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.

Evolution of glial cells: a non-bilaterian perspective.

Nervous systems of bilaterian animals generally consist of two cell types: neurons and glial cells. Despite accumulating data about the many important functions glial cells serve in bilaterian nervous systems, the evolutionary origin of this abundant cell type remains unclear. Current hypotheses regarding glial evolution are mostly based on data from model bilaterians. Non-bilaterian animals have been largely overlooked in glial studies and have been subjected only to morphological analysis. Here, we provide a comprehensive overview of conservation of the bilateral gliogenic genetic repertoire of non-bilaterian phyla (Cnidaria, Placozoa, Ctenophora, and Porifera). We overview molecular and functional features of bilaterian glial cell types and discuss their possible evolutionary history. We then examine which glial features are present in non-bilaterians. Of these, cnidarians show the highest degree of gliogenic program conservation and may therefore be crucial to answer questions about glial evolution.

Parallel Evolution of Transcription Factors in Basal Metazoans.

Transcription factors (TFs) play a pivotal role as regulators of gene expression, orchestrating the formation and maintenance of diverse animal body plans and innovations. However, the precise contributions of TFs and the underlying mechanisms driving the origin of basal metazoan body plans, particularly in ctenophores, remain elusive. Here, we present a comprehensive catalog of TFs in 2 ctenophore species, Pleurobrachia bachei and Mnemiopsis leidyi, revealing 428 and 418 TFs in their respective genomes. In contrast, morphologically simpler metazoans have a reduced TF representation compared to ctenophores, cnidarians, and bilaterians: the sponge Amphimedon encodes 277 TFs, and the placozoan Trichoplax adhaerens encodes 274 TFs. The emergence of complex ctenophore tissues and organs coincides with significant lineage-specific diversification of the zinc finger C2H2 (ZF-C2H2) and homeobox superfamilies of TFs. Notable, the lineages leading to Amphimedon and Trichoplax exhibit independent expansions of leucine zipper (BZIP) TFs. Some lineage-specific TFs may have evolved through the domestication of mobile elements, thereby supporting alternative mechanisms of parallel TF evolution and body plan diversification across the Metazoa.

Expression and Functional Analysis of Ctenophore Glutamate Receptor Genes.

The functional analysis of ctenophore neurotransmitter receptors, transporters, and ion channels can be greatly simplified by use of heterologous expression systems. Heterologous expression allows the characterization of individual membrane proteins, expressed at high levels in cells, where background activity by endogenous ion channels and transporters is with few exceptions minimal. The goal of such experiments is to gain an in-depth understanding of the behavior and regulation of individual molecular species, which is challenging in native tissue, but especially so in the case of ctenophores and other marine organisms. Coupled with transcriptome analysis, and immunohistochemical studies of receptor expression in vivo, experiments with heterologous expression systems can provide valuable insight into cellular activity, prior to more challenging functional studies on native tissues.

Ctenophora: Illustrated Guide and Taxonomy.

Ctenophores or comb jellies represent the first diverging lineage of extant animals - sister to all other Metazoa. As a result, they occupy a unique place in the biological sciences. Despite their importance, this diverse group of marine predators has remained relatively poorly known, with both the species and higher-level taxonomy of the phylum in need of attention. We present a checklist of the phylum based on a review of the current taxonomic literature and illustrate their diversity with images. The current classification presented remains substantially in conflict with recent phylogenetic results, and many of the taxa are not monophyletic or untested. This chapter summarizes the existing classification focusing on recognized families and genera with 185 currently accepted, extant species listed. We provide illustrative examples of ctenophore diversity covering all but one of the 33 families and 47 of the 48 genera, as well as about 25-30 undescribed species. We also list the 14 recognized ctenophore fossil species and note others that have been controversially attributed to the phylum. Analyses of unique ctenophore adaptations are critical to understanding early animal evolution and adaptive radiation of this clade of basal metazoans.

Gene Expression Patterns in the Ctenophore Pleurobrachia bachei: In Situ Hybridization.

In situ hybridization is a powerful and precise tool for revealing cell- and tissue-specific gene expression and a critical approach to validating single-cell RNA-seq (scRNA-seq). However, applying it to highly fragile animals such as ctenophores is challenging. Here, we present an in situ hybridization protocol for adult Pleurobrachia bachei (Cydippida)-a notable reference species representing the earliest-branching metazoan lineage, Ctenophora, sister to the rest of Metazoa. We provided expression patterns for several markers of cell phenotypes, as illustrated examples. The list includes predicted small secretory molecules/neuropeptides, WntX, genes encoding RNA-binding proteins (Musashi, Elav, Dicer, Argonaut), Neuroglobin, and selected transcription factors such as BarX. Both cell- and organ-specific expression of these genes further support the convergent evolution of many ctenophore innovations, which are remarkably distinct from tissue and organ specification in other basal metazoan lineages.

DNA Isolation Long-Read Genomic Sequencing in Ctenophores.

Long-read sequencing has proven the necessity for high-quality genomic assemblies of reference species, including enigmatic ctenophores. Obtaining high-molecular-weight genomic DNA is pivotal to this process and has proven highly problematic for many species. Here, we discuss different methodologies for gDNA isolation and present a protocol for isolating gDNA for several members of the phylum Ctenophora. Specifically, we describe a Pacific Biosciences library construction method used in conjunction with gDNA isolation methods that have proven successful in obtaining high-quality genomic assemblies in ctenophores.

Expression, Purification, and Determination of Sensitivity to Calcium Ions of Ctenophore Photoproteins.

Light-sensitive Ca2+-regulated photoproteins of ctenophores are single-chain polypeptide proteins of 206-208 amino acids in length comprising three canonical EF-hand Ca2+-binding sites, each of 12 contiguous residues. These photoproteins are a stable complex of apoprotein and 2-hydroperoxy adduct of coelenterazine. Addition of calcium ions to photoprotein is only required to trigger bright bioluminescence. However, in contrast to the related Ca2+-regulated photoproteins of jellyfish their capacity to bioluminescence disappears on exposure to light over the entire absorption spectral range of ctenophore photoproteins. Here, we describe protocols for expression of gene encoding ctenophore photoprotein in Escherichia coli cells, obtaining of the recombinant apoprotein of high purity and its conversion into active photoprotein with synthetic coelenterazine as well as determination of its sensitivity to calcium ions using light-sensitive Ca2+-regulated photoprotein berovin from ctenophore Beroe abyssicola as an illustrative case.

RNA Isolation from Ctenophores.

RNA-seq or transcriptome analysis of individual cells and small cell populations is essential for virtually any biomedical field. Here, we examine and discuss the different methods of RNA isolation specific to ctenophores. We present a convenient, inexpensive, and reproducible protocol for RNA-seq libraries that are designed for low quantities of samples. We demonstrated these methods on early (one, two, four, eight cells) embryonic and developmental stages, tissues, and even a single aboral organ from the ctenophore Pleurobrachia bachei and other ctenophore species (e.g., Mnemiopsis, Bolinopsis, and Beroe).

Characterization of the Mitochondrial Proteome in the Ctenophore Mnemiopsis leidyi Using MitoPredictor.

Mitochondrial proteomes have been experimentally characterized for only a handful of animal species. However, the increasing availability of genomic and transcriptomic data allows one to infer mitochondrial proteins using computational tools. MitoPredictor is a novel random forest classifier, which utilizes orthology search, mitochondrial targeting signal (MTS) identification, and protein domain content to infer mitochondrial proteins in animals. MitoPredictor's output also includes an easy-to-use R Shiny applet for the visualization and analysis of the results. In this article, we provide a guide for predicting and analyzing the mitochondrial proteome of the ctenophore Mnemiopsis leidyi using MitoPredictor.

Gap Junctions in Ctenophora.

Gap junction proteins form specialized intercellular communication channels, including electrical synapses, that regulate cellular metabolism and signaling. We present a molecular inventory of the gap junction proteins-innexins (INX-like) in ctenophores, focusing on two reference species, Pleurobrachia bachei and Mnemiopsis leidyi. Innexins were identified in more than 15 ctenophore species, including such genera as Euplokamis, Pukia, Hormiphora, Bolinopsis, Cestum, Ocyropsis, Dryodora, Beroe, benthic ctenophores, Coeloplana and Vallicula, and undescribed species of Mertensiidae. The observed diversity of innexins resulted from the independent expansion of this family from the common ancestor of ctenophores. Innexins show the conserved topology with four transmembrane domains connected by two extracellular loops, which bridge intracellular gaps. However, INX-like genes have highly diverse exon organization and low percentage identity for their amino acid sequences within the same species and between ctenophore species. Such a broad scope of molecular diversity differs from innexins in other phyla. We predicted posttranslational modifications in innexins: 249 and 188 for M. leidyi and P. bachei, respectively. Neither their number nor their locations were conserved within or between species. When the number of posttranslational modifications is factored into the innexins' radiation, the potential for molecular and physiological diversity within gap junctions of ctenophores is almost unfathomable. RNA-seq and in situ hybridization data revealed that innexins are expressed across embryogenesis, including early cleavage stages and gastrulation. They are abundant in all adult tissues, with the highest expression level in the aboral organ (the major integrative center and the gravity sensor in ctenophores), followed by tentacles and comb plates. Nevertheless, each organ and tissue has a unique combination of innexins, suggesting their involvement in complex integrative functions and behaviors of ctenophores.

Functional Screening of cDNA Expression Library for Novel Ctenophore Photoproteins.

The functional screening of cDNA libraries (or functional cloning) enables isolation of cDNA genes encoding novel proteins with unknown amino acid sequences. This approach is the only way to identify a protein sequence in the event of shortage of biological material for obtaining pure target protein in amounts sufficient to determine its primary structure, since sensitive functional test for a target protein is only required to successfully perform functional cloning. Commonly, bioluminescent proteins from representatives belonging to different taxa significantly differ in sequences due to independent origin of bioluminescent systems during evolution. Nonetheless, these proteins are frequently similar in functions and can use even the same substrate of bioluminescence reaction, allowing the use of the same functional test for screening. The cDNA genes encoding unknown light-emitting proteins can be identified during functional screening with high sensitivity, which is provided by modern light recording equipment making possible the detection of a very small amount of a target protein. Here, we present the protocols for isolation of full-size cDNA genes for the novel bioluminescent protein family of light-sensitive Ca2+-regulated photoproteins in the absence of any sequence information by functional screening of plasmid cDNA expression library. The protocols describe all the steps from gathering animals to isolation of individual E. coli colonies carrying full-size cDNA genes using photoprotein berovin from ctenophore Beroe abyssicola as an illustrative example.

DNA Methylation in Ctenophores.

Epigenomic regulation and dynamic DNA methylation, in particular, are widespread mechanisms orchestrating the genome operation across time and species. Whole-genome bisulfite sequencing (WGBS) is currently the only method for unbiasedly capturing the presence of 5-methylcytosine (5-mC) DNA methylation patterns across an entire genome with single-nucleotide resolution. Bisulfite treatment converts unmethylated cytosines to uracils but leaves methylated cytosines intact, thereby creating a map of all methylated cytosines across a genome also known as a methylome. These epigenomic patterns of DNA methylation have been found to regulate gene expression and influence gene evolution rates between species. While protocols have been optimized for vertebrate methylome production, little adaptation has been done for invertebrates. Creating a methylome reference allows comparisons to be made between rates of transcription and epigenomic patterning in animals. Here we present a method of library construction for bisulfite sequencing optimized for non-bilateral metazoans such as the ctenophore, Mnemiopsis leidyi. We have improved upon our previously published method by including spike-in genomic DNA controls to measure methylation conversion rates. By pooling two bisulfite conversion reactions from the same individual, we also produced sequencing libraries that yielded a higher percentage of sequenced reads uniquely mapping to the reference genome. We successfully detected 5-mC in whole-animal methylomes at CpG, CHG, and CHH sites and visualized datasets using circos diagrams. The proof-of-concept tests were performed both under control conditions and following injury tests with changes in methylation patterns of genes encoding innexins, toxins and neuropeptides. Our approach can be easily adapted to produce epigenomes from other fragile marine animals.

Ocean to Tree: Leveraging Single-Molecule RNA-Seq to Repair Genome Gene Models and Improve Phylogenomic Analysis of Gene and Species Evolution.

Understanding gene evolution across genomes and organisms, including ctenophores, can provide unexpected biological insights. It enables powerful integrative approaches that leverage sequence diversity to advance biomedicine. Sequencing and bioinformatic tools can be inexpensive and user-friendly, but numerous options and coding can intimidate new users. Distinct challenges exist in working with data from diverse species but may go unrecognized by researchers accustomed to gold-standard genomes. Here, we provide a high-level workflow and detailed pipeline to enable animal collection, single-molecule sequencing, and phylogenomic analysis of gene and species evolution. As a demonstration, we focus on (1) PacBio RNA-seq of the genome-sequenced ctenophore Mnemiopsis leidyi, (2) diversity and evolution of the mechanosensitive ion channel Piezo in genetic models and basal-branching animals, and (3) associated challenges and solutions to working with diverse species and genomes, including gene model updating and repair using single-molecule RNA-seq. We provide a Python Jupyter Notebook version of our pipeline (GitHub Repository: Ctenophore-Ocean-To-Tree-2023 https://github.com/000generic/Ctenophore-Ocean-To-Tree-2023 ) that can be run for free in the Google Colab cloud to replicate our findings or modified for specific or greater use. Our protocol enables users to design new sequencing projects in ctenophores, marine invertebrates, or other novel organisms. It provides a simple, comprehensive platform that can ease new user entry into running their evolutionary sequence analyses.

Brief History of Ctenophora.

Ctenophores are the descendants of the earliest surviving lineage of ancestral metazoans, predating the branch leading to sponges (Ctenophore-first phylogeny). Emerging genomic, ultrastructural, cellular, and systemic data indicate that virtually every aspect of ctenophore biology as well as ctenophore development are remarkably different from what is described in representatives of other 32 animal phyla. The outcome of this reconstruction is that most system-level components associated with the ctenophore organization result from convergent evolution. In other words, the ctenophore lineage independently evolved as high animal complexities with the astonishing diversity of cell types and structures as bilaterians and cnidarians. Specifically, neurons, synapses, muscles, mesoderm, through gut, sensory, and integrative systems evolved independently in Ctenophora. Rapid parallel evolution of complex traits is associated with a broad spectrum of unique ctenophore-specific molecular innovations, including alternative toolkits for making an animal. However, the systematic studies of ctenophores are in their infancy, and deciphering their remarkable morphological and functional diversity is one of the hot topics in biological research, with many anticipated surprises.

Extracellular DNA traps in a ctenophore demonstrate immune cell behaviors in a non-bilaterian.

The formation of extracellular DNA traps (ETosis) is a first response mechanism by specific immune cells following exposure to microbes. Initially characterized in vertebrate neutrophils, cells capable of ETosis have been discovered recently in diverse non-vertebrate taxa. To assess the conservation of ETosis between evolutionarily distant non-vertebrate phyla, we observed and quantified ETosis using the model ctenophore Mnemiopsis leidyi and the oyster Crassostrea gigas. Here we report that ctenophores - thought to have diverged very early from the metazoan stem lineage - possess immune-like cells capable of phagocytosis and ETosis. We demonstrate that both Mnemiopsis and Crassostrea immune cells undergo ETosis after exposure to diverse microbes and chemical agents that stimulate ion flux. We thus propose that ETosis is an evolutionarily conserved metazoan defense against pathogens.

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.

An AI-generated proteome-scale dataset of predicted protein structures for the ctenophore Mnemiopsis leidyi.

This Dataset Brief describes the computational prediction of protein structures for the ctenophore Mnemiopsis leidyi. Here, we report the proteome-scale generation of 15,333 protein structure predictions using AlphaFold, as well as an updated implementation of publicly available search, manipulation, and visualization tools for these protein structure predictions through the Mnemiopsis Genome Project Portal (https://research.nhgri.nih.gov/mnemiopsis). The utility of these predictions is demonstrated by highlighting comparisons to experimentally determined structures for the light-sensitive protein mnemiopsin 1 and the ionotropic glutamate receptor (iGluR). The application of these novel protein structure prediction methods will serve to further position non-bilaterian species such as Mnemiopsis as powerful model systems for the study of early animal evolution and human health.

The ctenophore Mnemiopsis leidyi deploys a rapid injury response dating back to the last common animal ancestor.

Regenerative potential is widespread but unevenly distributed across animals. However, our understanding of the molecular mechanisms underlying regenerative processes is limited to a handful of model organisms, restricting robust comparative analyses. Here, we conduct a time course of RNA-seq during whole body regeneration in Mnemiopsis leidyi (Ctenophora) to uncover gene expression changes that correspond with key events during the regenerative timeline of this species. We identified several genes highly enriched in this dataset beginning as early as 10 minutes after surgical bisection including transcription factors in the early timepoints, peptidases in the middle timepoints, and cytoskeletal genes in the later timepoints. We validated the expression of early response transcription factors by whole mount in situ hybridization, showing that these genes exhibited high expression in tissues surrounding the wound site. These genes exhibit a pattern of transient upregulation as seen in a variety of other organisms, suggesting that they may be initiators of an ancient gene regulatory network linking wound healing to the initiation of a regenerative response.

Functional analysis of ctenophore Shaker K+ channels: N-type inactivation in the animal roots.

Here we explore the evolutionary origins of fast N-type ball-and-chain inactivation in Shaker (Kv1) K+ channels by functionally characterizing Shaker channels from the ctenophore (comb jelly) Mnemiopsis leidyi. Ctenophores are the sister lineage to other animals and Mnemiopsis has >40 Shaker-like K+ channels, but they have not been functionally characterized. We identified three Mnemiopsis channels (MlShak3-5) with N-type inactivation ball-like sequences at their N termini and functionally expressed them in Xenopus oocytes. Two of the channels, MlShak4 and MlShak5, showed rapid inactivation similar to cnidarian and bilaterian Shakers with rapid N-type inactivation, whereas MlShak3 inactivated ∼100-fold more slowly. Fast inactivation in MlShak4 and MlShak5 required the putative N-terminal inactivation ball sequences. Furthermore, the rate of fast inactivation in these channels depended on the number of inactivation balls/channel, but the rate of recovery from inactivation did not. These findings closely match the mechanism of N-type inactivation first described for Drosophila Shaker in which 1) inactivation balls on the N termini of each subunit can independently block the pore, and 2) only one inactivation ball occupies the pore binding site at a time. These findings suggest classical N-type activation evolved in Shaker channels at the very base of the animal phylogeny in a common ancestor of ctenophores, cnidarians, and bilaterians and that fast-inactivating Shakers are therefore a fundamental type of animal K+ channel. Interestingly, we find evidence from functional co-expression experiments and molecular dynamics that MlShak4 and MlShak5 do not co-assemble, suggesting that Mnemiopsis has at least two functionally independent N-type Shaker channels.