Yue Him Wong

The molecular control and ancestral state of dorsal–ventral patterning within spiralians remain unclear due to the remarkable diversity across species. Here we present a chromosome-level genome for the brachiopod Lingula anatina and apply functional transcriptomics to study dorsal–ventral patterning under BMP signalling control. We uncover asymmetrical activation of BMP signalling at the dorsal side of the gastrula, governed by ventral chordin expression and a ‘seesaw’ of BMP ligands. Using small-molecule drugs and recombinant proteins, we show that high BMP activity inhibits genes typically associated with neural patterning during gastrula and larval stages, similar to deuterostomes and non-spiralian protostomes. Our findings suggest deep conservation of this mechanism across all three major bilaterian clades, supported by striking similarities in BMP-regulated gene sets between brachiopods and Xenopus . We argue that the spiralian ancestor retained the ancestral bilaterian mechanism, although downstream network components have undergone developmental system drift.

The endoparasitic rhizocephalan Parasacculina sinensis has a radically simplified morphology and primarily infests decapods crustaceans. Rhizocephalan barnacles usually absorb nutrients from the host through a complex rootlet system (the interna), and also change the morphology, physiology and behavior of their hosts. However, little is known about the transcriptomic landscape, ultrastructural details and gene expression of the interna rootlets in the group. In this study, we investigated the structural and molecular signatures of the interna of P. sinensis by using detailed histological staining and transcriptomic analyses. The interconnected F-actin nodal network, lipid droplets, and nucleus of interna rootlets were visualized using fluorescence straining. We successfully obtained a clean transcriptome of P. sinensis and conducted functional analyses of interna embedded within host hepatopancreas, claw muscle, and eyestalk. The gene ontology (GO) terms related to translation, metabolic process, biosynthetic process, cellular process were highly expressed in the top 10% transcripts from the interna. The GO category of shared differential expression of genes (DEGs) among internae was related to embryonic development. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway neuroactive ligand-receptor interaction and the GO term neurotransmitter transporter activity were identified in the shared DEGs among internae. The interna entangled within host hepatopancreas, eyestalk and claw muscle fibers had similarities and differences in the functional biology. Additionally, the interna specific candidate genes probably involved in host immune, lipid metabolism, molting and growth were identified. Our study demonstrates an in-depth function of interna rootlets of P. sinensis and reveals potential mechanisms of parasite host control. This study provides novel information to further investigate the evolutionary drivers of parasitism in barnacles.

Marseilleviruses are a group of double-strand DNA viruses that infect amoeba within the Nucleocytoviricota phylum and are ubiquitous in water and soil globally. Here, we report four novel strains isolated from mangroves in Guangdong province, China, namely, futianmevirus, futianmfvirus, dashavirus str. E, and xiwanvirus. Viral particles presented about 220∼240 nm icosahedrally shaped capsids and were wrapped by membranes to form giant vesicles. Based on stability assays, viral particles were halotolerant and acid-tolerant, but sensitive to chloroform and high temperature, while giant vesicles conferred thermal and acid/alkaline resistance to particles. Genomics and phylogenetic analyses showed that the four strains formed divergent branches within different lineages of marseillevirus. Notably, to our knowledge, futianmevirus was the first reported marseillevirus lacking translation elongation factor EF-1alpha (EF1A). Our in silico analysis of marseillevirus coded translation-associated homolgs suggested their conserved functions. Additionally, we predicted at least four novel proteins that were structurally similar to components of the protozoan ribosome. Overall, not only our data comprehensively described the diversity of marseillevirus biological properties, but also proposed a new perspective on the giant virus translation system. Importance: The family Marseilleviridae was the second reported family of giant viruses and distributed globally. In this work, we reported the four novel marseilleviruses isolated from saltwater samples of mangrove. Difference of biological properties between giant vesicles and viral particles revealed the environment fitness of marseillevirus. On the other hand, sensitivity to chloroform indicated the importance of lipid components for viral infection. Additionally, our comparative genomics, phylogenetic analysis, and protein structure comparison revealed the diverse translation-associated gene sets of marseilleviruses. The prediction of ribosome components expands the knowledge about the giant viral translation-associated proteins, and will be helpful in future to reveal how giant viruses hijack the amoeba translation system.

Bone morphogenetic protein (BMP) signalling is crucial in regulating dorsal–ventral patterning and cell fate determination during early development in bilaterians. Interactions between BMP ligands and their main antagonist, Chordin, establish BMP gradients, subdivide embryos into distinct territories and organise body plans. However, the molecular control and evolutionary origins of dorsal–ventral patterning within spiralians, one of the three major bilaterian groups, have been obscured by their unique embryonic development. Here we present the chromosome-level genome of a spiralian with deuterostome-like development, the brachiopod Lingula anatina , and apply functional transcriptomics to study dorsal–ventral patterning under the control of BMP signalling. We uncover the presence of a dorsal–ventral BMP signalling gradient in the L. anatina gastrula with bmp2/4 and chordin expressed at its dorsal and ventral sides, respectively. Using small-molecule drugs, exogenous recombinant BMP proteins and RNA sequencing, we show that a high level of BMP pathway activation inhibits the expression of neural genes during gastrula and larval stages. We also show that BMP signalling splits the developing larval shell field into two valves. The discovery of a BMP-mediated dorsal–ventral patterning system in a spiralian, similar to those observed in deuterostomes and non-spiralian protostomes, suggests deep conservation of this mechanism across all three major bilaterian clades. This is further supported by striking similarities in the gene sets regulated by BMP signalling in brachiopods and the vertebrate model Xenopus . We argue that the spiralian ancestor retained the basal bilaterian mechanism of dorsal–ventral patterning, although downstream components of the BMP–Chordin network have undergone dynamic evolutionary changes.

BackgroundAs a group of sessile crustaceans that were being misclassified as mollusks by Carl Linnaeus, barnacles produce calcareous shell plates which, in most species, are permanently attached to the substratum. As biomineralization has independently evolved in multiple marine invertebrate taxa, a key question is how biomineralization has driven the evolution of genetic toolkits underlying shell formation. Here, we explore the shell proteome of the deep-sea acorn barnacleBathylasma hirsutum(Hoek, 1883) using an integrated transcriptomic-proteomic approach and compare the properties of barnacle shell proteins with molluscan shell matrix proteins.ResultsWe identified 31B. hirsutumbarnacle shell proteins (BSPs), including a series of key biomineralization proteins, such as carbonic anhydrase and C-type lectin. More than half of barnacle specific shell proteins (BSSPs) exhibit unknown functions. The amino acid composition of these BSSPs were biased toward A, D, E, G, S, P and Q, and were acidic and hydrophilic. Almost all BSSPs were detected with repetitive low complexity domains. Similar to molluscan shell matrix proteins, RLCDs in D-, and E-rich BSSPs constituted up to 50% amino acid of the whole protein. RLCDs in Q-rich proteins also exhibited similarity to a Q-rich abalone shell matrix protein and an insect cuticle protein.ConclusionFrom theB. hirsutumshell proteome, certain proteins such as carbonic anhydrase, C-type lectin, and peroxidase were implicated in shell formation or protein cross-linking across sessile invertebrate taxa. Despite the lack of sequence homology, D- and Q-rich BSSPs share similar features with molluscan shell matrix proteins in sequence redundancy, amino acid bias and thereby protein isoelectric point and hydropathy. Such convergence may reflect that similar selection pressures shape the molecular evolution of biomineralization and shell formation genes in marine invertebrates.

Acquisition of new genes often results in the emergence of novel functions and is a key step in lineage‐specific adaptation. As a group of sessile crustaceans, barnacles establish permanent attachment through initial cement secretion at the larval phase followed by continuous cement secretion in juveniles and adults. However, the origins and evolution of barnacle larval and adult cement proteins remain poorly understood. By performing microdissection of larval cement glands, transcriptome and shotgun proteomics and immunohistochemistry validation, we identified 30 larval and 27 adult cement proteins of the epibiotic turtle barnacle Chelonibia testudinaria, of which the majority are stage‐ and barnacle‐specific. While only two proteins, SIPC and CP100K, were expressed in both larvae and adults, detection of protease inhibitors and the cross‐linking enzyme lysyl oxidase paralogs in larvae and adult cement. Other barnacle‐specific cement proteins such as CP100k and CP52k likely share a common origin dating back at least to the divergence of Rhizocephala and Thoracica. Different CP52k paralogues could be detected in larval and adult cement, suggesting stage‐specific cement proteins may arise from duplication followed by changes in expression timing of the duplicates. Interestingly, the biochemical properties of larval‐ and adult‐specific CP52k paralogues exhibited remarkable differences. We conclude that barnacle larval and adult cement systems evolved independently, and both emerged from co‐option of existing genes and de novo formation, duplication and functional divergence of lineage‐specific cement protein genes. Our findings provide important insights into the evolutionary mechanisms of bioadhesives in sessile marine invertebrates.

Acquisition of new genes often results in the emergence of novel functions and is a key step in lineage-specific adaptation. As the only group of sessile crustaceans, barnacles establish permanent attachment through initial cement secretion at the larval phase followed by continuous cement secretion in juveniles and adults. However, the origins and evolution of barnacle larval and adult cement proteins remain poorly understood. By performing microdissection of larval cement glands, transcriptome and shotgun proteomics and immunohistochemistry validation, we identified 30 larval and 27 adult cement proteins of the epibiotic turtle barnacle Chelonibia testudinaria, of which the majority are stage- and barnacle-specific. While only two proteins, SIPC and CP100K, were expressed in both larvae and adults, detection of protease inhibitors and the cross-linking enzyme lysyl oxidase paralogs in larvae and adult cement suggested functional convergence. Other barnacle specific cement proteins such as CP100k and CP52k likely share a common origin dating back at least to the divergent of Rhizocephala and Thoracica. Different CP52k paralogs could be detected in larval and adult cement, suggesting stage-specific cement proteins may arise from duplication followed by changes in expression timing of the duplicates. Interestingly, the biochemical properties of larval- and adult-specific CP52k paralogs exhibited remarkable differences, reflecting the composition of cement in different life stages of turtle barnacle might be chemically different. We conclude that de novo gene formation and duplicate neofunctionalization are pivotal to the evolution of lineage-specific cement toolkits in barnacles, which may explain how barnacles can inhabit diverse marine substrata.

The arborescent bryozoanBugulina neritinais a cosmopolitan fouling species in sub-tropical to sub-temperate waters. The butenolide compound 5-octylfuran-2(5H)-one (hereafter named butenolide) reportedly inhibits larval settlement ofB. neritina, but its effect on the larval behavioral and transcriptomic responses remained unclear. We report that 10 μg mL^-1or higher concentration of butenolide and/or prolonged treatment (10 h or longer) resulted in significant increase in larval mortality and prominent spiral larval swimming behavior. The transcriptomic analyses not only revealed up-regulation of typical stress-related protein genes in response to 10 mg mL^-1butenolide treatment, but also indicated up-regulation ofmucin, synaptic genes and nitric oxide signaling genes. In addition, the expression of developmental genes and lipid biosynthesis genes were also affected. Overall, our larval behavior and transcriptome analyses reflected the impact of butenolide on the metabolism, neuronal and molecular signaling inB. neritinalarvae.