Independent Innexin Radiation Shaped Signaling in Ctenophores

Ctenophores and parahoxozoans independently evolved functionally diverse voltage-gated K+ channels

The ctenophore species Mnemiopsis leidyi is known to have a large set of voltage-gated K+ channels, but little is known about the functional diversity of these channels or their evolutionary history in other ctenophore species. Here, we searched the genomes of two additional ctenophore species, Beroe ovata and Hormiphora californensis, for voltage-gated K+ channels and functionally expressed a subset of M. leidyi channels. We found that the last common ancestor of these three disparate ctenophore lineages probably had at least 33 voltage-gated K+ channels. Two of these genes belong to the EAG family, and the remaining 31 belong to the Shaker family and form a single clade within the animal/choanoflagellate Shaker phylogeny. We additionally found evidence for 10 of these Shaker channels in a transcriptome of the early branching ctenophore lineage Euplokamis dunlapae, suggesting that the diversification of these channels was already underway early in ctenophore evolution. We functionally expressed 16 Mnemiopsis Shakers and found that they encode a diverse array of voltage-gated K+ conductances with functional orthologs for many classic Shaker family subtypes found in cnidarians and bilaterians. Analysis of Mnemiopsis transcriptome data show these 16 Shaker channels are expressed in a wide variety of cell types, including neurons, muscle, comb cells, and colloblasts. Ctenophores therefore appear to have independently evolved much of the voltage-gated K+ channel diversity that is shared between cnidarians and bilaterians.

Temporal changes in the transcriptome profile of Macrobrachium rosenbergii in response to decapod iridescent virus 1 infection

The farming of Macrobrachium rosenbergii faces significant challenges due to infections caused by Decapod iridovirus 1 (DIV1). To gain deeper insights into the dynamic immune regulatory processes of M. rosenbergii in response to DIV1 infection, RNA sequencing (RNA-seq) was employed to profile the transcriptome in the hepatopancreas at 24, 48, 72, and 96 hours post-infection (hpi). Time-course analysis revealed 3,339 differentially expressed genes (DEGs), which exhibited distinct expression patterns across various stages of infection. At 24 hpi and 48 hpi, the top 20 enriched pathways included 3 immunity-related pathways (Lysosome, Phagosome, C-type lectin receptor signaling) and 7 metabolism-related pathways at 24 hpi, and 5 metabolism-related pathways at 48 hpi. In contrast, in the later stages of infection (72 hpi), 13 of the top 17 enriched pathways associated with DEGs were metabolism-related, including those involved in antioxidant defense, such as the Peroxisome, Cysteine and methionine metabolism, and Glutathione metabolism. At 96 hpi, pathways related to ECM-receptor interaction, Purine metabolism, and Lysosome were significantly enriched. Among the DEGs, a total of 16 genes were consistently identified across all time points, with 14 of these genes, including alpha-2-macroglobulin-like, alpha-amylase 1-like, putative aldolase class 2 protein PA3430, platelet-derived growth factor subunit B-like, serum amyloid A-5 protein-like, phenoloxidase-activating enzyme-like, pantetheinase-like, and perlucin-like protein, demonstrating sustained upregulation at all time points. In contrast, the gene encoding rhodanese domain-containing protein CG4456-like was consistantly downregulated. Additionally, weighted gene co-expression network analysis (WGCNA) indicated several hub genes that were tightly connected to intercellular communication, such as innexin shaking-B-like and innexin inx3-like, and endochitinase A1-like. The gene expression changes varied over time, exhibiting a dynamic, time-dependent pattern that underscores the complexity of host-pathogen interactions. These results provide new insights into the cellular mechanisms influenced by DIV1 throughout the infection process, offering valuable knowledge for developing virus control strategies in shrimp aquaculture.

Light sensitivity in Beroidae ctenophores: Insights from laboratory studies and genomics

Light detection underlies a variety of animal behaviors, including those related to spatial orientation, feeding, avoidance of predators, and reproduction. Ctenophores are likely the oldest animal group in which light sensitivity based on opsins evolved, so they may still have the ancestral molecular mechanisms for photoreception. However, knowledge about ctenophore photosensitivity, associated morphological structures, molecular mechanisms involved, and behavioral reactions is limited and fragmented. We present the initial experiments on the responses of adult Beroe ovata to high-intensity light exposure with different spectra and photosensitivity in various parts of the animal's body. Ctenophores have shown a consistent behavioral response when their aboral organ is exposed to a household-grade laser in the violet spectrum. To investigate the genes responsible for the photosensitivity of Beroidae, we have analyzed transcriptome and genome-wide datasets. We identified three opsins in Beroe that are homologous to those found in Mnemiopsis leidyi (Lobata) and Pleurobrachia bachei (Cydippida). These opsins form clades Ctenopsin1, 2, and 3, respectively. Ctenopsin3 is significantly distinct from other ctenophore opsins and clustered outside the main animal opsin groups. The Ctenopsin1 and Ctenopsin2 groups are sister clusters within the canonical animal opsin tree. These two groups could have originated from gene duplication in the common ancestor of the species we studied and then developed independently in different lineages of Ctenophores. So far, there is no evidence of additional expansion of the opsin family in ctenophore evolution. The involvement of ctenophore opsins in photoreception is discussed by analyzing their protein structures.

Evolutionary origin of the nervous system from Ctenophora prospective

Nervous system is one of the key adaptations underlying the evolutionary success of the majority of animal groups. Ctenophores (or comb jellies) are gelatinous marine invertebrates that were probably the first lineage to diverge from the rest of animals. Due to the key phylogenetic position and multiple unique adaptations, the noncentralized nervous system of comb jellies has been in the center of the debate around the origin of the nervous system in the animal kingdom and whether it happened only once or twice. Here, we discuss the latest findings in ctenophore neuroscience and multiple challenges on the way to build a clear evolutionary picture of the origin of the nervous system.

Morphological and dietary changes encoded in the genome of Beroe ovata, a ctenophore-eating ctenophore

As the sister group to all other animals, ctenophores (comb jellies) are important for understanding the emergence and diversification of numerous animal traits. Efforts to explore the evolutionary processes that promoted diversification within Ctenophora are hindered by undersampling genomic diversity within this clade. To address this gap, we present the sequence, assembly and initial annotation of the genome of Beroe ovata. Beroe possess unique morphology, behavior, ecology and development. Unlike their generalist carnivorous kin, beroid ctenophores feed exclusively on other ctenophores. Accordingly, our analyses revealed a loss of chitinase, an enzyme critical for the digestion of most non-ctenophore prey, but superfluous for ctenophorivores. Broadly, our genomic analysis revealed that extensive gene loss and changes in gene regulation have shaped the unique biology of B. ovata. Despite the gene losses in B. ovata, our phylogenetic analyses on photosensitive opsins and several early developmental regulatory genes show that these genes are conserved in B. ovata. This additional sampling contributes to a more complete reconstruction of the ctenophore ancestor and points to the need for extensive comparisons within this ancient and diverse clade of animals. To promote further exploration of these data, we present BovaDB (http://ryanlab.whitney.ufl.edu/bovadb/), a portal for the B. ovata genome.

Syncytial nerve net in a ctenophore adds insights on the evolution of nervous systems

A fundamental breakthrough in neurobiology has been the formulation of the neuron doctrine by Santiago Ramón y Cajal, which stated that the nervous system is composed of discrete cells. Electron microscopy later confirmed the doctrine and allowed the identification of synaptic connections. In this work, we used volume electron microscopy and three-dimensional reconstructions to characterize the nerve net of a ctenophore, a marine invertebrate that belongs to one of the earliest-branching animal lineages. We found that neurons in the subepithelial nerve net have a continuous plasma membrane that forms a syncytium. Our findings suggest fundamental differences of nerve net architectures between ctenophores and cnidarians or bilaterians and offer an alternative perspective on neural network organization and neurotransmission.