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The marine animal phylum Placozoa is characterized by a poorly explored cryptic biodiversity combined with very limited knowledge of their ecology. While placozoans are typically found as part of the epibenthos of coastal waters, known placozoan predators, namely small, shell‐less sea slugs belonging to the family Rhodopidae (Mollusca: Gastropoda: Heterobranchia), inhabit the interstitium of seafloor sediment. In order to gain further insights into this predator–prey relationship and to expand our understanding of placozoan ecological niches, we screened publicly available whole‐body metagenomic data from two rhodopid specimens collected from coastal sediments. Our analysis not only revealed the signatures of three previously unknown placozoan lineages in these sea slug samples but also enabled the assembly of three complete and two partial mitochondrial chromosomes belonging to four previously described placozoan genera, substantially extending the picture of placozoan biodiversity. Our findings further refine the molecular phylogeny of the Placozoa, corroborate the recently established taxonomic ranks in this phylum, and provide molecular support that known placozoan clades should be referred to as genera. We finally discuss the main finding of our study – the presence of placozoans in the sea floor sediment interstitium – in the context of their ecological, biological, and natural history implications. [ABSTRACT FROM AUTHOR]

Mounting evidence suggests that animals and their associated bacteria interact via intricate molecular mechanisms, and it is hypothesized that disturbances to the microbiome influence animal development. Here, we show that the loss of a key photosymbiont (i.e. bleaching) upon shading correlates with a stark body-plan reorganization in the common aquarium cyanosponge Lendenfeldia chondrodes. The morphological changes observed in shaded sponges include the development of a thread-like morphology that contrasts with the flattened, foliose morphology of control specimens. The microanatomy of shaded sponges markedly differed from that of control sponges, with shaded specimens lacking a well-developed cortex and choanosome. Also, the palisade of polyvacuolar gland-like cells typical in control specimens was absent in shaded sponges. The morphological changes observed in shaded specimens are coupled with broad transcriptomic changes and include the modulation of signaling pathways involved in animal morphogenesis and immune response, such as the Wnt, transforming growth factor β (TGF- β), and TLR–ILR pathways. This study provides a genetic, physiological, and morphological assessment of the effect of microbiome changes on sponge postembryonic development and homeostasis. The correlated response of the sponge host to the collapse of the population of symbiotic cyanobacteria provides evidence for a coupling between the sponge transcriptomic state and the state of its microbiome. This coupling suggests that the ability of animals to interact with their microbiomes and respond to microbiome perturbations has deep evolutionary origins in this group. [ABSTRACT FROM AUTHOR]

The use of RNA sequencing (RNA‐Seq) data and the generation of de novo transcriptome assemblies have been pivotal for studies in ecology and evolution. This is especially true for nonmodel organisms, where no genome information is available. In such organisms, studies of differential gene expression, DNA enrichment bait design and phylogenetics can all be accomplished with de novo transcriptome assemblies. Multiple tools are available for transcriptome assembly, but no single tool can provide the best assembly for all data sets. Therefore, a multi‐assembler approach, followed by a reduction step, is often sought to generate an improved representation of the assembly. To reduce errors in these complex analyses while at the same time attaining reproducibility and scalability, automated workflows have been essential in the analysis of RNA‐Seq data. However, most of these tools are designed for species where genome data are used as reference for the assembly process, limiting their use in nonmodel organisms. We present TransPi, a comprehensive pipeline for de novo transcriptome assembly, with minimum user input but without losing the ability of a thorough analysis. A combination of different model organisms, k‐mer sets, read lengths and read quantities was used for assessing the tool. Furthermore, a total of 49 nonmodel organisms, spanning different phyla, were also analysed. Compared to approaches using single assemblers only, TransPi produces higher BUSCO completeness percentages, and a concurrent significant reduction in duplication rates. TransPi is easy to configure and can be deployed seamlessly using Conda, Docker and Singularity. [ABSTRACT FROM AUTHOR]

Conservation scientists are producing valuable science in Mongolia and elsewhere, and they are advocating for conservation more aggressively than ever before (United Nations [31]; Nelson and Vucetich [25]; Kotcher et al. [21]; Brussard and Tull [7]; Scott et al. [29]). Despite diving headlong into the conservation crisis already evident over 35 years ago, conservation scientists have not stemmed the bleeding, let alone provided a chance for healing. Yet too often conservation scientists are drive-by scientists, conducting research and publishing studies that do not help the public or decision-makers make more sustainable decisions (Donohue et al. [11]). [Extracted from the article]

Brasilicardin A (1) consists of an unusual anti/syn/anti‐perhydrophenanthrene skeleton with a carbohydrate side chain and an amino acid moiety. It exhibits potent immunosuppressive activity, yet its mode of action differs from standard drugs that are currently in use. Further pre‐clinical evaluation of this promising, biologically active natural product is hampered by restricted access to the ready material, as its synthesis requires both a low‐yielding fermentation process using a pathogenic organism and an elaborate, multi‐step total synthesis. Our semi‐synthetic approach included a) the heterologous expression of the brasilicardin A gene cluster in different non‐pathogenic bacterial strains producing brasilicardin A aglycone (5) in excellent yield and b) the chemical transformation of the aglycone 5 into the trifluoroacetic acid salt of brasilicardin A (1 a) via a short and straightforward five‐steps synthetic route. Additionally, we report the first preclinical data for brasilicardin A. [ABSTRACT FROM AUTHOR]

Brasilicardin A (BraA) is a promising immunosuppressive compound produced naturally by the pathogenic bacterium Nocardia terpenica IFM 0406. Heterologous host expression of brasilicardin gene cluster showed to be efficient to bypass the safety issues, low production levels and lack of genetic tools related with the use of native producer. Further improvement of production yields requires better understanding of gene expression regulation within the BraA biosynthetic gene cluster (Bra‐BGC); however, the only so far known regulator of this gene cluster is Bra12. In this study, we discovered the protein LysRNt, a novel member of the LysR‐type transcriptional regulator family, as a regulator of the Bra‐BGC. Using in vitro approaches, we identified the gene promoters which are controlled by LysRNt within the Bra‐BGC. Corresponding genes encode enzymes involved in BraA biosynthesis as well as the key Bra‐BGC regulator Bra12. Importantly, we provide in vivo evidence that LysRNt negatively affects production of brasilicardin congeners in the heterologous host Amycolatopsis japonicum. Finally, we demonstrate that some of the pathway related metabolites, and their chemical analogs, can interact with LysRNt which in turn affects its DNA‐binding activity. [ABSTRACT FROM AUTHOR]

Understanding the temporal changes of the Earth's magnetic field intensity is one of the main goals of modern palaeomagnetism. For most palaeointensity methods to yield reliable results, the magnetic minerals must obey a set of rules. One of these rules is the additivity of partial thermal (TRM) or anhysteretic remanent magnetizations (ARM). Additivity was previously shown for partial TRM in single-domain particles and more generally for ARMs. Additivity between these two low-field remanences, however, has not been investigated, yet. This paper presents a series of rock magnetic experiments on natural low Ti titanomagnetites (Curie temperature between 534 °C and 561 °C) examining the effects of high temperatures on alternating field (AF) demagnetization and acquisition of an ARM. One of our sample sets comes from a borehole drilled through the impact melt sheet of the Manicouagan crater (Canada), the other from the Rocche Rosse lava flow on the island of Lipari (Italy). Hysteresis parameters indicate the magnetic carriers in the pseudo-single-domain range showing no evidence for oxidation. Thermal demagnetization at 300 °C and 500 °C before AF demagnetization shifts the coercivity spectra towards higher fields. AF demagnetization experiments at 500 °C show a significant (by a factor between 1.4 and >7.6) reduction in median destructive field and a shift towards lower coercivities. A linear relationship was found between the peak magnetic field required to demagnetize a fraction of a full TRM of a sample at a specific temperature and the one necessary to demagnetize the same fraction at room temperature after heating to that temperature. The comparison of full ARM and partial TRM at successively higher temperatures with a hybrid hTARM reveals that combined additivity between the two kinds of remanences is fulfilled. These results open the possibility to demagnetize highly coercive minerals, such as hematite and goethite, which is often not achievable at elevated temperatures. Furthermore, the additivity of TRM and ARM remanences may be used to develop novel hybrid TRM/ARM palaeointensity methods for samples, where heating is problematic (e.g. in meteorites). [ABSTRACT FROM AUTHOR]

Resolving the relationships of animals (Metazoa) is crucial to our understanding of the origin of key traits such as muscles, guts, and nerves. However, a broadly accepted metazoan consensus phylogeny has yet to emerge. In part, this is because the genomes of deeply diverging and fast-evolving lineages may undergo significant gene turnover, reducing the number of orthologs shared with related phyla. This can limit the usefulness of traditional phylogenetic methods that rely on alignments of orthologous sequences. Phylogenetic analysis of gene content has the potential to circumvent this orthology requirement, with binary presence/absence of homologous gene families representing a source of phylogenetically informative characters. Applying binary substitution models to the gene content of 26 complete animal genomes, we demonstrate that patterns of gene conservation differ markedly depending on whether gene families are defined by orthology or homology, that is, whether paralogs are excluded or included. We conclude that the placement of some deeply diverging lineages may exceed the limit of resolution afforded by the current methods based on comparisons of orthologous protein sequences, and novel approaches are required to fully capture the evolutionary signal from genes within genomes. [ABSTRACT FROM AUTHOR]

Placozoans are a phylum of nonbilaterian marine animals currently represented by a single described species, Trichoplax adhaerens, Schulze 1883. Placozoans arguably show the simplest animal morphology, which is identical among isolates collected worldwide, despite an apparently sizeable genetic diversity within the phylum. Here, we use a comparative genomics approach for a deeper appreciation of the structure and causes of the deeply diverging lineages in the Placozoa. We generated a high-quality draft genome of the genetic lineage H13 isolated from Hong Kong and compared it to the distantly related T. adhaerens. We uncovered substantial structural differences between the two genomes that point to a deep genomic separation and provide support that adaptation by gene duplication is likely a crucial mechanism in placozoan speciation. We further provide genetic evidence for reproductively isolated species and suggest a genus-level difference of H13 to T. adhaerens, justifying the designation of H13 as a new species, Hoilungia hongkongensis nov. gen., nov. spec., now the second described placozoan species and the first in a new genus. Our multilevel comparative genomics approach is, therefore, likely to prove valuable for species distinctions in other cryptic microscopic animal groups that lack diagnostic morphological characters, such as some nematodes, copepods, rotifers, or mites. [ABSTRACT FROM AUTHOR]

The phylum Placozoa holds a key position for our understanding of the evolution of mitochondrial genomes in Metazoa. Placozoans possess large mitochondrial genomes which harbor several remarkable characteristics such as a fragmented cox1 gene and trans-splicing cox1 introns. A previous study also suggested the existence of cox1 mRNA editing in Trichoplax adhaerens, yet the only formally described species in the phylum Placozoa. We have analyzed RNA-seq data of the undescribed sister species, Placozoa sp. H2 (“Panama” clone), with special focus on the mitochondrial mRNA. While we did not find support for a previously postulated cox1 mRNA editing mechanism, we surprisingly found two independent transcripts representing intermediate cox1 mRNA splicing stages. Both transcripts consist of partial cox1 exon as well as overlapping intron fragments. The data suggest that the cox1 gene harbors a single base pair (cytosine) micro exon. Furthermore, conserved group I intron structures flank this unique micro exon also in other placozoans. We discuss the evolutionary origin of this micro exon in the context of a self-splicing intron gain in the cox1 gene of the last common ancestor of extant placozoans. [ABSTRACT FROM AUTHOR]

Abstract: Impact melt breccias from the Rochechouart (France) meteorite crater possess paleomagnetic directions with both normal and reverse polarities, raising the question whether shock from the collision initiated a geomagnetic field reversal. Stepwise thermal demagnetization together with a suite of rock magnetic experiments, optical microscopy, Raman spectroscopy and electron microprobe analyses identify adjacent, multiphase, titanohematite in the samples containing normal and mixed polarities—typical of lithologies bearing self-reversal behavior stemming from magnetic exchange interaction. Melt breccias possessing mostly titanium-free hematite as the magnetic remanence carrier have solely reverse-polarity directions, leading to the conclusion that the Rochechouart meteorite impact did not spawn a geomagnetic event. Samples displaying paleomagnetic directions with normal or mixed polarity yield unreliable paleointensity data. 30 samples with reverse polarity that pass stringent data selection criteria from Thellier–Thellier paleointensity experiments with alteration, tail and additivity checks define an average field value of . This translates into a virtual dipole moment of , which is relatively low, but within uncertainty of other Mesozoic paleointensity data. [Copyright &y& Elsevier]

The enigmatic animal phylum Placozoa holds a key position in the metazoan Tree of Life. A simple bauplan makes it appear to be the most basal metazoan known and genetic evidence also points to a position close to the last common metazoan ancestor. Trichoplax adhaerens is the only formally described species in the phylum to date, making the Placozoa the only monotypic phylum in the animal kingdom. However, recent molecular genetic as well as morphological studies have identified a high level of diversity, and hence a potential high level of taxonomic diversity, within this phylum. Different taxa, possibly at different taxonomic levels, are awaiting description. In this review we firstly summarize knowledge on the morphology, phylogenetic position and ecology of the Placozoa. Secondly, we give an overview of placozoan morphological and genetic diversity and finally present an updated distribution of placozoan populations. We conclude that there is great potential and need to erect new taxa and to establish a firm system for this taxonomic tabula rasa. [ABSTRACT FROM AUTHOR]

It is generally believed that the last eukaryotic common ancestor (LECA) was a unicellular organism with motile cilia. In the vertebrates, the winged-helix transcription factor FoxJ1 functions as the master regulator of motile cilia biogenesis. Despite the antiquity of cilia, their highly conserved structure, and their mechanism of motility, the evolution of the transcriptional program controlling ciliogenesis has remained incompletely understood. In particular, it is presently not known how the generation of motile cilia is programmed outside of the vertebrates, and whether and to what extent the FoxJ1-dependent regulation is conserved. We have performed a survey of numerous eukaryotic genomes and discovered that genes homologous to foxJ1 are restricted only to organisms belonging to the unikont lineage. Using a mis-expression assay, we then obtained evidence of a conserved ability of FoxJ1 proteins from a number of diverse phyletic groups to activate the expression of a host of motile ciliary genes in zebrafish embryos. Conversely, we found that inactivation of a foxJ1 gene in Schmidtea mediterranea, a platyhelminth (flatworm) that utilizes motile cilia for locomotion, led to a profound disruption in the differentiation of motile cilia. Together, all of these findings provide the first evolutionary perspective into the transcriptional control of motile ciliogenesis and allow us to propose a conserved FoxJ1-regulated mechanism for motile cilia biogenesis back to the origin of the metazoans. [ABSTRACT FROM AUTHOR]

Unraveling animal life cycles and embryonic development is basic to understanding animal biology and often sheds light on phylogenetic relationships. A key group for understanding the evolution of the Metazoa is the early branching phylum Placozoa, which has attracted rapidly increasing attention. Despite over a hundred years of placozoan research the life cycle of this enigmatic phylum remains unknown. Placozoa are a unique model system for which the nuclear genome was published before the basic biology (i.e. life cycle and development) has been unraveled. Four organismal studies have reported the development of oocytes and one genetic study has nourished the hypothesis of sexual reproduction in natural populations at least in the past. Here we report new observations on sexual reproduction and embryonic development in the Placozoa and support the hypothesis of current sexual reproduction. The regular observation of oocytes and expressed sperm markers provide support that placozoans reproduce sexually in the field. Using whole genome and EST sequences and additional cDNA cloning we identified five conserved sperm markers, characteristic for different stages in spermatogenesis. We also report details on the embryonic development up to a 128-cell stage and new ultrastructural features occurring during early development. These results suggest that sperm and oocyte generation and maturation occur in different placozoans and that clonal lineages reproduce bisexually in addition to the standard mode of vegetative reproduction. The sum of observations is best congruent with the hypothesis of a simple life cycle with an alternation of reproductive modes between bisexual and vegetative reproduction. [ABSTRACT FROM AUTHOR]

Total evidence analyses reveal a surprise: Higher animals did not evolve from any known lower animal group. [ABSTRACT FROM AUTHOR]

Methanol dried over powdered 4 Å molecular sieves can be used for a selective mono-de- O -acetylation of the phenolic acetyl group of the per- O -acetyl protected brasilicardin A carbohydrate side chain. This reaction opens a practical procedure for a synthetic access to derivates of the immunosuppressive and cytotoxic natural product brasilicardin A. [Display omitted] • Selective mono-de-O-acetylation method of the per-O-acetyl protected brasilicardin A carbohydrate side chain. • Strategy for the derivatization of the phenolic hydroxyl group of the brasilicardin A side chain is presented. • Our finding enables a straight-forward methodology for the synthesis of brasilicardin A congeners. [ABSTRACT FROM AUTHOR]

We report the mitochondrial genomes of two freshwater sponges,Spongilla lacustrisandEphydatia cf. muelleri. The genomes contain 14 protein-coding genes and are similar in structure to other published mitochondrial genomes from freshwater sponges. TheE. cf. muelleridescribed here is remarkably similar in coding regions to the published genome, but differs in number and length of hairpin-forming repeats between genes. [ABSTRACT FROM PUBLISHER]

Genome sequencing of arguably the simplest known animal, Trichoplax adhaerens, uncovered a rich array of transcription factor and signalling pathway genes. Although the existence of such genes allows speculation about the presence of complex regulatory events, it does not reveal the level of actual protein expression and functionalization through posttranslational modifications. Using high-resolution mass spectrometry, we here semi-quantify 6,516 predicted proteins, revealing evidence of horizontal gene transfer and the presence at the protein level of nodes important in animal signalling pathways. Moreover, our data demonstrate a remarkably high activity of tyrosine phosphorylation, in line with the hypothesized burst of tyrosine-regulated signalling at the instance of animal multicellularity. Together, this Trichoplax proteomics data set offers significant new insight into the mechanisms underlying the emergence of metazoan multicellularity and provides a resource for interested researchers. [ABSTRACT FROM AUTHOR]