: Introductionmentioning

confidence: 99%

A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis

Schultz

Francis

McBroome

et al. 2021

G3 Genes|Genomes|Genetics

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“…Candidate genes were identified using in-depth literature searches, published N. vectensis egg proteome 51 and transcriptome 37 datasets as well as BLAST of the publicly available genome 66,67 . Orthology was confirmed by reciprocal pBLAST using the NCBI BLAST platform (http://www.ncbi.nlm.nih.gov/blast/) and phylogenetic analyses.…”

Section: Methodsmentioning

confidence: 99%

Evolutionary conserved aspects of animal nutrient uptake and transport in sea anemone vitellogenesis

Lebouvier

Miramón-Puértolas

Steinmetz

2022

Preprint

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Vitellogenesis, the accumulation of egg yolk, relies on the transport of dietary nutrients from the gut to the ovary through the circulatory system in many bilaterians (e.g. vertebrates, arthropods). How these dietary nutrients and yolk precursors are absorbed and transported in cnidarians (e.g. corals, sea anemones, jellyfish), which are bi-layered and lack a circulatory system, is however only poorly understood. Here, we studied the tissues and molecules that facilitate the uptake and transport of dietary nutrients, especially lipids, towards the oocytes in the sea anemone Nematostella vectensis to better understand the evolution of systemic nutrient transport in animals. We identified the somatic gonad epithelium as one of several gastrodermal tissues specialized in phagocytosis, micropinocytosis and intracellular digestion. We showed more specifically that dietary fatty acids are absorbed by the ApolipoproteinB- and Vitellogenin-expressing somatic gonad epithelium. Their subsequent, rapid transport into the extracellular matrix (ECM) and endocytosis into oocytes is likely mediated by an evolutionary conserved Vitellogenin (Vtg)-Very Low-Density Lipoprotein Receptor (VLDLR) ligand/receptor pair. We propose that ECM-based, Vtg/VLDLR-mediated lipoprotein transport during vitellogenesis predates the cnidarian-bilaterian split and provided a mechanistic basis to evolve sophisticated circulatory systems in bilaterians.

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“…RNA Pol II was detected at putative enhancers in N. vectensis , suggestive of enhancer-promoter looping ( Schwaiger et al, 2014 ). Cnidarians typically do not encode orthologs of the chromatin organizers CTCF ( Heger et al, 2012 ; Zimmermann et al, 2020 ) and SATB1/2 (current analysis) family proteins. There is evidence to suggest that CTCF-less genomes do not form TADs, which are recurring chromatin domains first evidenced by Hi-C data ( Dixon et al, 2012 ; Kenny et al, 2020 ).…”

Section: Chromatin Organizationmentioning

confidence: 96%

Epigenetic Regulation in Hydra: Conserved and Divergent Roles

Pillai

Gungi

Reddy

et al. 2021

Front. Cell Dev. Biol.

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Transitions in gene regulatory processes responsible for the emergence of specialized cell types and spatiotemporal regulation of developmental signaling prior to the divergence of Cnidaria and Bilateria are poorly understood. As a sister group of Bilateria, the phylum Cnidaria can provide significant insights into these processes. Among the cnidarians, hydrae have been studied for >250 years to comprehend the mechanisms underlying their unique immortality and robust regenerative capacity. Studies on Hydra spp. and other pre-bilaterians alike have advanced our understanding of the evolutionary underpinnings governing eumetazoan tissue development, homeostasis, and regeneration. In addition to its regenerative potential, Hydra exhibits continuously active axial patterning due to its peculiar tissue dynamics. These distinctive physiological processes necessitate large scale gene expression changes that are governed by the multitude of epigenetic mechanisms operating in cells. This review highlights the contemporary knowledge of epigenetic regulation in Hydra with contemporary studies from other members of Cnidaria, as well as the interplay between regulatory mechanisms wherever demonstrated. The studies covered in the scope of this review reveal both ancestral and divergent roles played by conserved epigenetic mechanisms with emphasis on transcriptional regulation. Additionally, single-cell transcriptomics data was mined to predict the physiological relevance of putative gene regulatory components, which is in agreement with published findings and yielded insights into the possible functions of the gene regulatory mechanisms that are yet to be deciphered in Hydra, such as DNA methylation. Finally, we delineate potentially rewarding epigenetics research avenues that can further leverage the unique biology of Hydra.

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Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny

Cited by 56 publications

References 172 publications

A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis

A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis

Evolutionary conserved aspects of animal nutrient uptake and transport in sea anemone vitellogenesis

Epigenetic Regulation in Hydra: Conserved and Divergent Roles

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