Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri

Kenny, Nathan J.; Francis, Warren R.; Rivera‐Vicéns, Ramón E.; Juravel, Ksenia; Mendoza, Alex de; Díez‐Vives, Cristina; Lister, Ryan; Bezares-Calderón, Luis A; Grombacher, Lauren; Roller, Maša; Barlow, Lael D.; Camilli, Sara; Ryan, Joseph F.; Wörheide, Gert; Hill, Andrew P.; Riesgo, Ana; Leys, Sally P.

doi:10.1038/s41467-020-17397-w

Cited by 77 publications

(48 citation statements)

References 68 publications

(94 reference statements)

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“…To our knowledge, only one other study has addressed the higher-order chromosomal organization in a non-bilaterian [24]. In this work, Kenny and colleagues searched for TADs in their chromosome-level assembly of the sponge E. muelleri.…”

Section: Sea Anemone Genomes Lack Evidence For Topologically Associatmentioning

confidence: 99%

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Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny

Zimmermann

Robb

Genikhovich

et al. 2020

Preprint

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Cnidaria (sea anemones, jellyfish, corals and hydra) form a close sister group to Bilateria. Within this clade, the sea anemone Nematostella vectensis has emerged as a slow evolving model for investigating characteristics of the cnidarian-bilaterian common ancestor, which diverged near the Cambrian explosion. Here, using long read sequencing and high throughput chromosome conformation capture, we generate high quality chromosome-level genome assemblies for N. vectensis and the closely related edwardsiid sea anemone, Scolanthus callimorphus. In both cases we find a robust set of 15 chromosomes comprising a stable linkage group detectable within all major clades of sequenced cnidarian genomes. Further, both genomes show remarkable chromosomal conservation with chordates. In contrast with Bilateria, we report that extended Hox and NK gene clusters are chromosomally linked but do not retain a tight spatial conservation. Accordingly, there is a lack of evidence for topologically associated domains, which have been implicated in the evolutionary pressure to retain tight microsyntenic gene clusters. We also uncover ultra-conserved noncoding elements at levels previously undetected in non-chordate lineages. Both genomes are accessible through an actively updated genome browser and database at https://simrbase.stowers.org

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Section: Sea Anemone Genomes Lack Evidence For Topologically Associatmentioning

confidence: 99%

“…BUSCOs found in genomes obtained from previous studies [10,14,19,23,24,64,65,[104][105][106][107][108][109] were used to generate multiple alignments. Genes were aligned with mafft version 7.427 using the E-INS-i model and a maximum 1000 refinement iterations [22].…”

Section: Divergence Estimatesmentioning

confidence: 99%

Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny

Zimmermann

Robb

Genikhovich

et al. 2020

Preprint

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“…In order to gain a better understanding of the evolutionary fate of RLRs and the position of N. vectensis homologs within the family of these viral nucleic acid sensors, we reconstructed previous phylogenetic trees with an addition of numerous recently available sequences. Instead of including other distantly related DExD/H helicases, such as RNA-specific endoribonuclease Dicer or elongation initiation factor 4A (eIF4A), we performed phylogenetic analysis exclusively of RLRs with the sequences of sponges, one of the first two metazoan phyla to diverge 31,32 , set as an outgroup ( Fig. 1a ).…”

Section: Resultsmentioning

confidence: 99%

Functional characterization of the cnidarian antiviral immune response reveals ancestral complexity

Lewandowska

Sharoni

Admoni

et al. 2020

Preprint

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Animals developed a broad repertoire of innate immune sensors and downstream effector cascades for defense against RNA viruses. Yet, this system highly varies between different bilaterian animals, masking its ancestral state. In this study we aimed to characterize the antiviral immune response of the cnidarian Nematostella vectensis and decipher the function of the retinoic acid-inducible gene I-like receptors (RLRs) known to detect viral double-stranded RNA (dsRNA) in bilaterians, but activate different antiviral pathways in vertebrates and nematodes. We show that a mimic of long viral dsRNA triggers a complex antiviral immune response bearing features distinctive for both vertebrate and invertebrate systems. Furthermore, the results of affinity assays and knockdown experiments provide functional evidence for the conserved role of RLRs in initiating immune response to dsRNA that originated before the cnidarian-bilaterian split and lay a strong foundation for future research on the evolution of the immune responses to RNA viruses.

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“…Eukaryotic species were selected for based on factors including importance as experimental organisms, phylogenetic diversity and sequence/assembly quality. This included recently published sequence data from the protozoan alga Euglena gracilis [ 36 ] and the freshwater sponge Ephydatia muelleri [ 37 ]. Details regarding all genomic and transcriptomic data sources are provided in Table S1.…”

Section: Methodsmentioning

confidence: 99%

Evolution and diversification of the nuclear envelope

Padilla-Mejía

Макаров

Barlow

et al. 2021

Nucleus

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Eukaryotic cells arose ~1.5 billion years ago, with the endomembrane system a central feature, facilitating evolution of intracellular compartments. Endomembranes include the nuclear envelope (NE) dividing the cytoplasm and nucleoplasm. The NE possesses universal features: a double lipid bilayer membrane, nuclear pore complexes (NPCs), and continuity with the endoplasmic reticulum, indicating common evolutionary origin. However, levels of specialization between lineages remains unclear, despite distinct mechanisms underpinning various nuclear activities. Several distinct modes of molecular evolution facilitate organellar diversification and to understand which apply to the NE, we exploited proteomic datasets of purified nuclear envelopes from model systems for comparative analysis. We find enrichment of core nuclear functions amongst the widely conserved proteins to be less numerous than lineage-specific cohorts, but enriched in core nuclear functions. This, together with consideration of additional evidence, suggests that, despite a common origin, the NE has evolved as a highly diverse organelle with significant lineage-specific functionality.

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Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri

Cited by 77 publications

References 68 publications

Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny

Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny

Functional characterization of the cnidarian antiviral immune response reveals ancestral complexity

Evolution and diversification of the nuclear envelope

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