Deciphering temporal gene expression dynamics in multiple coral species exposed to heat stress: Implications for predicting resilience.

Coral reefs are facing unprecedented threats due to global climate change, particularly elevated sea surface temperatures causing coral bleaching. Understanding coral responses at the molecular level is crucial for predicting their resilience and developing effective conservation strategies. In this study, we conducted a comprehensive gene expression analysis of four coral species to investigate their long-term molecular response to heat stress. We identified distinct gene expression patterns among the coral species, with laminar corals exhibiting a stronger response compared to branching corals. Heat shock proteins (HSPs) showed an overall decreasing expression trend, indicating the high energy cost associated with sustaining elevated HSP levels during prolonged heat stress. Peroxidases and oxidoreductases involved in oxidative stress response demonstrated significant upregulation, highlighting their role in maintaining cellular redox balance. Differential expression of genes related to calcium homeostasis and bioluminescence suggested distinct mechanisms for coping with heat stress among the coral species. Furthermore, the impact of heat stress on coral biomineralization varied, with downregulation of carbonic anhydrase and skeletal organic matrix proteins indicating reduced capacity for biomineralization in the later stages of heat stress. Our findings provide insights into the molecular mechanisms underlying coral responses to heat stress and highlight the importance of considering species-specific responses in assessing coral resilience. The identified biomarkers may serve as indicators of heat stress and contribute to early detection of coral bleaching events. These findings contribute to our understanding of coral resilience and provide a basis for future research aimed at enhancing coral survival in the face of climate change.

Comparative transcriptome analysis reveals deep molecular landscapes in stony coral Montipora clade.

Introduction: Coral reefs, among the most invaluable ecosystems in the world, face escalating threats from climate change and anthropogenic activities. To decipher the genetic underpinnings of coral adaptation and resilience, we undertook comprehensive transcriptome profiling of two emblematic coral species, Montipora foliosa and Montipora capricornis, leveraging PacBio Iso-Seq technology. These species were strategically selected for their ecological significance and their taxonomic proximity within the Anthozoa class. Methods: Our study encompassed the generation of pristine transcriptomes, followed by thorough functional annotation via diverse databases. Subsequently, we quantified transcript abundance and scrutinized gene expression patterns, revealing notable distinctions between the two species. Results: Intriguingly, shared orthologous genes were identified across a spectrum of coral species, highlighting a substantial genetic conservation within scleractinian corals. Importantly, a subset of genes, integral to biomineralization processes, emerged as exclusive to scleractinian corals, shedding light on their intricate evolutionary history. Furthermore, we discerned pronounced upregulation of genes linked to immunity, stress response, and oxidative-reduction processes in M. foliosa relative to M. capricornis. These findings hint at the presence of more robust mechanisms in M. foliosa for maintaining internal equilibrium and effectively navigating external challenges, underpinning its potential ecological advantage. Beyond elucidating genetic adaptation in corals, our research underscores the urgency of preserving genetic diversity within coral populations. Discussion: These insights hold promise for informed conservation strategies aimed at safeguarding these imperiled ecosystems, bearing ecological and economic significance. In synthesis, our study seamlessly integrates genomic inquiry with ecological relevance, bridging the gap between molecular insights and the imperative to conserve coral reefs in the face of mounting threats.

Coaxial electrostatic spray-based preparation of localization missile liposomes on a microfluidic chip for targeted treatment of triple-negative breast cancer.

Due to triple-negative breast cancer (TNBC) lacking specific targets for efficient therapies, nanoparticles have been widely developed to enhance efficacy and reduce the toxicity of chemotherapeutics. We prepared unique liposomes containing PTX and DOX by microfluidics-based coaxial electrostatic spray method, which have a uniform particle size, high drug loading capacity, and good stability. Meanwhile, the cRGD peptide was fused with the lipid membrane to form PTX/DOX@cRGD-Lipo, which played a GPS role in locating tumor neovascularization and further targeting TNBC cells where both overexpress αvß3. The PTX/DOX@cRGD-Lipo showed synergistic anti-tumor activity of double drugs and enhanced tumor cell apoptosis. Fluorescence microscopy and flow cytometry showed that the co-loaded targeted liposomes could be effectively absorbed by MDA-MB-231 and 4T1 cells and then released the content. In addition, the PTX/DOX@cRGD-Lipo presented excellent targeting biodistribution in vivo and a higher tumor growth inhibition rate in the orthotopic tumor mouse model. All results suggested that the double drug-loaded targeted liposome could be a promising treatment modality for TNBC.

Polyp-Canal Reconstruction Reveals Evolution Toward Complexity in Corals.

Modern scleractinian corals are classified into robust, complex, and basal clades through comparative molecular studies. However, only few morphological or biological criteria can systematically determine the evolutionary trajectories of these major scleractinian coral clades. Here, we obtained the structural information of 21 scleractinian coral species representing robust and complex clades: High-resolution micro-computed tomography was used to reconstruct the polyp-canal systems in their colonies and to visualize the dynamic polyp growth processes. We found that the emergence of mesh-like canals may distinguish representatives of complex and robust clades. The differences in polyp-canal connections suggest distinct evolutionary trajectories among coral species: The formation of the canal network promoted the development of more complex coral structures, and coral polyps within this network formed calices of very similar volume, following precise axial growth directions. The influence of individual polyps on the coral colony becomes less significant as coral structures become more complex, and coral species with more complicated polyp-canal systems occupied niches more efficiently. This work supplements current evolutionary studies on reef-building corals, providing insight for further studies on coral growth patterns.

Three amphioxus reference genomes reveal gene and chromosome evolution of chordates.

The slow-evolving invertebrate amphioxus has an irreplaceable role in advancing our understanding of the vertebrate origin and innovations. Here we resolve the nearly complete chromosomal genomes of three amphioxus species, one of which best recapitulates the 17 chordate ancestor linkage groups. We reconstruct the fusions, retention, or rearrangements between descendants of whole-genome duplications, which gave rise to the extant microchromosomes likely existed in the vertebrate ancestor. Similar to vertebrates, the amphioxus genome gradually establishes its three-dimensional chromatin architecture at the onset of zygotic activation and forms two topologically associated domains at the Hox gene cluster. We find that all three amphioxus species have ZW sex chromosomes with little sequence differentiation, and their putative sex-determining regions are nonhomologous to each other. Our results illuminate the unappreciated interspecific diversity and developmental dynamics of amphioxus genomes and provide high-quality references for understanding the mechanisms of chordate functional genome evolution.

Utilizing an artificial intelligence system to build the digital structural proteome of reef-building corals.

BACKGROUND: Reef-building corals play an important role in the marine ecosystem, and analyzing their proteomes from a structural perspective will exert positive effects on exploring their biology. Here we integrated mass spectrometry with newly published ColabFold to obtain digital structural proteomes of dominant reef-building corals. RESULTS: Of the 8,382 homologous proteins in Acropora muricata, Montipora foliosa, and Pocillopora verrucosa identified, 8,166 received predicted structures after about 4,060 GPU hours of computation. The resulting dataset covers 83.6% of residues with a confident prediction, while 25.9% have very high confidence. CONCLUSIONS: Our work provides insight-worthy predictions for coral research, confirms the reliability of ColabFold in practice, and is expected to be a reference case in the impending high-throughput era of structural proteomics.

Full-Length Transcriptome Maps of Reef-Building Coral Illuminate the Molecular Basis of Calcification, Symbiosis, and Circadian Genes.

Coral transcriptomic data largely rely on short-read sequencing, which severely limits the understanding of coral molecular mechanisms and leaves many important biological questions unresolved. Here, we sequence the full-length transcriptomes of four common and frequently dominant reef-building corals using the PacBio Sequel II platform. We obtain information on reported gene functions, structures, and expression profiles. Among them, a comparative analysis of biomineralization-related genes provides insights into the molecular basis of coral skeletal density. The gene expression profiles of the symbiont Symbiodiniaceae are also isolated and annotated from the holobiont sequence data. Finally, a phylogenetic analysis of key circadian clock genes among 40 evolutionarily representative species indicates that there are four key members in early metazoans, including cry genes; Clock or Npas2; cyc or Arntl; and tim, while per, as the fifth member, occurs in Bilateria. In summary, this work provides a foundation for further work on the manipulation of skeleton production or symbiosis to promote the survival of these important organisms.

Symbiodiniaceae microRNAs and their targeting sites in coral holobionts: A transcriptomics-based exploration.

Corals should make excellent models for cross-kingdom research because of their natural animal-photobiont holobiont composition, yet a lack of studies and experimental data restricts their use. Here we integrate new full-length transcriptomes and small RNAs of four common reef-building corals with the published Cladocopium genomes to gain deeper insight into gene regulation in coral-Symbiodiniaceae holobionts. Eleven novel Symbiodiniaceae miRNAs get identified, and enrichment results of their target genes show that they might play a role in downregulating rejection from host coral cells, protecting symbiont from autophagy and apoptosis in parallel. This work provides evidence for the early origin of cross-kingdom regulation as a mechanism of self-defense autotrophs can use against heterotrophs, sheds more light on coral-Symbiodiniaceae holobionts, and contributes valuable data for further coral research.

Full-Length Transcriptome Sequencing Reveals Tissue-Specific Gene Expression Profile of Mangrove Clam Geloina erosa.

Mollusca is the second largest animal phylum and represents one of the most evolutionarily successful animal groups. Geloina erosa, a species of Corbiculidae, plays an important role in mangrove ecology. It is highly adaptable and can withstand environmental pollution and microbial infections. However, there is no reference genome or full-length transcriptome available for G. erosa. This impedes the study of the biological functions of its different tissues because transcriptome research requires reference genome or full-length transcriptome as a reference to improve accuracy. In this study, we applied a combination of Illumina and PacBio single-molecule real-time sequencing technologies to sequence the full-length transcriptomes of G. erosa tissues. Transcriptomes of nine samples obtained from three tissues (hepatopancreas, gill, and muscle) were sequenced using Illumina. Furthermore, we obtained 87,310 full-length reads non-chimeric sequences. After removing redundancy, 22,749 transcripts were obtained. The average Q score of 30 was 94.48%. In total, 271 alternative splicing events were predicted. There were 14,496 complete regions and 3,870 lncRNAs. Differential expression analysis revealed tissue-specific physiological functions. The gills mainly express functions related to filtration, metabolism, identifying pathogens and activating immunity, and neural activity. The hepatopancreas is the main tissue related to metabolism, it also involved in the immune response. The muscle mainly express functions related to muscle movement and control, it contains more energy metabolites that gill and hepatopancreas. Our research provides an important reference for studying the gene expression of G. erosa under various environmental stresses. Moreover, we present a reliable sequence that will provide an excellent foundation for further research on G. erosa.

Deep whole-genome resequencing sheds light on the distribution and effect of amphioxus SNPs.

BACKGROUND: Amphioxus is a model organism for vertebrate evolutionary research. The significant contrast between morphological phenotypic similarity and high-level genetic polymorphism among amphioxus populations has aroused scientists' attention. Here we resequenced 21 amphioxus genomes to over 100X depth and mapped them to a haploid reference. RESULTS: More than 11.5 million common SNPs were detected in the amphioxus population, which mainly affect genes enriched in ion transport, signal transduction and cell adhesion, while protein structure analysis via AlphaFold2 revealed that these SNPs fail to bring effective structural variants. CONCLUSIONS: Our work provides explanation for "amphioxus polymorphism paradox" in a micro view, and generates an enhanced genomic dataset for amphioxus research.

Full-Length Transcriptome Sequencing of the Scleractinian Coral Montipora foliosa Reveals the Gene Expression Profile of Coral-Zooxanthellae Holobiont.

Coral-zooxanthellae holobionts are one of the most productive ecosystems in the ocean. With global warming and ocean acidification, coral ecosystems are facing unprecedented challenges. To save the coral ecosystems, we need to understand the symbiosis of coral-zooxanthellae. Although some Scleractinia (stony corals) transcriptomes have been sequenced, the reliable full-length transcriptome is still lacking due to the short-read length of second-generation sequencing and the uncertainty of the assembly results. Herein, PacBio Sequel II sequencing technology polished with the Illumina RNA-seq platform was used to obtain relatively complete scleractinian coral M. foliosa transcriptome data and to quantify M. foliosa gene expression. A total of 38,365 consensus sequences and 20,751 unique genes were identified. Seven databases were used for the gene function annotation, and 19,972 genes were annotated in at least one database. We found 131 zooxanthellae transcripts and 18,829 M. foliosa transcripts. A total of 6328 lncRNAs, 847 M. foliosa transcription factors (TFs), and 2 zooxanthellae TF were identified. In zooxanthellae we found pathways related to symbiosis, such as photosynthesis and nitrogen metabolism. Pathways related to symbiosis in M. foliosa include oxidative phosphorylation and nitrogen metabolism, etc. We summarized the isoforms and expression level of the symbiont recognition genes. Among the membrane proteins, we found three pathways of glycan biosynthesis, which may be involved in the organic matter storage and monosaccharide stabilization in M. foliosa. Our results provide better material for studying coral symbiosis.

FEM: mining biological meaning from cell level in single-cell RNA sequencing data.

BACKGROUND: One goal of expression data analysis is to discover the biological significance or function of genes that are differentially expressed. Gene Set Enrichment (GSE) analysis is one of the main tools for function mining that has been widely used. However, every gene expressed in a cell is valuable information for GSE for single-cell RNA sequencing (scRNA-SEQ) data and not should be discarded. METHODS: We developed the functional expression matrix (FEM) algorithm to utilize the information from all expressed genes. The algorithm converts the gene expression matrix (GEM) into a FEM. The FEM algorithm can provide insight on the biological significance of a single cell. It can also integrate with GEM for downstream analysis. RESULTS: We found that FEM performed well with cell clustering and cell-type specific function annotation in three datasets (peripheral blood mononuclear cells, human liver, and human pancreas).

Micro-CT reconstruction reveals the colony pattern regulations of four dominant reef-building corals.

Colonies are the basic geometric building blocks of coral reefs. However, the forming regulations of both colonies and reefs are still not understood adequately. Therefore, in this study, we reconstructed 25 samples using high-resolution micro-computed tomography to investigate coral growth patterns and parameters. Our skeleton and canal reconstructions revealed the characteristics of different coral species, and we further visualized the growth axes and growth rings to understand the coral growth directions. We drew a skeleton grayscale map and calculated the coral skeleton void ratios to ascertain the skeletal diversity, devising a method to quantify coral growth. On the basis of the three-dimensional (3D) reconstructions and growth parameters, we investigated the growth strategies of different coral species. This research increases the breadth of knowledge on how reef-building corals grow their colonies, providing information on reef-forming regulations. The data in this paper contain a large amount of coral growth information, which can be used in further research on reef-forming patterns under different conditions. The method used in this study can also be applied to animals with porous skeletons.

Exploring Nanotechnological Detection Background of Heat Shock Proteins (HSPs) in Coral Acropora muricata.

Coral reefs are cornerstone of global marine ecosystems, providing shelter for over one third of marine organisms. Currently, along with global warming and increased human activities, large-scale decline of coral reefs has become a severe ecosystem problem, and now quantitative detection of heat shock protein (HSP) gene by nanotechnology has become a research hotspot in this field. However, Acropora muricata is one of the most important dominant reef-building corals in Indo- Pacific region, encounter an urgent obstacle on the HSP detection research by nanoscience and nanotechnology for lack of sequence background. Here, we combined PacBio single molecular real-time (SMRT) and HiSeq X Ten sequencing technologies to perform full-length transcriptome sequencing of heat shock proteins in Acropora muricata, a reef-building coral dominant in many Indo-Pacific reefs, to annotate them. Thirteen functional heat shock proteins (HSPs) were identified using phylogenetic analysis, classified into three subgroups as HSP60, HSP70 and HSP90. HSPs are widely distributed in all animal phyla, having evolved from the last prokaryotic common ancestor. Additionally, phylogenetic and tertiary nanostructure analyses suggested that HSP70 is the most diverse HSP in A. muricata, with extensive sequence and structure differences indicating adaptations to warming water and suggesting its utility in studies of El Niño and other warming events. A greater understanding of the HSP gene family is likely to also be of value in studies of coral nanotechnological detection that can be used to protect reef ecosystems.

BENviewer: a gene interaction network visualization server based on graph embedding model.

BENviewer is a brand-new online gene interaction network visualization server based on graph embedding models. With mature graph embedding algorithms applied on several interaction network databases, it provides human-friendly 2D visualization based on more than 2000 biological pathways, and these results present not only genes involved but also tightness of interactions in an intuitive way. As a unique visualization server introducing graph embedding application for the first time, it is expected to help researchers gain deeper insights into biological networks beyond generating results explainable by existing knowledge. Additionally, operation flow for users is simplified to greater extent in its current version; meanwhile URL optimization contributes to data acquisition in batch for further analysis. BENviewer is freely available at http://www.bmeonline.cn/BENviewer, besides it is open-sourced at https://github.com/SKLB-lab/BENviewer, http://benviewer.bmeonline.cn.

Microfluidic-based fabrication and characterization of drug-loaded PLGA magnetic microspheres with tunable shell thickness.

To overcome the shortcoming of conventional transarterial chemoembolization (cTACE) like high systemic release, a novel droplet-based flow-focusing microfluidic device was fabricated and the biocompatible poly(lactic-co-glycolic acid) (PLGA) magnetic drug-eluting beads transarterial chemoembolization (TACE) microspheres with tunable size and shell thickness were prepared via this device. Paclitaxel, as a model active, was loaded through O/O/W emulsion method with high efficiency. The size and the shell thickness vary when adjusting the flow velocity and/or solution concentration, which caters for different clinical requirements to have different drug loading and release behavior. Under the designed experimental conditions, the average diameter of the microspheres is 60 ± 2 µm and the drug loading efficiency has reached 6%. The drug release behavior of the microspheres shows the combination of delayed release and smoothly sustained release profiles and the release kinetics differ within different shell thickness. The microspheres also own the potential of magnetic resonance imaging (MRI) visuality because of the loaded magnetic nanoparticles. The microsphere preparation method and device we proposed are simple, feasible, and effective, which have a good application prospect.

Binding Pattern Reconstructions of FGF-FGFR Budding-Inducing Signaling in Reef-Building Corals.

Reef-building corals play an important role in marine ecosystems. However, owing to climate change, ocean acidification, and predation by invasive crown-of-thorns starfish, these corals are declining. As marine animals comprise polyps, reproduction by asexual budding is pivotal in scleractinian coral growth. The fibroblast growth factor (FGF) signaling pathway is essential in coral budding morphogenesis. Here, we sequenced the full-length transcriptomes of four common and frequently dominant reef-building corals and screened out the budding-related FGF and FGFR genes. Thereafter, three-dimensional (3D) models of FGF and FGFR proteins as well as FGF-FGFR binding models were reconstructed. Based on our findings, the FGF8-FGFR3 binding models in Pocillopora damicornis, Montipora capricornis, and Acropora muricata are typical receptor tyrosine kinase-signaling pathways that are similar to the Kringelchen (FGFR) in hydra. However, in P. verrucosa, FGF8 is not the FGFR3 ligand, which is found in other hydrozoan animals, and its FGFR3 must be activated by other tyrosine kinase-type ligands. Overall, this study provides background on the potentially budding propagation signaling pathway activated by the applications of biological agents in reef-building coral culture that could aid in the future restoration of coral reefs.

High-Strength Hydrogel Adhesive Formed via Multiple Interactions for Persistent Adhesion under Saline.

Hydrogel adhesives have been widely used in wet environments. Nonetheless, strong and stable persistent adhesion remains a challenge. Here, we report a facile yet powerful strategy to construct high-strength hydrogel adhesives for durable adhesion in a saline environment. Such a hydrogel consists of two polymer networks: a hydrophobic-associated polyacrylamide network of covalent and noncovalent cross-links and an alginate network cross-linked by divalent cations in saline. Meanwhile, polydopamine nanoparticles formed through in-situ self-polymerization are distributed evenly throughout the system to provide underwater adhesion. A low and controllable swelling rate and high compressive strength of hydrogels can be achieved via this multiple interaction strategy. Ultimately, this strategy contributes to the persistent underwater adhesion of hydrogels, and the decreasing rate of lap-shear adhesion strength of hydrogels is only 24.79 ± 8.01% after saline immersion for up to 21 days. Moreover, good cytocompatibility of hydrogels is helpful for their application in the biomedical field.

Single symbiotic cell transcriptome sequencing of coral.

Zooxanthellae and coral can form an intracellular symbiotic system. Yet, little is known about the molecular mechanism underlying this symbiosis. In this study, we characterized the symbiosis based on analyses of gene expression at the single-cell level. Among 9110 single coral cells, we identified 4871 symbiotic cells based on the detection of both coral and zooxanthellae gene transcripts within a single cell. Using the bioinformatics tool Seurat, symbiotic cells were further clustered into five groups, 52 genes exhibited differential expression between groups. We proposed an index called the "symbiosis index", to indicate the degree of gene expression of both species in a single symbiotic cell. Interestingly, the index differed distinctly among the five groups. The symbiosis index was highly correlated with the expression of the coral gene gfas1.m1.6761 (ANKRD40), which encodes ankyrin repeat domain-containing protein 40 and is involved in DNA replication (r = 0.76). Two metabolism-related genes, DAGLA and betaGlu, were highly expressed in cells with a high symbiosis index. Four zooxanthellae genes, PRPF19, ATRN, aAA-ATPases and AK812-SmicGene44833, exhibited substantial changes in expression levels when zooxanthellae lived within coral. A trajectory analysis suggested that cells with a higher symbiosis index may be derived from those with a lower index during coral colony development. Taken together, our results provide evidence for zooxanthellae residing within coral, forming a symbiotic system. The symbiosis index is an effective indicator of different cell groups, with lineage relationships among groups. Additionally, we identified specific genes that exhibit expression changes in the symbiotic system.