Formation of adult organs through metamorphosis in ascidians

Transcriptome Analysis Reveals the Requirement of the TGFβ Pathway in Ascidian Tail Regression

Metamorphosis is a common developmental process in invertebrate development. It is essential for the degeneration of larval organs, formation of adult organs, and adaptation transformation of the living environment. However, the underlying molecular regulatory mechanism remains to be elucidated. In this study, we used tail regression of ascidian Styela clava as a model to understand the gene regulation pathway and molecular mechanism in organ metamorphosis. The TGFβ signaling pathway was screened and demonstrated to be involved in tail regression based on RNA sequencing on the different larval stages and verification with inhibitor treatment experiments. We further investigated the downstream gene network of the TGFβ signaling pathway through comparative transcriptome data analysis on the TGFβ pathway inhibition samples. Together with qRT-PCR verification, we identified four critical gene functional categories, including ion transporters/water channel, extracellular matrix structural constituent, extracellular matrix organization, and cell polarity establishment. Furthermore, a cross-species comparative analysis between Ciona robusta and S. clava was performed to understand the conservation and divergence of gene regulation in ascidians. Overall, our work identifies a crucial gene regulation pathway in ascidian tail regression and provides several potential downstream targets for understanding the molecular mechanism of larval metamorphosis.

A simple inland culture system provides insights into ascidian post-embryonic developmental physiology

Maintenance and breeding of experimental organisms are fundamental to life sciences, but both initial and running costs, and hands-on zootechnical demands can be challenging for many laboratories. Here, we first aimed to further develop a simple protocol for reliable inland culture of tunicate model species of the Ciona genus. We cultured both Ciona robusta and Ciona intestinalis in controlled experimental conditions, with a focus on dietary variables, and quantified growth and maturation parameters. From statistical analysis of these standardized datasets, we gained insights into the post-embryonic developmental physiology of Ciona and inferred an improved diet and culturing conditions for sexual maturation. We showed that body length is a critical determinant of both somatic and sexual maturation, which suggests the existence of systemic control mechanisms of resource allocation towards somatic growth or maturation and supports applying size selection as a predictor of reproductive fitness in our inland culture to keep the healthiest animals at low density in the system. In the end, we successfully established a new protocol, including size selection, to promote both sperm and egg production. Our protocol using small tanks will empower researchers to initiate inland Ciona cultures with low costs and reduced space constraints.

Specification and survival of post-metamorphic branchiomeric neurons in a non-vertebrate chordate

Tunicates are the sister group to the vertebrates, yet most species have a life cycle split between swimming larva and sedentary adult phases. During metamorphosis, larval neurons are replaced by adult-specific ones. The regulatory mechanisms underlying this replacement remain largely unknown. Using tissue-specific CRISPR/Cas9-mediated mutagenesis in the tunicate Ciona, we show that orthologs of conserved hindbrain and branchiomeric neuron regulatory factors Pax2/5/8 and Phox2 are required to specify the 'neck', a cellular compartment set aside in the larva to give rise to cranial motor neuron-like neurons post-metamorphosis. Using bulk and single-cell RNA-sequencing analyses, we characterize the transcriptome of the neck downstream of Pax2/5/8. We present evidence that neck-derived adult ciliomotor neurons begin to differentiate in the larva and persist through metamorphosis, contrary to the assumption that the adult nervous system is formed after settlement and the death of larval neurons during metamorphosis. Finally, we show that FGF signaling during the larval phase alters the patterning of the neck and its derivatives. Suppression of FGF converts neck cells into larval neurons that fail to survive metamorphosis, whereas prolonged FGF signaling promotes an adult neural stem cell-like fate.

Gradistics: An underappreciated dimension in evolutionary space

The growth of complexity is an unsolved and underappreciated problem. We consider possible causes of this growth, hypotheses testing, molecular mechanisms, complexity measures, cases of simplification, and significance for biomedicine. We focus on a general ability of regulation, which is based on the growing information storage and processing capacities, as the main proxy of complexity. Natural selection is indifferent to complexity. However, complexification can be inferred from the same first principle, on which natural selection is founded. Natural selection depends on potentially unlimited reproduction under limited environmental conditions. Because of the demographic pressure, the simple ecological niches become fulfilled and diversified (due to species splitting and divergence). Diversification increases complexity of biocenoses. After the filling and diversification of simple niches, the more complex niches can arise. This is the 'atomic orbitals' (AO) model. Complexity has many shortcomings but it has an advantage. This advantage is ability to regulatory adaptation, including behavioral, formed in the evolution by means of genetic adaptation. Regulatory adaptation is much faster than genetic one because it is based on the information previously accumulated via genetic adaptation and learning. Regulatory adaptation further increases complexity of biocenoses. This is the 'regulatory advantage' (RA) model. The comparison of both models allows testable predictions. We focus on the animal evolution because of the appearance of higher regulatory level (nervous system), which is absent in other lineages, and relevance to humans (including biomedical aspects).

Molecular Characterization and Expression Analysis of Putative Class C (Glutamate Family) G Protein-Coupled Receptors in Ascidian Styela clava

In this study, we performed the genome-wide domain analysis and sequence alignment on the genome of Styela clava, and obtained a repertoire of 204 putative GPCRs, which exhibited a highly reduced gene number compared to vertebrates and cephalochordates. In this repertoire, six Class C GPCRs, including four metabotropic glutamate receptors (Sc-GRMs), one calcium-sensing receptor (Sc-CaSR), and one gamma-aminobutyric acid (GABA) type B receptor 2-like (Sc-GABABR2-like) were identified, with the absence of type 1 taste and vomeronasal receptors. All the Sc-GRMs and Sc-CaSR contained the typical "Venus flytrap" and cysteine-rich domains required for ligand binding and subsequent propagation of conformational changes. In swimming larvae, Sc-grm3 and Sc-casr were mainly expressed at the junction of the sensory vesicle and tail nerve cord while the transcripts of Sc-grm4, Sc-grm7a, and Sc-grm7b appeared at the anterior trunk, which suggested their important functions in neurotransmission. The high expression of these Class C receptors at tail-regression and metamorphic juvenile stages hinted at their potential involvement in regulating metamorphosis. In adults, the transcripts were highly expressed in several peripheral tissues, raising the possibility that S. clava Class C GPCRs might function as neurotransmission modulators peripherally after metamorphosis. Our study systematically characterized the ancestral chordate Class C GPCRs to provide insights into the origin and evolution of these receptors in chordates and their roles in regulating physiological and morphogenetic changes relevant to the development and environmental adaption.

A microRNA Cluster-Lefty Pathway is Required for Cellulose Synthesis During Ascidian Larval Metamorphosis

Synthesis of cellulose and formation of tunic structure are unique traits in the tunicate animal group. However, the regulatory mechanism of tunic formation remains obscure. Here, we identified a novel microRNA cluster of three microRNAs, including miR4018a, miR4000f, and miR4018b in Ciona savignyi. In situ hybridization and promoter assays showed that miR4018a/4000f/4018b cluster was expressed in the mesenchymal cells in the larval trunk, and the expression levels were downregulated during the later tailbud stage and larval metamorphosis. Importantly, overexpression of miR4018a/4000f/4018b cluster in mesenchymal cells abolished the cellulose synthesis in Ciona larvae and caused the loss of tunic cells in metamorphic larvae, indicating the regulatory roles of miR4018a/4000f/4018b cluster in cellulose synthesis and mesenchymal cell differentiation into tunic cells. To elucidate the molecular mechanism, we further identified the target genes of miR4018a/4000f/4018b cluster using the combination approaches of TargetScan prediction and RNA-seq data. Left-right determination factor (Lefty) was confirmed as one of the target genes after narrow-down screening and an experimental luciferase assay. Furthermore, we showed that Lefty was expressed in the mesenchymal and tunic cells, indicating its potentially regulatory roles in mesenchymal cell differentiation and tunic formation. Notably, the defects in tunic formation and loss of tunic cells caused by overexpression of miR4018a/4000f/4018b cluster could be restored when Lefty was overexpressed in Ciona larvae, suggesting that miR4018a/4000f/4018b regulated the differentiation of mesenchymal cells into tunic cells through the Lefty signaling pathway during ascidian metamorphosis. Our findings, thus, reveal a novel microRNA-Lefty molecular pathway that regulates mesenchymal cells differentiating into tunic cells required for the tunic formation in tunicate species.

Effects of Exposure to Trade Antifouling Paints and Biocides on Larval Settlement and Metamorphosis of the Compound Ascidian Botryllus schlosseri

To evaluate the effects of antifouling paints and biocides on larval settlement and metamorphosis, newly hatched swimming larvae of the compound ascidian Botryllus schlosseri, a dominant species of soft-fouling in coastal communities, were exposed to (i) substrata coated with seven antifouling paints on the market containing different biocidal mixtures and types of matrices and (ii) sea water containing various concentrations of eight biocidal constituents. All antifouling paints showed high performance, causing 100% mortality and metamorphic inhibition, with ≥75% not-settled dead larvae. All antifouling biocides prevented the settlement of larvae. The most severe larval malformations, i.e., (i) the formation of a bubble encasing the cephalenteron and (ii) the inhibition of tail resorption, were observed after exposure to metal and organometal compounds, including tributyltin (TBT) at 1 μM (325.5 µg L−1), zinc pyrithione (ZnP) at 1 μM (317.7 µg L−1), and CuCl at 0.1 μM (98.99 µg L−1), and to antimicrobials and fungicides, including Sea-Nine 211 at 1 μM (282.2 µg L−1) and Chlorothalonil at 1 μM (265.9 µg L−1). The herbicides seemed to be less active. Irgarol 1051 was not lethal at any of the concentrations tested. Diuron at 250 μM (58.2 mg L−1) and 2,3,5,6-tetrachloro-4-(methylsulphonyl)pyridine (TCMS pyridine) at 50 μM (14.8 mg L−1) completely inhibited larval metamorphosis. These results may have important implications for the practical use of different antifouling components, highlighting the importance of their testing for negative impacts on native benthic species.

Growth of Biological Complexity from Prokaryotes to Hominids Reflected in the Human Genome

The growth of complexity in evolution is a most intriguing phenomenon. Using gene phylostratigraphy, we showed this growth (as reflected in regulatory mechanisms) in the human genome, tracing the path from prokaryotes to hominids. Generally, the different regulatory gene families expanded at different times, yet only up to the Euteleostomi (bony vertebrates). The only exception was the expansion of transcription factors (TF) in placentals; however, we argue that this was not related to increase in general complexity. Surprisingly, although TF originated in the Prokaryota while chromatin appeared only in the Eukaryota, the expansion of epigenetic factors predated the expansion of TF. Signaling receptors, tumor suppressors, oncogenes, and aging- and disease-associated genes (indicating vulnerabilities in terms of complex organization and strongly enrichment in regulatory genes) also expanded only up to the Euteleostomi. The complexity-related gene properties (protein size, number of alternative splicing mRNA, length of untranslated mRNA, number of biological processes per gene, number of disordered regions in a protein, and density of TF–TF interactions) rose in multicellular organisms and declined after the Euteleostomi, and possibly earlier. At the same time, the speed of protein sequence evolution sharply increased in the genes that originated after the Euteleostomi. Thus, several lines of evidence indicate that molecular mechanisms of complexity growth were changing with time, and in the phyletic lineage leading to humans, the most salient shift occurred after the basic vertebrate body plan was fixed with bony skeleton. The obtained results can be useful for evolutionary medicine.

Transcription Factors of the bHLH Family Delineate Vertebrate Landmarks in the Nervous System of a Simple Chordate

Tunicates are marine invertebrates whose tadpole-like larvae feature a highly simplified version of the chordate body plan. Similar to their distant vertebrate relatives, tunicate larvae develop a regionalized central nervous system and form distinct neural structures, which include a rostral sensory vesicle, a motor ganglion, and a caudal nerve cord. The sensory vesicle contains a photoreceptive complex and a statocyst, and based on the comparable expression patterns of evolutionarily conserved marker genes, it is believed to include proto-hypothalamic and proto-retinal territories. The evolutionarily conserved molecular fingerprints of these landmarks of the vertebrate brain consist of genes encoding for different transcription factors, and of the gene batteries that they control, and include several members of the bHLH family. Here we review the complement of bHLH genes present in the streamlined genome of the tunicate Ciona robusta and their current classification, and summarize recent studies on proneural bHLH transcription factors and their expression territories. We discuss the possible roles of bHLH genes in establishing the molecular compartmentalization of the enticing nervous system of this unassuming chordate.

Hox13 is essential for formation of a sensory organ at the terminal end of the sperm duct in Ciona

Species-specific traits are thought to have been acquired by natural selection. Transcription factors play central roles in the evolution of species-specific traits. Hox genes encode a set of conserved transcription factors essential for establishing the anterior-posterior body axis of animals. Changes in the expression or function of Hox genes can lead to the diversification of animal-body plans. The tunicate ascidian Ciona intestinalis Type A has an orange-colored structure at the sperm duct terminus. This orange-pigmented organ (OPO) is the characteristic that can distinguish this ascidian from other closely related species. The OPO is formed by the accumulation of orange-pigmented cells (OPCs) that are present throughout the adult body. We show that Hox13 is essential for formation of the OPO. Hox13 is expressed in the epithelium of the sperm duct and neurons surrounding the terminal openings for sperm ejection, while OPCs themselves do not express this gene. OPCs are mobile cells that can move through the body vasculature by pseudopodia, suggesting that the OPO is formed by the accumulation of OPCs guided by Hox13-positive cells. Another ascidian species, Ciona savignyi, does not have an OPO. Like Hox13 of C. intestinalis, Hox13 of C. savignyi is expressed at the terminus of its sperm duct; however, its expression domain is limited to the circular area around the openings. The genetic changes responsible for the acquisition or loss of OPO are likely to occur in the expression pattern of Hox13.

Molecular and evolutionary aspects of the protochordate digestive system

The digestive system is a functional unit consisting of an endodermal tubular structure (alimentary canal) and accessory organs that function in nutrition processing in most triploblastic animals. Various morphologies and apparatuses are formed depending on the phylogenetical relationship and food habits of the specific species. Nutrition processing and morphogenesis of the alimentary canal and accessory organs have both been investigated in vertebrates, mainly humans and mammals. When attempting to understand the evolutionary processes that led to the vertebrate digestive system, however, it is useful to examine other chordates, specifically protochordates, which share fundamental functional and morphogenetic molecules with vertebrates, which also possess non-duplicated genomes. In protochordates, basic anatomical and physiological studies have mainly described the characteristic traits of suspension feeders. Recent progress in genome sequencing has allowed researchers to comprehensively detail protochordate genes and has compared the genetic backgrounds among chordate nutrition processing and alimentary canal/accessory organ systems based on genomic information. Gene expression analyses have revealed spatiotemporal gene expression profiles in protochordate alimentary canals. Additionally, to investigate the basis of morphological diversity in the chordate alimentary canal and accessory organs, evolutionary developmental research has examined developmental transcription factors related to morphogenesis and anterior-posterior pattering of the alimentary canal and accessory organs. In this review, we summarize the current knowledge of molecules involved in nutrition processing and the development of the alimentary canal and accessory organs with innate immune and endocrine roles in protochordates and we explore the molecular basis for understanding the evolution of the chordate digestive system.

De novo neurogenesis in a budding chordate: Co-option of larval anteroposterior patterning genes in a transitory neurogenic organ

During metamorphosis of solitary ascidians, part of the larval tubular nervous system is recruited to form the adult central nervous system (CNS) through neural stem-like cells called ependymal cells. The anteroposterior (AP) gene expression patterning of the larval CNS regionalize the distribution of the ependymal cells, which contains the positional information of the neurons of the adult nervous system. In colonial ascidians, the CNS of asexually developed zooids has the same morphology of the one of the post-metamorphic zooids. However, its development follows a completely different organogenesis that lacks embryogenesis, a larval phase and metamorphosis. In order to describe neurogenesis during asexual development (blastogenesis), we followed the expression of six CNS AP patterning genes conserved in chordates and five neural-related genes to determine neural cell identity in Botryllus schlosseri. We observed that a neurogenesis occurs de novo on each blastogenic cycle starting from a neurogenic transitory structure, the dorsal tube. The dorsal tube partially co-opts the AP patterning of the larval CNS markers, and potentially combine the neurogenesis role and provider of positional clues for neuron patterning. This study shows how a larval developmental module is reused in a direct asexual development in order to generate the same structures.

De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution

Tunicates are marine invertebrates that compose the closest phylogenetic group to the vertebrates. These chordates present a particularly diverse range of regenerative abilities and life-history strategies. Consequently, tunicates provide an extraordinary perspective into the emergence and diversity of these traits. Here we describe the genome sequencing, annotation and analysis of the Stolidobranchian Botrylloides leachii. We have produced a high-quality 159 Mb assembly, 82% of the predicted 194 Mb genome. Analysing genome size, gene number, repetitive elements, orthologs clustering and gene ontology terms show that B. leachii has a genomic architecture similar to that of most solitary tunicates, while other recently sequenced colonial ascidians have undergone genome expansion. In addition, ortholog clustering has identified groups of candidate genes for the study of colonialism and whole-body regeneration. By analysing the structure and composition of conserved gene linkages, we observed examples of cluster breaks and gene dispersions, suggesting that several lineage-specific genome rearrangements occurred during tunicate evolution. We also found lineage-specific gene gain and loss within conserved cell-signalling pathways. Such examples of genetic changes within conserved cell-signalling pathways commonly associated with regeneration and development that may underlie some of the diverse regenerative abilities observed in tunicates. Overall, these results provide a novel resource for the study of tunicates and of colonial ascidians.