An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models

Cellulose nanocrystals in the development of biodegradable materials: A review on CNC resources, modification, and their hybridization

The escalating demand for sustainable materials has propelled cellulose into the spotlight as a promising alternative to petroleum-based products. As the most abundant organic polymer on Earth, cellulose is ubiquitous, found in plants, bacteria, and even a unique marine animal-the tunicate. Cellulose polymers naturally give rise to microscale semi-crystalline fibers and nanoscale crystalline regions known as cellulose nanocrystals (CNCs). Exhibiting rod-like structures with widths spanning 3 to 50 nm and lengths ranging from 50 nm to several microns, CNC characteristics vary based on the cellulose source. The degree of crystallinity, crucial for CNC properties, fluctuates between 49 and 95 % depending on the source and synthesis method. CNCs, with their exceptional properties such as high aspect ratio, relatively low density (≈1.6 g cm-3), high axial elastic modulus (≈150 GPa), significant tensile strength, and birefringence, emerge as ideal candidates for biodegradable fillers in nanocomposites and functional materials. The percolation threshold, a mathematical concept defining long-range connectivity between filler and polymer, governs the effectiveness of reinforcement in nanocomposites. This threshold is intricately influenced by the aspect ratio and molecular interaction strength, impacting CNC performance in polymeric and pure nanocomposite materials. This comprehensive review explores diverse aspects of CNCs, encompassing their derivation from various sources, methods of modification (both physical and chemical), and hybridization with heterogeneous fillers. Special attention is devoted to the hybridization of CNCs derived from tunicates (TCNC) with those from wood (WCNC), leveraging the distinct advantages of each. The overarching objective is to demonstrate how this hybridization strategy mitigates the limitations of WCNC in composite materials, offering improved interaction and enhanced percolation. This, in turn, is anticipated to elevate the reinforcing effects and pave the way for the development of nanocomposites with tunable viscoelastic, physicochemical, and mechanical properties.

Divergence time estimates for the hypoxia-inducible factor-1 alpha (HIF1α) reveal an ancient emergence of animals in low-oxygen environments

Unveiling the tempo and mode of animal evolution is necessary to understand the links between environmental changes and biological innovation. Although the earliest unambiguous metazoan fossils date to the late Ediacaran period, molecular clock estimates agree that the last common ancestor (LCA) of all extant animals emerged ~850 Ma, in the Tonian period, before the oldest evidence for widespread ocean oxygenation at ~635-560 Ma in the Ediacaran period. Metazoans are aerobic organisms, that is, they are dependent on oxygen to survive. In low-oxygen conditions, most animals have an evolutionarily conserved pathway for maintaining oxygen homeostasis that triggers physiological changes in gene expression via the hypoxia-inducible factor (HIFa). However, here we confirm the absence of the characteristic HIFa protein domain responsible for the oxygen sensing of HIFa in sponges and ctenophores, indicating the LCA of metazoans lacked the functional protein domain as well, and so could have maintained their transcription levels unaltered under the very low-oxygen concentrations of their environments. Using Bayesian relaxed molecular clock dating, we inferred that the ancestral gene lineage responsible for HIFa arose in the Mesoproterozoic Era, ~1273 Ma (Credibility Interval 957-1621 Ma), consistent with the idea that important genetic machinery associated with animals evolved much earlier than the LCA of animals. Our data suggest at least two duplication events in the evolutionary history of HIFa, which generated three vertebrate paralogs, products of the two successive whole-genome duplications that occurred in the vertebrate LCA. Overall, our results support the hypothesis of a pre-Tonian emergence of metazoans under low-oxygen conditions, and an increase in oxygen response elements during animal evolution.

Bioactive Molecules from the Innate Immunity of Ascidians and Innovative Methods of Drug Discovery: A Computational Approach Based on Artificial Intelligence

The study of bioactive molecules of marine origin has created an important bridge between biological knowledge and its applications in biotechnology and biomedicine. Current studies in different research fields, such as biomedicine, aim to discover marine molecules characterized by biological activities that can be used to produce potential drugs for human use. In recent decades, increasing attention has been paid to a particular group of marine invertebrates, the Ascidians, as they are a source of bioactive products. We describe omics data and computational methods relevant to identifying the mechanisms and processes of innate immunity underlying the biosynthesis of bioactive molecules, focusing on innovative computational approaches based on Artificial Intelligence. Since there is increasing attention on finding new solutions for a sustainable supply of bioactive compounds, we propose that a possible improvement in the biodiscovery pipeline might also come from the study and utilization of marine invertebrates' innate immunity.

A New Molecular Phylogeny of Salps (Tunicata: Thalicea: Salpida) and the Evolutionary History of Their Colonial Architecture

Salps are marine pelagic tunicates with a complex life cycle, including a solitary and colonial stage composed of asexually budded individuals. These colonies develop into species-specific architectures with distinct zooid orientations, including transversal, oblique, linear, helical, and bipinnate chains, as well as whorls and clusters. The evolutionary history of salp colony architecture has remained obscured due to the lack of an ontology to characterize architectures, as well as a lack of phylogenetic taxon sampling and resolution of critical nodes. We (1) collected and sequenced eight species of salps that had never been sequenced before, (2) inferred the phylogenetic relationships among salps, and (3) reconstructed the evolutionary history of salp colony architecture. We collected salp specimens via offshore SCUBA diving, dissected tissue samples, extracted their DNA, amplified their 18S gene, and sequenced them using Sanger technology. We inferred the phylogeny of Salpida based on 18S using both Maximum Likelihood and Bayesian approaches. Using this phylogeny, we reconstructed the ancestral states of colony architecture using a Bayesian ordered Markov model informed by the presence and absence of specific developmental mechanisms that lead to each architecture. We find that the ancestral salp architecture is either oblique or linear, with every other state being derived. Moreover, linear chains have evolved independently at least three times. While transversal chains are developmentally basal and hypothesized to be ancestral, our phylogenetic topology and reconstructions strongly indicate that they are evolutionarily derived through the loss of zooid torsion. These traits are likely critical to multijet locomotory performance and evolving under natural selection. Our work showcases the need to study the broader diversity of salp species to gain a comprehensive understanding of their organismal biology, evolutionary history, and ecological roles in pelagic ecosystems.

Ciona robusta macrophage migration inhibitory factor (Mif1 and Mif2) genes are differentially regulated in the lipopolysaccharide-challenged pharynx

The effects of lipopolysaccharide (LPS) on Mif (macrophage migration inhibitory factor) gene expression in the pharynx (haemapoetic tissue) of Ciona robusta were investigated using quantitative reverse-transcription PCR (qRT-PCR) and in situ hybridisation (ISH). To verify the induction of an inflammatory response in the pharynx, a qRT-PCR analysis was performed to evaluate the change in the expression of proinflammatory marker genes such as Mbl, Ptx-like, Tnf-α and Nf-kb, which were shown to be upregulated 1 h post LPS challenge. The change in the expression of the two Mif paralogs in the pharynx was assessed before and after stimulation, and qRT-PCR and ISH results showed that, although Mif2 and Mif2 were expressed in clusters of haemocytes in pharynx vessels, only Mif1 expression increased after LPS stimulation. This indicates that the Mif genes are differently regulated and respond to different ambient inputs that need further analysis.

A Developmental Ontology for the Colonial Architecture of Salps

AbstractColonial animals are composed of clonal individuals that remain physically connected and physiologically integrated. Salps are tunicates with a dual life cycle, including an asexual solitary stage that buds sexual colonies composed of jet-propelling zooids that efficiently swim together as a single unit by multijet propulsion. Colonies from different species develop distinct architectures characterized by their zooid arrangement patterns, but this diversity has received little attention. Thus, these architectures have never been formally defined using a framework of variables and axes that would allow comparative analyses. We set out to define an ontology of the salp colony architecture morphospace and describe the developmental pathways that build the different architectures. To inform these definitions, we collected and photographed live specimens of adult and developing colonies through offshore scuba diving. Since all salp colonies begin their development as a transversal double chain, we characterized each adult colonial architecture as a series of developmental transitions, such as rotations and translations of zooids, relative to their orientation at this early shared stage. We hypothesize that all adult architectures are either final or intermediate stages within three developmental pathways toward bipinnate, cluster, or helical forms. This framework will enable comparative studies on the biomechanical implications, ecological functions, evolutionary history, and engineering applications of the diversity of salp colony architectures.

Transcriptomic and Bioinformatic Analyses Identifying a Central Mif-Cop9-Nf-kB Signaling Network in Innate Immunity Response of Ciona robusta

The Ascidian C. robusta is a powerful model for studying innate immunity. LPS induction activates inflammatory-like reactions in the pharynx and the expression of several innate immune genes in granulocyte hemocytes such as cytokines, for instance, macrophage migration inhibitory factors (CrMifs). This leads to intracellular signaling involving the Nf-kB signaling cascade that triggers downstream pro-inflammatory gene expression. In mammals, the COP9 (Constitutive photomorphogenesis 9) signalosome (CSN) complex also results in the activation of the NF-kB pathway. It is a highly conserved complex in vertebrates, mainly engaged in proteasome degradation which is essential for maintaining processes such as cell cycle, DNA repair, and differentiation. In the present study, we used bioinformatics and in-silico analyses combined with an in-vivo LPS exposure strategy, next-generation sequencing (NGS), and qRT-PCR to elucidate molecules and the temporal dynamics of Mif cytokines, Csn signaling components, and the Nf-κB signaling pathway in C. robusta. A qRT-PCR analysis of immune genes selected from transcriptome data revealed a biphasic activation of the inflammatory response. A phylogenetic and STRING analysis indicated an evolutionarily conserved functional link between the Mif-Csn-Nf-kB axis in ascidian C. robusta during LPS-mediated inflammation response, finely regulated by non-coding molecules such as microRNAs (miRNAs).

Dolioletta advena sp. nov., a New Species of Doliolid (Tunicata, Thaliacea) from the Adriatic Sea

The Adriatic Sea, as a part of Mediterranean, is one of the best investigated areas in the world regarding zooplankton. Nevertheless, in the last decade four new species of gelatinous zooplankton were described from the Adriatic Sea. Whether these species are newcomers or they were simply overlooked is still under investigations. Here we provide a description of a new species of Doliolida from the genus Dolioletta, Dolioletta advena sp. nov., found in the Adriatic Sea in August 2021, in a period of high sea temperatures and salinities, suggesting its thermal predilection. Its blastozooids dominated the studied doliolid blastozooid communities in the South Adriatic, except in the 50–100 m depth layer at a coastal Lokrum station. Blastozooids of D. advena sp. nov. possess unique morphological features which easily distinguish it from other doliolid species: the most prominent feature being the curved digestive tract where the intestine does not form a tight coil as in other Dolioletta species. The placement of this species in the genus Dolioletta is corroborated by COI phylogenetic analysis which showed that D. advena sp. nov. forms a well-supported monophyletic clade with Dolioletta gegenbauri (81% bootstrap support). In addition to D. advena sp. nov. COI sequence, we provide COI sequences of five doliolid and one pyrosomatid species, which will greatly improve the availability of thaliacean sequences for metabarcoding studies. The origin of D. advena sp. nov. is unknown, but given the fact that doliolids are well investigated in the Mediterranean Sea, it is likely that it arrived with sea currents either through the Suez Canal or the Strait of Gibraltar. Future investigations will confirm or reject this hypothesis.

Morphological Study and 3D Reconstruction of the Larva of the Ascidian Halocynthia roretzi

The swimming larva represents the dispersal phase of ascidians, marine invertebrates belonging to tunicates. Due to its adhesive papillae, the larva searches the substrate, adheres to it, and undergoes metamorphosis, thereby becoming a sessile filter feeding animal. The larva anatomy has been described in detail in a few species, revealing a different degree of adult structure differentiation, called adultation. In the solitary ascidian Halocynthia roretzi, a species reared for commercial purposes, embryogenesis has been described in detail, but information on the larval anatomy is still lacking. Here, we describe it using a comparative approach, utilizing 3D reconstruction, as well as histological/TEM observations, with attention to its papillae. The larva is comparable to those of other solitary ascidians, such as Ciona intestinalis. However, it displays a higher level of adultation for the presence of the atrium, opened outside by means of the atrial siphon, and the peribranchial chambers. It does not reach the level of complexity of the larva of Botryllus schlosseri, a phylogenetically close colonial ascidian. Our study reveals that the papillae of H. roretzi, previously described as simple and conform, exhibit dynamic changes during settlement. This opens up new considerations on papillae morphology and evolution and deserves to be further investigated.

Transcriptomic Analyses Reveal 2 and 4 Family Members of Cytochromes P450 (CYP) Involved in LPS Inflammatory Response in Pharynx of Ciona robusta

Cytochromes P450 (CYP) are enzymes responsible for the biotransformation of most endogenous and exogenous agents. The expression of each CYP is influenced by a unique combination of mechanisms and factors including genetic polymorphisms, induction by xenobiotics, and regulation by cytokines and hormones. In recent years, Ciona robusta, one of the closest living relatives of vertebrates, has become a model in various fields of biology, in particular for studying inflammatory response. Using an in vivo LPS exposure strategy, next-generation sequencing (NGS) and qRT-PCR combined with bioinformatics and in silico analyses, compared whole pharynx transcripts from naïve and LPS-exposed C. robusta, and we provide the first view of cytochrome genes expression and miRNA regulation in the inflammatory response induced by LPS in a hematopoietic organ. In C. robusta, cytochromes belonging to 2B,2C, 2J, 2U, 4B and 4F subfamilies were deregulated and miRNA network interactions suggest that different conserved and species-specific miRNAs are involved in post-transcriptional regulation of cytochrome genes and that there could be an interplay between specific miRNAs regulating both inflammation and cytochrome molecules in the inflammatory response in C. robusta.

Symbiotic Associations in Ascidians: Relevance for Functional Innovation and Bioactive Potential

Associations between different organisms have been extensively described in terrestrial and marine environments. These associations are involved in roles as diverse as nutrient exchanges, shelter or adaptation to adverse conditions. Ascidians are widely dispersed marine invertebrates associated to invasive behaviours. Studying their microbiomes has interested the scientific community, mainly due to its potential for bioactive compounds production-e.g., ET-73 (trabectedin, Yondelis), an anticancer drug. However, these symbiotic interactions embrace several environmental and biological functions with high ecological relevance, inspiring diverse biotechnological applications. We thoroughly reviewed microbiome studies (microscopic to metagenomic approaches) of around 171 hosts, worldwide dispersed, occurring at different domains of life (Archaea, Bacteria, Eukarya), to illuminate the functions and bioactive potential of associated organisms in ascidians. Associations with Bacteria are the most prevalent, namely with Cyanobacteria, Proteobacteria, Bacteroidetes, Actinobacteria and Planctomycetes phyla. The microbiomes of ascidians belonging to Aplousobranchia order have been the most studied. The integration of worldwide studies characterizing ascidians' microbiome composition revealed several functions including UV protection, bioaccumulation of heavy metals and defense against fouling or predators through production of natural products, chemical signals or competition. The critical assessment and characterization of these communities is extremely valuable to comprehend their biological/ecological role and biotechnological potential.

Robustness of phylogenetic inference to model misspecification caused by pairwise epistasis

Likelihood-based phylogenetic inference posits a probabilistic model of character state change along branches of a phylogenetic tree. These models typically assume statistical independence of sites in the sequence alignment. This is a restrictive assumption that facilitates computational tractability, but ignores how epistasis, the effect of genetic background on mutational effects, influences the evolution of functional sequences. We consider the effect of using a misspecified site-independent model on the accuracy of Bayesian phylogenetic inference in the setting of pairwise-site epistasis. Previous work has shown that as alignment length increases, tree reconstruction accuracy also increases. Here, we present a simulation study demonstrating that accuracy increases with alignment size even if the additional sites are epistatically coupled. We introduce an alignment-based test statistic that is a diagnostic for pairwise epistasis and can be used in posterior predictive checks.

Evolutionary and transcriptional analyses of a pentraxin-like component family involved in the LPS inflammatory response of Ciona robusta

Pentraxins (PTXs) are a superfamily of conserved proteins which are components of the humoral arm of innate immunity. They are considered to be functional ancestors of antibodies and are classified into short and long types. In this study, we show that a pentraxin-like component (Ptx-like) with a C-terminal PTX domain, highly homologous to the short PTX of H. sapiens CRP, and a long N-terminal domain typical of long PTXs, is involved in the inflammatory response of Ciona robusta under LPS exposure in vivo. Analyses of protein domains as well as 3D modelling and phylogenetic tree supported the close relationship of Ptx-like with mammalian CRP, suggesting that C. robusta Ptx-like shares a common ancestor in the chordate lineages. qRT-PCR analysis showed that Ptx-like was transcriptionally upregulated during the inflammatory process induced by LPS inoculation and that it is involved in the initial phase as well as the secondary phase of the inflammatory response in which matrix remodelling and the achievement of homeostasis occur. In situ hybridisation assays revealed that gene transcription was upregulated in the pharynx post-LPS challenge in vivo, and that Ptx-like was expressed by clusters of haemocytes, mainly granulocytes, inside the pharynx vessels. We also found transcript-expressing granulocytes flowing in the musculature and in the lacunae of the circulatory system. These data supported that Ptx-like is a potential molecule of the acute-phase response in C. robusta immune defence systems against bacterial infection.

ceRNA Network Regulation of TGF-β, WNT, FOXO, Hedgehog Pathways in the Pharynx of Ciona robusta

The transforming growth factor-β (TGF-β) family of cytokines performs a multifunctional signaling, which is integrated and coordinated in a signaling network that involves other pathways, such as Wintless, Forkhead box-O (FOXO) and Hedgehog and regulates pivotal functions related to cell fate in all tissues. In the hematopoietic system, TGF-β signaling controls a wide spectrum of biological processes, from immune system homeostasis to the quiescence and self-renewal of hematopoietic stem cells (HSCs). Recently an important role in post-transcription regulation has been attributed to two type of ncRNAs: microRNAs and pseudogenes. Ciona robusta, due to its philogenetic position close to vertebrates, is an excellent model to investigate mechanisms of post-transcriptional regulation evolutionarily highly conserved in immune homeostasis. The combined use of NGS and bioinformatic analyses suggests that in the pharynx, the hematopoietic organ of Ciona robusta, the Tgf-β, Wnt, Hedgehog and FoxO pathways are involved in tissue homeostasis, as they are in human. Furthermore, ceRNA network interactions and 3'UTR elements analyses of Tgf-β, Wnt, Hedgehog and FoxO pathways genes suggest that different miRNAs conserved (cin-let-7d, cin-mir-92c, cin-mir-153), species-specific (cin-mir-4187, cin-mir-4011a, cin-mir-4056, cin-mir-4150, cin-mir-4189, cin-mir-4053, cin-mir-4016, cin-mir-4075), pseudogenes (ENSCING00000011392, ENSCING00000018651, ENSCING00000007698) and mRNA 3'UTR elements are involved in post-transcriptional regulation in an integrated way in C. robusta.

Cytochrome c oxydase I phylogenetic analysis of Haemogregarina parasites (Apicomplexa, Coccidia, Eucoccidiorida, Haemogregarinidae) confirms the presence of three distinct species within the freshwater turtles of Tunisia

Species of Haemogregarina are apicomplexan blood parasites that use vertebrates as intermediate hosts. Due to limited interspecific morphological characters within the genus during the last decade, 18S rRNA gene sequences were widely used for species identification. As coinfection patterns were recently reported from nuclear molecular data for two sympatric freshwater turtles Mauremys leprosa and Emys orbicularis from Tunisia, our objectives were to design COI specific primers to confirm the presence of three distinct species in both host species. Blood samples were collected from 22 turtles, from which DNAs were extracted and used as templates for amplification. Following different rounds of PCR and nested PCR, we designed specific Haemogregarina COI primers that allowed the sequencing of nine distinct haplotypes. Phylogenetic Bayesian analysis revealed the occurrence of three well-differentiated sublineages that clustered together into a single clade. Based on pairwise genetic distances (p-distance), we confirmed the occurrence of three distinct but phylogenetically closely related species coinfecting M. leprosa and E. orbicularis in the same aquatic environments. Our results demonstrate that the use of fast evolving genes within Haemogregarina will help to investigate the parasite diversity within both intermediate vertebrate and definitive invertebrate hosts, and to assess the evolution, historical biogeography and specificity of haemogregarines.

An elongated COI fragment to discriminate botryllid species and as an improved ascidian DNA barcode

Botryllids are colonial ascidians widely studied for their potential invasiveness and as model organisms, however the morphological description and discrimination of these species is very problematic, leading to frequent specimen misidentifications. To facilitate species discrimination and detection of cryptic/new species, we developed new barcoding primers for the amplification of a COI fragment of about 860 bp (860-COI), which is an extension of the common Folmer's barcode region. Our 860-COI was successfully amplified in 177 worldwide-sampled botryllid colonies. Combined with morphological analyses, 860-COI allowed not only discriminating known species, but also identifying undescribed and cryptic species, resurrecting old species currently in synonymy, and proposing the assignment of clade D of the model organism Botryllus schlosseri to Botryllus renierii. Importantly, within clade A of B. schlosseri, 860-COI recognized at least two candidate species against only one recognized by the Folmer's fragment, underlining the need of further genetic investigations on this clade. This result also suggests that the 860-COI could have a greater ability to diagnose cryptic/new species than the Folmer's fragment at very short evolutionary distances, such as those observed within clade A. Finally, our new primers simplify the amplification of 860-COI even in non-botryllid ascidians, suggesting their wider usefulness in ascidians.

Phylogenetic comparison of egg transparency in ascidians by hyperspectral imaging

The transparency of animals is an important biological feature. Ascidian eggs have various degrees of transparency, but this characteristic has not yet been measured quantitatively and comprehensively. In this study, we established a method for evaluating the transparency of eggs to first characterize the transparency of ascidian eggs across different species and to infer a phylogenetic relationship among multiple taxa in the class Ascidiacea. We measured the transmittance of 199 eggs from 21 individuals using a hyperspectral camera. The spectrum of the visual range of wavelengths (400–760 nm) varied among individuals and we calculated each average transmittance of the visual range as bio-transparency. When combined with phylogenetic analysis based on the nuclear 18S rRNA and the mitochondrial cytochrome c oxidase subunit I gene sequences, the bio-transparencies of 13 species were derived from four different families: Ascidiidae, Cionidae, Pyuridae, and Styelidae. The bio-transparency varied 10–90% and likely evolved independently in each family. Ascidiella aspersa showed extremely high (88.0 ± 1.6%) bio-transparency in eggs that was maintained in the “invisible” larva. In addition, it was indicated that species of the Ascidiidae family may have a phylogenetic constraint of egg transparency.

Hidden diversity in Antarctica: Molecular and morphological evidence of two different species within one of the most conspicuous ascidian species

The Southern Ocean is one of the most isolated marine ecosystems, characterized by high levels of endemism, diversity, and biomass. Ascidians are among the dominant groups in Antarctic benthic assemblages; thus, recording the evolutionary patterns of this group is crucial to improve our current understanding of the assembly of this polar ocean. We studied the genetic variation within Cnemidocarpa verrucosa sensu lato, one of the most widely distributed abundant and studied ascidian species in Antarctica. Using a mitochondrial and a nuclear gene (COI and 18S), the phylogeography of fifteen populations distributed along the West Antarctic Peninsula and Burdwood Bank/MPA Namuncurá (South American shelf) was characterized, where the distribution of the genetic distance suggested the existence of, at least, two species within nominal C. verrucosa. When reevaluating morphological traits to distinguish between genetically defined species, the presence of a basal disk in one of the genotypes could be a diagnostic morphological trait to differentiate the species. These results are surprising due to the large research that has been carried out with the conspicuous C. verrucosa with no differentiation between species. Furthermore, it provides important tools to distinguish species in the field and laboratory. But also, these results give new insights into patterns of differentiation between closely related species that are distributed in sympatry, where the permeability of species boundaries still needs to be well understood.

Shotgun Proteomics of Ascidians Tunic Gives New Insights on Host-Microbe Interactions by Revealing Diverse Antimicrobial Peptides

Ascidians are marine invertebrates associated with diverse microbial communities, embedded in their tunic, conferring special ecological and biotechnological relevance to these model organisms used in evolutionary and developmental studies. Next-generation sequencing tools have increased the knowledge of ascidians’ associated organisms and their products, but proteomic studies are still scarce. Hence, we explored the tunic of three ascidian species using a shotgun proteomics approach. Proteins extracted from the tunic of Ciona sp., Molgula sp., and Microcosmus sp. were processed using a nano LC-MS/MS system (Ultimate 3000 liquid chromatography system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap mass spectrometer). Raw data was searched against UniProtKB – the Universal Protein Resource Knowledgebase (Bacteria and Metazoa section) using Proteome Discoverer software. The resulting proteins were merged with a non-redundant Antimicrobial Peptides (AMPs) database and analysed with MaxQuant freeware. Overall, 337 metazoan and 106 bacterial proteins were identified being mainly involved in basal metabolism, cytoskeletal and catalytic functions. 37 AMPs were identified, most of them attributed to eukaryotic origin apart from bacteriocins. These results and the presence of “Biosynthesis of antibiotics” as one of the most highlighted pathways revealed the tunic as a very active tissue in terms of bioactive compounds production, giving insights on the interactions between host and associated organisms. Although the present work constitutes an exploratory study, the approach employed revealed high potential for high-throughput characterization and biodiscovery of the ascidians’ tunic and its microbiome.

Transcriptional and in silico analyses of MIF cytokine and TLR signalling interplay in the LPS inflammatory response of Ciona robusta

The close phylogenetic relationship between Ciona robusta and vertebrates makes it a powerful model for studying innate immunity and the evolution of immune genes. To elucidate the nature and dynamics of the immune response, the molecular mechanisms by which bacterial infection is detected and translated into inflammation and how potential pattern recognition receptors (PRRs) are involved in pathogen recognition in tunicate C. robusta (formerly known as Ciona intestinalis), we applied an approach combining bacterial infections, next-generation sequencing, qRT-PCR, bioinformatics and in silico analyses (criteria of a p-value < 0.05 and FDR < 0.05). A STRING analysis indicated a functional link between components of the Tlr/MyD88-dependent signalling pathway (Tlr2, MyD88, and Irak4) and components of the Nf-κB signalling pathway (Nf-κB, IκBα, and Ikkα) (p-value < 0.05, FDR < 0.05). A qRT-PCR analysis of immune genes selected from transcriptome data revealed Mif as more frequently expressed in the inflammatory response than inflammation mediator or effector molecules (e.g., Il-17s, Tnf-α, Tgf-β, Mmp9, Tlrs, MyD88, Irak4, Nf-κB, and galectins), suggesting close interplay between Mif cytokines and Nf-κB signalling pathway components in the biphasic activation of the inflammatory response. An in silico analyses of the 3′-UTR of Tlr2, MyD88, IκBα, Ikk, and Nf-κB transcripts showed the presence of GAIT elements, which are known to play key roles in the regulation of immune gene-specific translation in humans. These findings provide a new level of understanding of the mechanisms involved in the regulation of the C. robusta inflammatory response induced by LPS and suggest that in C. robusta, as in humans, a complex transcriptional and post-transcriptional control mechanism is involved in the regulation of several inflammatory genes.

Conflict Resolution for Mesozoic Mammals: Reconciling Phylogenetic Incongruence Among Anatomical Regions

The evolutionary history of Mesozoic mammaliaformes is well studied. Although the backbone of their phylogeny is well resolved, the placement of ecologically specialized groups has remained uncertain. Functional and developmental covariation has long been identified as an important source of phylogenetic error, yet combining incongruent morphological characters altogether is currently a common practice when reconstructing phylogenetic relationships. Ignoring incongruence may inflate the confidence in reconstructing relationships, particularly for the placement of highly derived and ecologically specialized taxa, such as among australosphenidans (particularly, crown monotremes), haramiyidans, and multituberculates. The alternative placement of these highly derived clades can alter the taxonomic constituency and temporal origin of the mammalian crown group. Based on prior hypotheses and correlated homoplasy analyses, we identified cheek teeth and shoulder girdle character complexes as having a high potential to introduce phylogenetic error. We showed that incongruence among mandibulodental, cranial, and postcranial anatomical partitions for the placement of the australosphenidans, haramiyids, and multituberculates could largely be explained by apparently non-phylogenetic covariance from cheek teeth and shoulder girdle characters. Excluding these character complexes brought agreement between anatomical regions and improved the confidence in tree topology. These results emphasize the importance of considering and ameliorating major sources of bias in morphological data, and we anticipate that these will be valuable for confidently integrating morphological and molecular data in phylogenetic and dating analyses.

Evolution of Allorecognition in the Tunicata

Allorecognition, the ability to distinguish self or kin from unrelated conspecifics, plays several important biological roles in invertebrate animals. Two of these roles include negotiating limited benthic space for colonial invertebrates, and inbreeding avoidance through self-incompatibility systems. Subphylum Tunicata (Phylum Chordata), the sister group to the vertebrates, is a promising group in which to study allorecognition. Coloniality has evolved many times independently in the tunicates, and the best known invertebrate self-incompatibility systems are in tunicates. Recent phylogenomic studies have coalesced around a phylogeny of the Tunicata as well as the Order Stolidobranchia within the Tunicata, providing a path forward for the study of allorecognition in this group.

Phylogenetic analysis of phenotypic characters of Tunicata supports basal Appendicularia and monophyletic Ascidiacea

With approximately 3000 marine species, Tunicata represents the most disparate subtaxon of Chordata. Molecular phylogenetic studies support Tunicata as sister taxon to Craniota, rendering it pivotal to understanding craniate evolution. Although successively more molecular data have become available to resolve internal tunicate phylogenetic relationships, phenotypic data have not been utilized consistently. Herein these shortcomings are addressed by cladistically analyzing 117 phenotypic characters for 49 tunicate species comprising all higher tunicate taxa, and five craniate and cephalochordate outgroup species. In addition, a combined analysis of the phenotypic characters with 18S rDNA-sequence data is performed in 32 OTUs. The analysis of the combined data is congruent with published molecular analyses. Successively up-weighting phenotypic characters indicates that phenotypic data contribute disproportionally more to the resulting phylogenetic hypothesis. The strict consensus tree from the analysis of the phenotypic characters as well as the single most parsimonious tree found in the analysis of the combined dataset recover monophyletic Appendicularia as sister taxon to the remaining tunicate taxa. Thus, both datasets support the hypothesis that the last common ancestor of Tunicata was free-living and that ascidian sessility is a derived trait within Tunicata. "Thaliacea" is found to be paraphyletic with Pyrosomatida as sister taxon to monophyletic Ascidiacea and the relationship between Doliolida and Salpida is unresolved in the analysis of morphological characters; however, the analysis of the combined data reconstructs Thaliacea as monophyletic nested within paraphyletic "Ascidiacea". Therefore, both datasets differ in the interpretation of the evolution of the complex holoplanktonic life history of thaliacean taxa. According to the phenotypic data, this evolution occurred in the plankton, whereas from the combined dataset a secondary transition into the plankton from a sessile ascidian is inferred. Besides these major differences, both analyses are in accord on many phylogenetic groupings, although both phylogenetic reconstructions invoke a high degree of homoplasy. In conclusion, this study represents the first serious attempt to utilize the potential phylogenetic information present in phenotypic characters to elucidate the inter-relationships of this diverse marine taxon in a consistent cladistic framework.

Inferring Tunicate Relationships and the Evolution of the Tunicate Hox Cluster with the Genome of Corella inflata

Tunicates, the closest living relatives of vertebrates, have served as a foundational model of early embryonic development for decades. Comparative studies of tunicate phylogeny and genome evolution provide a critical framework for analyzing chordate diversification and the emergence of vertebrates. Toward this goal, we sequenced the genome of Corella inflata (Ascidiacea, Phlebobranchia), so named for the capacity to brood self-fertilized embryos in a modified, "inflated" atrial chamber. Combining the new genome sequence for Co. inflata with publicly available tunicate data, we estimated a tunicate species phylogeny, reconstructed the ancestral Hox gene cluster at important nodes in the tunicate tree, and compared patterns of gene loss between Co. inflata and Ciona robusta, the prevailing tunicate model species. Our maximum-likelihood and Bayesian trees estimated from a concatenated 210-gene matrix were largely concordant and showed that Aplousobranchia was nested within a paraphyletic Phlebobranchia. We demonstrated that this relationship is not an artifact due to compositional heterogeneity, as had been suggested by previous studies. In addition, within Thaliacea, we recovered Doliolida as sister to the clade containing Salpida and Pyrosomatida. The Co. inflata genome provides increased resolution of the ancestral Hox clusters of key tunicate nodes, therefore expanding our understanding of the evolution of this cluster and its potential impact on tunicate morphological diversity. Our analyses of other gene families revealed that several cardiovascular associated genes (e.g., BMP10, SCL2A12, and PDE2a) absent from Ci. robusta, are present in Co. inflata. Taken together, our results help clarify tunicate relationships and the genomic content of key ancestral nodes within this phylogeny, providing critical insights into tunicate evolution.

Phylogenetic Analyses of Sites in Different Protein Structural Environments Result in Distinct Placements of the Metazoan Root

Phylogenomics, the use of large datasets to examine phylogeny, has revolutionized the study of evolutionary relationships. However, genome-scale data have not been able to resolve all relationships in the tree of life; this could reflect, at least in part, the poor-fit of the models used to analyze heterogeneous datasets. Some of the heterogeneity may reflect the different patterns of selection on proteins based on their structures. To test that hypothesis, we developed a pipeline to divide phylogenomic protein datasets into subsets based on secondary structure and relative solvent accessibility. We then tested whether amino acids in different structural environments had distinct signals for the topology of the deepest branches in the metazoan tree. We focused on a dataset that appeared to have a mixture of signals and we found that the most striking difference in phylogenetic signal reflected relative solvent accessibility. Analyses of exposed sites (residues located on the surface of proteins) yielded a tree that placed ctenophores sister to all other animals whereas sites buried inside proteins yielded a tree with a sponge+ctenophore clade. These differences in phylogenetic signal were not ameliorated when we conducted analyses using a set of maximum-likelihood profile mixture models. These models are very similar to the Bayesian CAT model, which has been used in many analyses of deep metazoan phylogeny. In contrast, analyses conducted after recoding amino acids to limit the impact of deviations from compositional stationarity increased the congruence in the estimates of phylogeny for exposed and buried sites; after recoding amino acid trees estimated using the exposed and buried site both supported placement of ctenophores sister to all other animals. Although the central conclusion of our analyses is that sites in different structural environments yield distinct trees when analyzed using models of protein evolution, our amino acid recoding analyses also have implications for metazoan evolution. Specifically, our results add to the evidence that ctenophores are the sister group of all other animals and they further suggest that the placozoa+cnidaria clade found in some other studies deserves more attention. Taken as a whole, these results provide striking evidence that it is necessary to achieve a better understanding of the constraints due to protein structure to improve phylogenetic estimation.

The eventful history of nonembryonic development in tunicates

Tunicates encompass a large group of marine filter-feeding animals and more than half of them are able to reproduce asexually by a particular form of nonembryonic development (NED) generally called budding. The phylogeny of tunicates suggests that asexual reproduction is an evolutionarily plastic trait, a view that is further reinforced by the fact that budding mechanisms differ from one species to another, involving nonhomologous tissues and cells. In this review, we explore more than 150 years of literature to provide an overview of NED diversity and we present a comparative picture of budding tissues across tunicates. Based on the phylogenetic relationships between budding and nonbudding species, we hypothesize that NED diversity is the result of seven independent acquisitions and subsequent diversifications in the course of tunicate evolution. While this scenario represents the state-of-the-art of our current knowledge, we point out gray areas that need to be further explored to refine our understanding of tunicate phylogeny and NED. Tunicates, with their plastic evolution and diversity of budding, represent an ideal playground for evolutionary developmental biologists to unravel the genetic and molecular mechanisms regulating nonembryonic development, as well as to better understand how such a profound innovation in life-history has evolved in numerous metazoans.

Regulation and evolution of muscle development in tunicates

For more than a century, studies on tunicate muscle formation have revealed many principles of cell fate specification, gene regulation, morphogenesis, and evolution. Here, we review the key studies that have probed the development of all the various muscle cell types in a wide variety of tunicate species. We seize this occasion to explore the implications and questions raised by these findings in the broader context of muscle evolution in chordates.

A redescription of Syncarpacomposita (Ascidiacea, Stolidobranchia) with an inference of its phylogenetic position within Styelidae

Two species of styelid colonial ascidians in the genus Syncarpa Redikorzev, 1913 are known from the northwest Pacific. The valid status of the lesser known species, Syncarpacomposita (Tokioka, 1951) (type locality: Akkeshi, Japan), is assessed here. To assess the taxonomic identity of S.composita, we compared one of the syntypes and freshly collected topotypes of S.composita with a syntype of S.oviformis Redikorzev, 1913 (type locality: Ul’banskij Bay, Russia). Specimens of S.composita consistently differed from the syntype of S.oviformis in the number of oral tentacles, the number of size-classes of transverse vessels, and the number of anal lobes. In this paper, S.composita is redescribed as distinct from S.oviformis, and its phylogenetic position inferred within Styelidae based on the 18S rRNA and cytochrome c oxidase subunit I gene sequences. In our phylogenetic tree, Syncarpa formed a well-supported clade together with Dendrodoa MacLeay, 1824. In Syncarpa and Dendrodoa, a single gonad is situated on the right side of the body, which is unique among Styelidae, and thus can be a synapomorphy for this clade.

Convergent Acquisition of Nonembryonic Development in Styelid Ascidians

Asexual propagation and whole body regeneration are forms of nonembryonic development (NED) widespread across animal phyla and central in life history and evolutionary diversification of metazoans. Whereas it is challenging to reconstruct the gains or losses of NED at large phylogenetic scale, comparative studies could benefit from being conducted at more restricted taxonomic scale, in groups for which phylogenetic relationships are well established. The ascidian family of Styelidae encompasses strictly sexually reproducing solitary forms as well as colonial species that combine sexual reproduction with different forms of NED. To date, the phylogenetic relationships between colonial and solitary styelids remain controversial and so is the pattern of NED evolution. In this study, we built an original pipeline to combine eight genomes with 18 de novo assembled transcriptomes and constructed data sets of unambiguously orthologous genes. Using a phylogenomic super-matrix of 4,908 genes from these 26 tunicates we provided a robust phylogeny of this family of chordates, which supports two convergent acquisitions of NED. This result prompted us to further describe the budding process in the species Polyandrocarpa zorritensis, leading to the discovery of a novel mechanism of asexual development. Whereas the pipeline and the data sets produced can be used for further phylogenetic reconstructions in tunicates, the phylogeny provided here sets an evolutionary framework for future experimental studies on the emergence and disappearance of complex characters such as asexual propagation and whole body regeneration.

The gelatinase MMP-9like is involved in regulation of LPS inflammatory response in Ciona robusta

Matrix metalloproteinases (MMPs) are a family of endopeptidases collectively able to degrade the components of the extracellular matrix (ECM), with important roles in many biological processes, such as embryogenesis, normal tissue remodelling, angiogenesis and wound healing. New views on the function of MMPs reveal that they regulate inflammatory response and therefore might represent an early step in the evolution of the immune system. MMPs can affect the activity of cytokines involved in inflammation including TGF-β and TNF-α. MMPs are widely distributed in all kingdoms of life and have likely evolved from a single-domain protein which underwent successive rounds of duplications. In this study, we focused on the Ciona robusta (formerly known as Ciona intestinalis) MMP gelatinase homologue. Gene organization, phylogenetic analysis and 3D modeling supported the closest correlation of C. robusta gelatinase with the human MMP-9. Real-time PCR analysis and zymographic assay showed a prompt expression induced by LPS inoculation and an upregulation of enzymatic activity. Furthermore, we showed that before of the well-known increase of TGF-β and TNF-α levels, a MMP-9like boost occurred, suggesting a possible involvement of MMP-9like in regulating inflammatory response in C. robusta.

Developmental system drift in motor ganglion patterning between distantly related tunicates

BACKGROUND

The larval nervous system of the solitary tunicate Ciona is a simple model for the study of chordate neurodevelopment. The development and connectivity of the Ciona motor ganglion have been studied in fine detail, but how this important structure develops in other tunicates is not well known.

METHODS AND RESULTS

By comparing gene expression patterns in the developing MG of the distantly related tunicate Molgula occidentalis, we found that its patterning is highly conserved compared to the Ciona MG. MG neuronal subtypes in Molgula were specified in the exact same positions as in Ciona, though the timing of subtype-specific gene expression onset was slightly shifted to begin earlier, relative to mitotic exit and differentiation. In transgenic Molgula embryos electroporated with Dmbx reporter plasmids, we were also able to characterize the morphology of the lone pair of descending decussating neurons (ddNs) in Molgula, revealing the same unique contralateral projection seen in Ciona ddNs and their putative vertebrate homologs the Mauthner cells. Although Dmbx expression labels the ddNs in both species, cross-species transgenic assays revealed significant changes to the regulatory logic underlying Dmbx transcription. We found that Dmbx cis-regulatory DNAs from Ciona can drive highly specific reporter gene expression in Molgula ddNs, but Molgula sequences are not active in Ciona ddNs.

CONCLUSIONS

This acute divergence in the molecular mechanisms that underlie otherwise functionally conserved cis-regulatory DNAs supports the recently proposed idea that the extreme genetic plasticity observed in tunicates may be attributed to the extreme rigidity of the spatial organization of their embryonic cell lineages.

Ascidian Zic Genes

Ascidians are tunicates, which constitute the sister group of vertebrates. The ascidian genome contains two Zic genes, called Zic-r.a (also called Macho-1) and Zic-r.b (ZicL). The latter is a multi-copy gene, and the precise copy number has not yet been determined. Zic-r.a is maternally expressed, and soon after fertilization Zic-r.a mRNA is localized in the posterior pole of the zygote. Zic-r.a protein is translated there and is involved in specification of posterior fate; in particular it is important for specification of muscle fate. Zic-r.a is also expressed zygotically in neural cells of the tailbud stage. On the other hand, Zic-r.b is first expressed in marginal cells of the vegetal hemisphere of 32-cell embryos and then in neural cells that contribute to the central nervous system during gastrulation. Zic-r.b is required first for specification of mesodermal tissues and then for specification of the central nervous system. Their upstream and downstream genetic pathways have been studied extensively by functional assays, which include gene knockdown and chromatin immunoprecipitation assays. Thus, ascidian Zic genes play central roles in specification of mesodermal and neural fates.

Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity

Although animals are among the best studied organisms, we still lack a full description of their diversity, especially for microscopic taxa. This is partly due to the time-consuming and costly nature of surveying animal diversity through morphological and molecular studies of individual taxa. A powerful alternative is the use of high-throughput environmental sequencing, providing molecular data from all organisms sampled. We here address the unknown diversity of animal phyla in marine environments using an extensive dataset designed to assess eukaryotic ribosomal diversity among European coastal locations. A multi-phylum assessment of marine animal diversity that includes water column and sediments, oxic and anoxic environments, and both DNA and RNA templates, revealed a high percentage of novel 18S rRNA sequences in most phyla, suggesting that marine environments have not yet been fully sampled at a molecular level. This novelty is especially high among Platyhelminthes, Acoelomorpha, and Nematoda, which are well studied from a morphological perspective and abundant in benthic environments. We also identified, based on molecular data, a potentially novel group of widespread tunicates. Moreover, we recovered a high number of reads for Ctenophora and Cnidaria in the smaller fractions suggesting their gametes might play a greater ecological role than previously suspected.

Odontonia plurellicola sp. n. and Odontonia bagginsi sp. n., two new ascidian-associated shrimp from Ternate and Tidore, Indonesia, with a phylogenetic reconstruction of the genus (Crustacea, Decapoda, Palaemonidae)

Two new species of palaemonid shrimp associated with ascidian hosts, Odontonia bagginsisp. n. from Tidore and Odontonia plurellicolasp. n., from Ternate, Indonesia are described and figured. Through phylogenetic analyses based on both morphological and molecular datasets (mitochondrial Cytochrome c oxidase subunit I gene and the 16S mitochondrial ribosomal gene) of the genus Odontonia, the phylogenetic positions of the new species have been reconstructed. Scanning Electron Microscopy has been used to observe additional characters on dactyli of the ambulatory pereiopods. Odontonia plurellicolasp. n. appears to be more closely related to O. simplicipes and O. seychellensis, but it differs most notably in the morphology of the rostrum and mouthparts. Odontonia plurellicolasp. n. appears to be the only Odontonia species living inside a phlebobranch ascidian Plurella sp. Odontonia bagginsisp. n. is closely related to O. sibogae, but differs markedly in the abundance of setae on the propodi of the ambulatory pereiopods. In the present paper, O. maldivensis Fransen, 2006 is regarded as a junior synonym of O. rufopunctata Fransen, 2002 based on both morphological and molecular aspects.

Identification of CPE and GAIT elements in 3'UTR of macrophage migration inhibitory factor (MIF) involved in inflammatory response induced by LPS in Ciona robusta

Innate immune responses face infectious microorganisms by inducing inflammatory responses. Multiple genes within distinct functional categories are coordinately and temporally regulated by transcriptional 'on' and 'off' switches that account for the specificity of gene expression in response to external stimuli. Mechanisms that control transcriptional and post-transcriptional regulation are important in coordinating the initiation and resolution of inflammation. Macrophage migration inhibitory factor (MIF) is an important cytokine that, in Ciona robusta, is related to inflammatory response. It is well known that in C. robusta, formerly known as Ciona intestinalis, the pharynx is involved in the inflammatory reaction induced by lipopolysaccharide (LPS) injection in the body wall. Using this biological system, we describe the identification of two C. robusta MIFs (CrMIF1 and CrMIF2). The phylogenetic tree and modeling support a close relationship with vertebrate MIF family members. CrMIF1 and CrMIF2 possess two evolutionally conserved catalytic sites: a tautomerase and an oxidoreductase site with a conserved CXXC motif. Real-time PCR analysis shows a prompt expression induced by LPS inoculation in CrMIF1 and a late upregulation of CrMIF2 and in silico analyses of 3'UTR show a cis-acting GAIT element and a CPE element in 3'-UTR, which are not present in the 3'-UTR of CrMIF1, suggesting that different transcriptional and post-transcriptional control mechanisms are involved in the regulation of gene expression of MIF during inflammatory response in C. robusta.

A phylogenomic framework and timescale for comparative studies of tunicates

Background

Tunicates are the closest relatives of vertebrates and are widely used as models to study the evolutionary developmental biology of chordates. Their phylogeny, however, remains poorly understood, and to date, only the 18S rRNA nuclear gene and mitogenomes have been used to delineate the major groups of tunicates. To resolve their evolutionary relationships and provide a first estimate of their divergence times, we used a transcriptomic approach to build a phylogenomic dataset including all major tunicate lineages, consisting of 258 evolutionarily conserved orthologous genes from representative species.

Results

Phylogenetic analyses using site-heterogeneous CAT mixture models of amino acid sequence evolution resulted in a strongly supported tree topology resolving the relationships among four major tunicate clades: (1) Appendicularia, (2) Thaliacea + Phlebobranchia + Aplousobranchia, (3) Molgulidae, and (4) Styelidae + Pyuridae. Notably, the morphologically derived Thaliacea are confirmed as the sister group of the clade uniting Phlebobranchia + Aplousobranchia within which the precise position of the model ascidian genus Ciona remains uncertain. Relaxed molecular clock analyses accommodating the accelerated evolutionary rate of tunicates reveal ancient diversification (~ 450–350 million years ago) among the major groups and allow one to compare their evolutionary age with respect to the major vertebrate model lineages.

Conclusions

Our study represents the most comprehensive phylogenomic dataset for the main tunicate lineages. It offers a reference phylogenetic framework and first tentative timescale for tunicates, allowing a direct comparison with vertebrate model species in comparative genomics and evolutionary developmental biology studies.

Electronic supplementary material

The online version of this article (10.1186/s12915-018-0499-2) contains supplementary material, which is available to authorized users.

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.

Reporter Analyses Reveal Redundant Enhancers that Confer Robustness on Cis-Regulatory Mechanisms

Reporter analyses of Hox1 and Brachyury (Bra) genes have revealed examples of redundant enhancers that provide regulatory robustness. Retinoic acid (RA) activates through an RA-response element the transcription of Hox1 in the nerve cord of the ascidian Ciona intestinalis. We also found a weak RA-independent neural enhancer within the second intron of Hox1. The Hox1 gene in the larvacean Oikopleura dioica is also expressed in the nerve cord. The O. dioica genome, however, does not contain the RA receptor-encoding gene, and the expression of Hox1 has become independent of RA. We have found that the upstream sequence of the O. dioica Hox1 was able to activate reporter gene expression in the nerve cord of the C. intestinalis embryo, suggesting that an RA-independent regulatory system in the nerve cord might be common in larvaceans and ascidians. This RA-independent redundant regulatory system may have facilitated the Oikopleura ancestor losing RA signaling without an apparent impact on Hox1 expression domains. On the other hand, vertebrate Bra is expressed in the ventral mesoderm and notochord, whereas its ascidian ortholog is exclusively expressed in the notochord. Fibroblast growth factor (FGF) induces Bra in the ventral mesoderm in vertebrates, whereas it induces Bra in the notochord in ascidians. Disruption of the FGF signal does not completely silence Bra expression in ascidians, suggesting that FGF-dependent and independent enhancers might comprise a redundant regulatory system in ascidians. The existence of redundant enhancers, therefore, provides regulatory robustness that may facilitate the acquisition of new expression domains.

In situ metabolomic- and transcriptomic-profiling of the host-associated cyanobacteria Prochloron and Acaryochloris marina

The tropical ascidian Lissoclinum patella hosts two enigmatic cyanobacteria: (1) the photoendosymbiont Prochloron spp., a producer of valuable bioactive compounds and (2) the chlorophyll-d containing Acaryochloris spp., residing in the near-infrared enriched underside of the animal. Despite numerous efforts, Prochloron remains uncultivable, restricting the investigation of its biochemical potential to cultivation-independent techniques. Likewise, in both cyanobacteria, universally important parameters on light-niche adaptation and in situ photosynthetic regulation are unknown. Here we used genome sequencing, transcriptomics and metabolomics to investigate the symbiotic linkage between host and photoendosymbiont and simultaneously probed the transcriptional response of Acaryochloris in situ. During high light, both cyanobacteria downregulate CO2 fixing pathways, likely a result of O2 photorespiration on the functioning of RuBisCO, and employ a variety of stress-quenching mechanisms, even under less stressful far-red light (Acaryochloris). Metabolomics reveals a distinct biochemical modulation between Prochloron and L. patella, including noon/midnight-dependent signatures of amino acids, nitrogenous waste products and primary photosynthates. Surprisingly, Prochloron constitutively expressed genes coding for patellamides, that is, cyclic peptides of great pharmaceutical value, with yet unknown ecological significance. Together these findings shed further light on far-red-driven photosynthesis in natural consortia, the interplay of Prochloron and its ascidian partner in a model chordate photosymbiosis and the uncultivability of Prochloron.

Insight into higher-level phylogeny of Neuropterida: Evidence from secondary structures of mitochondrial rRNA genes and mitogenomic data

It is well known that the rRNA structure information is important to assist phylogenetic analysis through identifying homologous positions to improve alignment accuracy. In addition, the secondary structure of some conserved motifs is highly stable among distantly related taxa, which can provide potentially informative characters for estimating phylogeny. In this paper, we applied the high-throughput pooled sequencing approach to the determination of neuropteran mitogenomes. Four complete mitogenome sequences were obtained: Micromus angulatus (Hemerobiidae), Chrysoperla nipponensis (Chrysopidae), Rapisma sp. (Ithonidae), and Thaumatosmylus sp. (Osmylidae). This allowed us to sample more complete mitochondrial RNA gene sequences. Secondary structure diagrams for the complete mitochondrial small and large ribosomal subunit RNA genes of eleven neuropterid species were predicted. Comparative analysis of the secondary structures indicated a closer relationship of Megaloptera and Neuroptera. This result was congruent with the resulting phylogeny inferred from sequence alignments of all 37 mitochondrial genes, namely the hypothesis of (Raphidioptera + (Megaloptera + Neuroptera)).

Who Let the CAT Out of the Bag? Accurately Dealing with Substitutional Heterogeneity in Phylogenomic Analyses

As phylogenetic datasets have increased in size, site-heterogeneous substitution models such as CAT-F81 and CAT-GTR have been advocated in favor of other models because they purportedly suppress long-branch attraction (LBA). These models are two of the most commonly used models in phylogenomics, and they have been applied to a variety of taxa, ranging from Drosophila to land plants. However, many arguments in favor of CAT models have been based on tenuous assumptions about the true phylogeny, rather than rigorous testing with known trees via simulation. Moreover, CAT models have not been compared to other approaches for handling substitutional heterogeneity such as data partitioning with site-homogeneous substitution models. We simulated amino acid sequence datasets with substitutional heterogeneity on a variety of tree shapes including those susceptible to LBA. Data were analyzed with both CAT models and partitioning to explore model performance; in total over 670,000 CPU hours were used, of which over 97% was spent running analyses with CAT models. In many cases, all models recovered branching patterns that were identical to the known tree. However, CAT-F81 consistently performed worse than other models in inferring the correct branching patterns, and both CAT models often overestimated substitutional heterogeneity. Additionally, reanalysis of two empirical metazoan datasets supports the notion that CAT-F81 tends to recover less accurate trees than data partitioning and CAT-GTR. Given these results, we conclude that partitioning and CAT-GTR perform similarly in recovering accurate branching patterns. However, computation time can be orders of magnitude less for data partitioning, with commonly used implementations of CAT-GTR often failing to reach completion in a reasonable time frame (i.e., for Bayesian analyses to converge). Practices such as removing constant sites and parsimony uninformative characters, or using CAT-F81 when CAT-GTR is deemed too computationally expensive, cannot be logically justified. Given clear problems with CAT-F81, phylogenies previously inferred with this model should be reassessed. [Data partitioning; phylogenomics, simulation, site-heterogeneity, substitution models.].

ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets

ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates.

Microinjection of Exogenous DNA into Eggs of Halocynthia roretzi

Exogenous gene expression assays during development, including reporters under the control of 5' upstream enhancer regions of genes, constitute a powerful technique for understanding the mechanisms of tissue-specific gene expression regulation and determining the characteristics, behaviors, and functions of cells that express these genes. The simple marine chordate Halocynthia roretzi has been used for these transgenic analyses for a long time and is an excellent model system for such studies, especially in comparative analyses with other ascidians. In this study, I describe simple methods for microinjecting H. roretzi eggs with exogenous DNA, such as a promoter construct consisting of a 5' upstream region and a reporter gene, which are prerequisites for transgenic analyses. I also describe basic knowledge regarding this ascidian species, providing reasons why it is an ideal subject for developmental biology studies.

Hox gene cluster of the ascidian, Halocynthia roretzi, reveals multiple ancient steps of cluster disintegration during ascidian evolution

BACKGROUND

Hox gene clusters with at least 13 paralog group (PG) members are common in vertebrate genomes and in that of amphioxus. Ascidians, which belong to the subphylum Tunicata (Urochordata), are phylogenetically positioned between vertebrates and amphioxus, and traditionally divided into two groups: the Pleurogona and the Enterogona. An enterogonan ascidian, Ciona intestinalis (Ci), possesses nine Hox genes localized on two chromosomes; thus, the Hox gene cluster is disintegrated. We investigated the Hox gene cluster of a pleurogonan ascidian, Halocynthia roretzi (Hr) to investigate whether Hox gene cluster disintegration is common among ascidians, and if so, how such disintegration occurred during ascidian or tunicate evolution.

RESULTS

Our phylogenetic analysis reveals that the Hr Hox gene complement comprises nine members, including one with a relatively divergent Hox homeodomain sequence. Eight of nine Hr Hox genes were orthologous to Ci-Hox1, 2, 3, 4, 5, 10, 12 and 13. Following the phylogenetic classification into 13 PGs, we designated Hr Hox genes as Hox1, 2, 3, 4, 5, 10, 11/12/13.a, 11/12/13.b and HoxX. To address the chromosomal arrangement of the nine Hox genes, we performed two-color chromosomal fluorescent in situ hybridization, which revealed that the nine Hox genes are localized on a single chromosome in Hr, distinct from their arrangement in Ci. We further examined the order of the nine Hox genes on the chromosome by chromosome/scaffold walking. This analysis suggested a gene order of Hox1, 11/12/13.b, 11/12/13.a, 10, 5, X, followed by either Hox4, 3, 2 or Hox2, 3, 4 on the chromosome. Based on the present results and those previously reported in Ci, we discuss the establishment of the Hox gene complement and disintegration of Hox gene clusters during the course of ascidian or tunicate evolution.

CONCLUSIONS

The Hox gene cluster and the genome must have experienced extensive reorganization during the course of evolution from the ancestral tunicate to Hr and Ci. Nevertheless, some features are shared in Hox gene components and gene arrangement on the chromosomes, suggesting that Hox gene cluster disintegration in ascidians involved early events common to tunicates as well as later ascidian lineage-specific events.

Presence of the tunicate Asterocarpa humilis on ship hulls and aquaculture facilities in the coast of the Biobío Region, south central Chile

Non-native ascidians are important members of the fouling community associated with artificial substrata and man-made structures. Being efficient fouling species, they are easily spread by human-mediated transports (e.g., with aquaculture trade and maritime transports). This is exemplified by the ascidian Asterocarpa humilis which displays a wide distribution in the Southern Hemisphere and has been recently reported in the Northern Hemisphere (NW Europe). In continental Chile, its first report dates back from 2000 for the locality of Antofagasta (23°S). Although there was no evidence about the vectors of introduction and spread, nor the source, some authors suggested maritime transport by ship hulls and aquaculture devices as putative introduction pathways and vectors. In the present study, we report for the first time the presence of A. humilis on the hull of an international ship in a commercial port in Concepción bay (36°S), south central Chile. We also found one individual associated to a seashell farm, 70 km far from Concepción bay. Further individuals were subsequently identified within Concepción bay: one juvenile settled upon international harbor pilings and a dozen individuals along aquaculture seashell longlines. For the first specimens sampled, species identification was ascertained using both morphological criteria and molecular barcoding, using the mitochondrial gene cytochrome c oxidase subunit I (COI) and a nuclear gene (ribosomal RNA 18S). The nuclear 18S gene and the mitochondrial gene COI clearly assigned the specimens to A. humilis, confirming our morphological identification. Two haplotypes were obtained with COI corresponding to haplotypes previously obtained with European and Northern Chilean specimens. The present study thus reports for the first time the presence of A. humilis in the Araucanian ecoregion, documenting the apparent expansion of this non-native tunicate in Chile over 2,000 km, spanning over three ecoregions. In addition we reveal the potential implication of the international maritime transport as a vector of spread of this species along the Eastern Pacific coast, and the putative role of aquaculture facilities in promoting local establishments of non-native tunicates.

Structure and ultrastructure of eyes and brains of Thalia democratica (Thaliacea, Tunicata, Chordata)

Salps are marine planktonic chordates that possess an obligatory alternation of reproductive modes in subsequent generations. Within tunicates, salps represent a derived life cycle and are of interest in considerations of the evolutionary origin of complex anatomical structures and life history strategies. In the present study, the eyes and brains of both the sexual, aggregate blastozooid and the asexual, solitary oozooid stage of Thalia democratica (Forskål, ) were digitally reconstructed in detail based on serial sectioning for light and transmission electron microscopy. The blastozooid stage of T. democratica possesses three pigment cup eyes, situated in the anterior ventral part of the brain. The eyes are arranged in a way that the optical axes of each eye point toward different directions. Each eye is an inverse eye that consists of two different cell types: pigment cells (pigc) and rhabdomeric photoreceptor cells (prcs). The oozooid stage of T. democratica is equipped with a single horseshoe-shaped eye, positioned in the anterior dorsal part of the brain. The opening of the horseshoe-shaped eye points anteriorly. Similar to the eyes of the blastozooid, the eye of the oozooid consists of pigment cells and rhabdomeric photoreceptor cells. The rhabdomeric photoreceptor cells possess apical microvilli that form a densely packed presumably photosensitive receptor part adjacent to the concave side of the pigc. We suggest correspondences of the individual eyes in the blastozooid stage to respective parts of the single horseshoe-shaped eye in the oozooid stage and hypothesize that the differences in visual structures and brain anatomies evolved as a result of the aggregate life style of the blastozooid as opposed to the solitary life style of the oozooid.