Ximing GuoGene duplication in bivalve genomes and implications for adaptation Gregory WrayRapid and extensive changes in transcriptional regulation underlie life history evolution in sea urchins Naoki IrieDo echinoderm embryos follow hourglass-like divergence? Christopher LoweHemichordate genomics, development and evolution Senjie LinENDS (energy, nutrients, defense, sex) molecular ecological model towards understanding drivers of phytoplankton regime shift and HAB formation Jinfeng ZhouGenomics and Ecological Management of Marine Resources Chris HunterPracticing FAIR publishing Shi WangComprehensive profiling of molluscan ontogenetic transcriptomes provides insights into metazoan biphasic life-history evolution Jianhai XiangDe novo sequencing and assembly of whole genome reveals biological secrets in the shrimp Litopenaeus vannamei Li LiThe Adaptive Evolution of the Oyster: Genetic Divergence or Phenotypic Plasticity Way SungMutation Rate Evolution and Insights from Marine Organisms Tuo ShiA symbiotic view of corals’ response to environmental change: from genotypic diversity to phenotypic plasticity Xiaojun ZhangA genomic view of the escape response of shrimp Lingyu WangGenetic basis for extensive divergence in developmental gene expression during sea urchin life history evolution Ruibang LuoDeep Learning Enabled Rapid and Accurate genomic Variant Calling in Single Molecule Sequencing Hongmei ZhuDetecting large complex SVs using linked short reads Li DengstLFR scaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme Jeffery ChuUnravelling biodiversity through genomics Debashish BhattacharyaBuilding a photosynthetic organelle: insights from genome analysis of Archaeplastida and the amoeba Paulinella Xiaohua ZhangInsight into microbial metabolisms in the deepest seawater on earth Dazhi WangA draft map of the marine diatom proteome Sangseob LeeEnvironmental Impact Assessment of Harmful Marine Algae Bloom Species and the Relevant Biological Management as Ocean Ecological Environmental Improvement Lushan WangOmic analysis of algal degradation enzyme system in marine vibrios Thomas MockTemperature drives the diversity of co-occurrence networks between micro-eukaryotes and prokaryotes in the surface ocean Linlin ZhangMolecular Genetic Basis of Adaptive Traits Shengfeng HuangApeC: a novel protein domain mostly present in aquatic animals shows diverse functional implications Kai ChenSingle cell transcriptome lineages of a urochordate and the evo-devo insights Xiaoliang RenDirect full-length RNA sequencing reveals unexpected transcriptome complexity during C. elegans development Ryan RangeEvolution of Anterior-Posterior Axis Specification and Patterning: Insights from the Sea Urchin Embryo Bo DongMechanical and genomic regulatory mechanisms of ascidian notochord morphogenesis Peng XuThe allotetraploid origin and genome evolution of common carp Cyprinus carpio Songlin ChenFish Genomic Researches in China: Current Status and Prospect Yan HeGenomic and transcriptomic investigations reveal the adaptation of black rockfish (Sebastes schlegelii) to viviparity Dehai LiBioactive Secondary Metabolites from Deep-sea Derived Microorganisms, Discovery and Extending Jinbo YangIntelligent SuperComputing Pharmacomics in Marine Drug Discovery Pedro LeãoDiscovery of cyanobacteria natural products in the post-genomic era Carlos Daniel PerezCoral reefs: a living pharmacy Bingjie OuyangNext-generation diagnostic monoclonal antibody development based on cartilaginous fish genomes and phage display technology
Ximing GuoGene duplication in bivalve genomes and implications for adaptation
Gregory WrayRapid and extensive changes in transcriptional regulation underlie life history evolution in sea urchins
Naoki IrieDo echinoderm embryos follow hourglass-like divergence?
Christopher LoweHemichordate genomics, development and evolution
Senjie LinENDS (energy, nutrients, defense, sex) molecular ecological model towards understanding drivers of phytoplankton regime shift and HAB formation
Jinfeng ZhouGenomics and Ecological Management of Marine Resources
Chris HunterPracticing FAIR publishing
Shi WangComprehensive profiling of molluscan ontogenetic transcriptomes provides insights into metazoan biphasic life-history evolution
Jianhai XiangDe novo sequencing and assembly of whole genome reveals biological secrets in the shrimp Litopenaeus vannamei
Li LiThe Adaptive Evolution of the Oyster: Genetic Divergence or Phenotypic Plasticity
Way SungMutation Rate Evolution and Insights from Marine Organisms
Tuo ShiA symbiotic view of corals’ response to environmental change: from genotypic diversity to phenotypic plasticity
Xiaojun ZhangA genomic view of the escape response of shrimp
Lingyu WangGenetic basis for extensive divergence in developmental gene expression during sea urchin life history evolution
Ruibang LuoDeep Learning Enabled Rapid and Accurate genomic Variant Calling in Single Molecule Sequencing
Hongmei ZhuDetecting large complex SVs using linked short reads
Li DengstLFR scaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme
Jeffery ChuUnravelling biodiversity through genomics
Debashish BhattacharyaBuilding a photosynthetic organelle: insights from genome analysis of Archaeplastida and the amoeba Paulinella
Xiaohua ZhangInsight into microbial metabolisms in the deepest seawater on earth
Dazhi WangA draft map of the marine diatom proteome
Sangseob LeeEnvironmental Impact Assessment of Harmful Marine Algae Bloom Species and the Relevant Biological Management as Ocean Ecological Environmental Improvement
Lushan WangOmic analysis of algal degradation enzyme system in marine vibrios
Thomas MockTemperature drives the diversity of co-occurrence networks between micro-eukaryotes and prokaryotes in the surface ocean
Linlin ZhangMolecular Genetic Basis of Adaptive Traits
Shengfeng HuangApeC: a novel protein domain mostly present in aquatic animals shows diverse functional implications
Kai ChenSingle cell transcriptome lineages of a urochordate and the evo-devo insights
Xiaoliang RenDirect full-length RNA sequencing reveals unexpected transcriptome complexity during C. elegans development
Ryan RangeEvolution of Anterior-Posterior Axis Specification and Patterning: Insights from the Sea Urchin Embryo
Bo DongMechanical and genomic regulatory mechanisms of ascidian notochord morphogenesis
Peng XuThe allotetraploid origin and genome evolution of common carp Cyprinus carpio
Songlin ChenFish Genomic Researches in China: Current Status and Prospect
Yan HeGenomic and transcriptomic investigations reveal the adaptation of black rockfish (Sebastes schlegelii) to viviparity
Dehai LiBioactive Secondary Metabolites from Deep-sea Derived Microorganisms, Discovery and Extending
Jinbo YangIntelligent SuperComputing Pharmacomics in Marine Drug Discovery
Pedro LeãoDiscovery of cyanobacteria natural products in the post-genomic era
Carlos Daniel PerezCoral reefs: a living pharmacy
Bingjie OuyangNext-generation diagnostic monoclonal antibody development based on cartilaginous fish genomes and phage display technology
Bivalve molluscs are a lineage of ancient bilaterians well adapted to marine benthic life. Many bivalves live in intertidal zones and can tolerate wide fluctuations in temperature, salinity and air exposure. Bivalve molluscs are remarkable calcifiers that produce strong shells for protection and play an important role in the carbon cycle. They have no adaptive immunity but thrive in microbe-rich environments as filter-feeders. Molecular bases of bivalve adaptations are not well understood, but recent sequencing of several bivalve genomes has provided some insights. All bivalve genomes are highly polymorphic and contain surprisingly large numbers of genes due to duplication. Gene duplications are mostly lineage-specific and derived from retroposition and tandem-repetition. The duplicated genes are often associated with shell formation, stress and immune responses and may play an important role in bivalve adaptation. The duplicated genes show diverse expression profiles indicative of neofunctionalization or specialization for different environmental conditions. Paralogous duplication increases gene diversity and regulatory complexity that are essential for highly advanced or specialized functions. With planktonic larvae capable of wide dispersal over diverse environments and stationary adults incapable of avoidance, bivalves must rely on genetic diversity and phenotypic plasticity to coup with unpredictable and wildly fluctuating environmental conditions. The unique life history of bivalves and environmental heterogeneity they face create strong balancing selection that may favor the retention and diversification of certain duplicated genes that are critical to their adaptation.
Rapid and extensive changes in transcriptional regulation underlie life history evolution in sea urchins
Marine invertebrates exhibit an astonishing diversity of larval forms and life history modes. These adaptations in nutrition, dispersal, and defense can evolve even between closely related species. One of the most intensively-studied examples is the sea urchin genus Heliocidaris: H. tuberculata produces a large number of small, energy-poor eggs that develop into feeding larvae, while H. erythrogramma produces fewer, energy-rich eggs that develop into non-feeding larvae that are morphologically very different. This transition from ancestral feeding to derived non-feeding larvae has evolved independently dozens of times in echinoderms and many more times in other groups of marine invertebrates. It is thought to be an adaptation to environments where phytoplankton is an unreliable food source for larvae. To better understand the genetic, molecular, and developmental basis for this striking life history shift, we are producing high-quality reference genome assemblies for the two Heliocidaris species and an outgroup, Lytechinus variegatus. These resources allow us to apply a variety of ‘omic technologies in a comparative functional genomic context across early development in all three species. We find extensive differences among species in temporal and spatial patterns of gene expression and chromatin configuration during early development, with changes in developmental regulatory genes significantly enriched on the branch leading to H. erythrogramma. We developed a method to quantify evolutionary differences in molecular function across developmental time-courses, providing an unsupervised method for identifying candidate genes underlying trait differences. We have also drawn on the detailed developmental gene regulatory network (GRN) for a related species of sea urchin, Strongylocentrotus purpuratus, to identify candidate genes based on prior functional information. To understand the trait consequences of changes in the function of both sets of candidate genes, we carried out knock-down and genome-editing experiments. The results reveal that some regulatory interactions within the developmental GRN have been lost, gained, or shifted in time or space. These changes are particularly striking given that some are conserved among echinoderm species that diverged 10s-100s of millions of years ago but have changed in just a few million years specifically on the branch leading to the species with the derived life history mode. Together, these findings demonstrate that the evolution of non-feeding larvae in Heliocidaris involved modifications in the expression and function of many different genes that collectively produced the extensive changes in developmental mechanisms responsible for this evolutionarily and ecologically important life history shift.
Considering the signal cascades observed during animal development, it would be reasonable to assume that the earliest developmental stages (such as fertilized egg) are the most important, and tends to be conserved the most. However, comparative transcriptomic studies did not support this idea, showing that that mid-embryonic stages (especially organogenesis stages) are the most conserved stages during development (the developmental hourglass model). The model further predicts that anatomical features in this most conserved phase defines the body plan for each animal phylum, but is this really true? Supporting evidence has been obtained in vertebrates, however, how about in echinoderms? Do they show pentameric bodyplan establishing phase as the most conserved gene expression profile? To answer the question, we have sequenced and analyzed genomes and developmental transcriptomes of echinoderms from five extant groups. We will also talk about possible evolutionary mechanism (including contribution from pleiotropic constraints) that made embryos to follow the hourglass model.
Hemichordates are the sister group of echinoderms and closely related to chordates. Their key phylogenetic position makes them an important group for untangling the mysteries of chordate evolution and the origins of vertebrates. However, the hemichordate body plan and adult morphological characters are difficult to directly compare with chordates due to major organizational differences. Our work in 2 species of enteropneusts, from genomes to developmental biology, has investigated the underlying gene regulatory networks that establishes their respective body plans. This has revealed deep regulatory conservation despite the body plan organizational disparities between the two phyla, and provides a cryptic molecular anatomy to make fundamental comparisons between groups. I will present our latest findings, with a focus on the patterning and establishment of the hemichordate nervous system, to provide insights into the early steps in the evolution of the vertebrate nervous system.
ENDS (energy, nutrients, defense, sex) molecular ecological model towards understanding drivers of phytoplankton regime shift and HAB formation
Diatoms and dinoflagellates are two major groups of phytoplankton that play pivotal roles in coastal marine biogeochemistry. Dinoflagellates are ecologically very successful, occupying diverse econiches and showing uptick trends in the backdrop of global warming and environmental changes. While diatoms usually dominate coastal phytoplankton communities, dinoflagellates at times outcompete diatoms in seasonal succession or harmful algal bloom events. Yet our understanding on how dinoflagellates gain competitive edges and thrive in their diverse habitats is still very limited. While diatom ecology has benefited from genomics and functional genetics, such contemporary molecular tools are not as accessible for dinoflagellates. Nevertheless, recent (slow but steady) advances have brought insights into how dinoflagellates regulate gene expression, acquire resources, and adapt to their life styles (e.g. symbiosis with corals). Recent findings have led me to posit that dinoflagellates are genetically wired to be advantageous in energy and nutrient acquisition in resource-limited environments, in anti-microbial defense, and possibly in sexual reproduction for population proliferation, namely an E-N-D-S model. I will present genomic, transcriptomics, and physiological as well as in situ data to provide support for the ENDS model to shed light on metabolic drivers of phytoplankton regime shift and HAB formation.
With the ocean comprising almost 71% of the Earth’s surface, its role in sustaining life on the Earth and their activities cannot be underestimated. Yet the advent of the Sixth Biological Extinction has so far imposed unprecedented pressure on the marine ecosystem and marine biodiversity. In this May, the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) released its first milestone report “IPBES Global Assessment”, which had been carefully compiled by 145 expert authors from 50 countries over a period of three years, and warned that “around 1 million animal and plant species are now threatened with extinction, many within decades, more than ever before in human history”; that is, a third of all marine mammals, more than 40% of amphibian species and almost 33% of reef-forming corals are threatened, in relation to the marine ecosystem. Science-based solutions to the current crisis of Climate and Biodiversity Emergency therefore have emerged, and their values increasingly emphasized. President Xi Jinping’s ideology of Ecological Civilization places Scientific Management at the core, so it is with leading international conventions and organizations, e.g. the UN Convention on Biological Diversity (CBD), Convention on Migratory Species (CMS), International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA) and the International Union for Conservation of Nature (IUCN) etc. In the field of Genomics, which was introduced in 1986 by the American scientist Thomas Roderick, its application, development and innovation in ecosystem and biodiversity conservation have been breathtaking. But in the face of ever-rising temperature and biodiversity loss, it remains imperative that questions like how Genomics may be applied to determine aquatic species’ susceptibility to environmental change, how it may contribute to ecosystem stability, how season/annual movements of migratory species and their habitats may be better understood based on genomic analysis, as well as how Genomics may contribute to the sustainable management of marine resources, sustainable fisheries and dietary pattern, the rescue and wild-release of endangered species and the formulation of policies and regulations, should warrant prioritized investigation and further exploration.
So you've heard about the buzz word "FAIR" and want to be on that band-wagon, but how ? what exactly does FAIR mean? what do you need to do to be FAIR?I will provide the answers to these questions and more, with a focus on how we do things differently to other journals at GigaScience. To give you a taste; essentially FAIR is a set of guiding principals, essentially it means "be a good scientist", do things transparently and reproducibly, and share everything openly to enable others to follow-up your work. GigaScience not only publishes the narrative (article) but also the underlying data and results through GigaDB. Trained biocurators assess the manuscripts to ensure transparency and reproducibility, and where appropriate help organise and curate data to promote reuse and therefore impact. Never ones to be content with the status-quo, GigaScience are now proud to introduce the future of publishing; GigaByte, a new journal from the GigaScience team will be lauching in early 2020.
Comprehensive profiling of molluscan ontogenetic transcriptomes provides insights into metazoan biphasic life-history evolution
The transient larva-bearing biphasic life cycle is the hallmark of many major invertebrate groups in the ocean, which is central for metazoan evolution and adult morphological plasticity. The evolutionary origin of marine larvae and tremendous adult morphological diversity have puzzled researchers for centuries. Here we investigate these central issues from an omics perspective on the largest marine phylum Mollusca that is characterized by a trochophora larva and highly variable adult forms. We conduct the comprehensive evo-devo profiling of molluscan transcriptomes, with a primary focus on the scallop Patinopecten yessoensis. The trochophore stage is revealed as a rapidly evolved, “intercalated” larval stage with its prototype presumably originating from the stem derivative of Metazoa and cell communication genes are likely crucial for larval origin. The extraordinary incorporation of highly expressed novel genes into the larval stage potentially contributes to molluscan lineage and morphological diversification. Our evolutionary transcriptome analyses argue against the prevailing “larva-first” hypothesis by suggesting an “adult-first” evolutionary scenario (i.e., larval intercalation into a direct-developing life cycle of metazoan ancestor). Our study demonstrates the power and invaluable framework by generating the comprehensive transcriptome atlas for molluscan evo-devo studies. The molluscan transcriptome atlas and core gene sets provide vital resources for filling the large void in our understanding of animal life history evolution and developmental regulation.
De novo sequencing and assembly of whole genome reveals biological secrets in the shrimp Litopenaeus vannamei
Crustacea, the subphylum of Arthropoda which dominates the aquatic environment, is of major importance in ecology and fisheries. Here we report on the genome sequence of the Pacific white shrimp Litopenaeus vannamei, covering ~1.66 Gb (scaffold N50 605.56 Kb) with 25,596 protein-coding genes and the highest proportion of simple sequence repeats (>23.93%) among sequenced animals. The noted expansion of genes related to vision and locomotion is probably central for its benthic adaptation. Frequent molting of the shrimp is associated with an intensified ecdysone signal pathway through gene expansion and positive selection. As an important aquaculture organism, L. vannamei has been subjected to high selection pressure during the past 30 years of breeding, and this has had a significant impact on its genome. Decoding the L. vannamei genome not only provides an insight into the genetic underpinnings of specific biological processes, but also provides valuable information for enhancing crustacean aquaculture.
The environment of the intertidal zone is highly variable in spatial and temporal scales. As the dominate species, the oyster provides an ideal model to study the adaptive evolution of the marine organism. Local adaptation and the phenotypic plasticity are two evolutionary form, and the dissection of their contribution and their mechanism to the evolution is the center of the biological science. Omics technology provide new ways to understand the evolutionary process.
The micoevolution of the Pacific oyster, Crasstrea gigas and other genus Crasosstrea species were studied. Genome re-sequencing of the wild propulsions of C. gigas revealed small genetic divergence that coincided with phenotypic divergence across environmental gradients, suggesting selection and local adaptation are pervasive and, together with limited gene flow, influence population structure. Plasticity in gene expression is positively correlated with evolved divergence, indicating that plasticity is adaptive and favoured by organisms under dynamic environments. In the case of divergence between C. gigas and its subspecies C. angula, genome-wide gene expression profiles were identified and differences in genetic background is the dominant effector, which reflects the divergent statues between the related species. Multiple Omics suggest that energy regulation and cell hemostasis play significant role in the adaptation, and acetylation and methylation -mediated process are involved.
Mutations are a primary source of genetic variation and they contribute to the vast phenotypic and genotypic variation that can be found within natural populations. Mutation-accumulation (MA) experiments combined with high-throughput genomic sequencing has revealed that genome-wide mutation rates vary by four orders of magnitude across known life. Furthermore, it has been revealed that the mutation rate varies significantly at both a contextual and spatiotemporal scale. In the few marine microorganisms where MA studies have been performed, the differences in mutation rate and patterns are magnified, suggesting that the enzymes involved in DNA synthesis and repair have unique properties in marine organisms. In this talk, I describe our current understanding of the rate and pattern of spontaneous mutations across the tree of life, and detail our high-throughput methods to measure and manipulate the rate and effect of mutations in both marine and non-marine microorganisms.
A symbiotic view of corals’ response to environmental change: from genotypic diversity to phenotypic plasticity
Collectively called zooxanthellae, photosynthetic dinoflagellates in the family Symbiodiniaceae are essential coral symbiont, the composition and diversity of which can fundamentally mediate corals’ response to environmental change. Corals containing previously rare, thermally tolerant algal symbionts are much more abundant on reefs that have been affected by severe bleaching and/or associated with extreme environments. Yet, the precise machinery underpinning this symbiotic regulation remains largely unknown. In order to better understand the synergistic coral-algal responses to environmental perturbations, we conducted a laboratory manipulative thermal stress experiment with the stony coral Pocillopora damicornis harboring distinct clades of Symbiodiniaceae (i.e., the presumably thermo-tolerant D vs. thermo-sensitive C) maintained at ambient (26 °C) or elevated (32 °C) temperature, respectively. Measurements of physiological parameters, such as photochemical quantum yield efficiency and rate of calcification, show that P. damicornis with dominant clade D symbiont (Durusdinium spp.) is more tolerant to increased temperature than its counterpart with clade C symbiont (Cladocopium spp.). Transcriptomic profiling of the coral holobiont further reveals that clade D-dominated coral has significantly more differentially expressed genes (DEGs), especially those involved in stress-response functions including anti-apoptosis, heat shock, anti-oxidation, and calcium ion binding under prolonged thermal stress. Taken together, our study provides a comprehensive assessment of the regulatory plasticity of coral symbioses, particularly the role of thermo-tolerant symbiont lineage in conferring increased resilience to safeguard corals against future ocean warming.
The sequencing of the Litopenaeus vannamei genome provides a unique opportunity to investigate the function and evolution of neural genes. The neurobiology of shrimps is of particular interest because they have a giant nerve fiber and escape response to avoid predation or escape from hostile environments. In the L. vannamei genome, the genes categories for signal recognition and neural development were significantly enriched. There were 24 genes related to signal recognition and nerve system among the 95 positively selected genes in the shrimp genome. Several notable gene families were drastically expanded, including GPCRs, transient receptor potential (TRP) channels, innexins, protocadherins, and C2H2 zinc-finger proteins (C2H2 ZNFs). These gene families were considered as the core neural development related genes across invertebrate bilaterians. L. vannamei genome encodes expanded ionotropic glutamate receptors (iGluRs) and glycine receptors (GlyRs) genes, which are involved in excitatory neurotransmission and regulating myelination. Compared with vertebrates and most protostomes that use acetylcholine (AcH) as neurotransmitter, arthropods use glutamate at the neuromuscular junction (NMJ). In addition, the gene families involved in muscle protein, such as actin, titin and myosin, were also expanded significantly in the L. vannamei genome. These features might equip the shrimp to rapidly perform neural signal transduction, enhancing its responsiveness and strengthening its locomotion, including escape reactions in adaptation to its benthic swimming life in shallow seawater.
Genetic basis for extensive divergence in developmental gene expression during sea urchin life history evolution
The genetic basis for divergence in developmental gene expression among species remains poorly understood, despite growing evidence that such changes underlie many interesting traits. Here we quantified gene expression in hybrids of Heliocidaris tuberculata and H. erythrogramma, two closely related sea urchins with highly divergent life histories. We find that the numerous changes in developmental gene expression that have evolved between these species result from many genetic differences affecting local transcription rather than a few with highly pleiotropic effects. Importantly, the genetic basis for expression divergence changes during development for many genes, indicating that the shifting composition of trans-acting factors during development mutes the pleiotropic consequences of many mutations that influence gene expression. Finally, we show that two prominent morphological traits in H. erythrogramma larvae associated with its derived life history are based largely on evolutionary changes in upstream regulators rather than the function or expression of terminal differentiation genes.
Single-Molecule Sequencing (SMS) such as PacBio and Oxford Nanopore are producing very long reads that span across a majority of the repetitive elements in complex genomes, enabling the reconstruction of the entire chromosomes in genome assembly. However, these new sequencing technologies are not impeccable – ONT reads has around 10% balanced and unbalanced base errors, which is over ten times higher than Illumina, making it unsuitable for small variant calling using either the traditional Bayesian model or local assembly method. Utilizing deep learning, we developed Clairvoyante (Luo et al., 2019), which is the first algorithm that calls small variants directly from the alignments of the SMS reads. We further improved our algorithm to make it not only more sensitive and accurate but also works on non-human species.
Large SVs excluding deletions are usually hard to identify using short read pairs produced by ordinary NGS libraries. They become detectable when linked reads are available including some complex SVs which are nested or close to one the other. After mapping linked reads to reference genome sequences, we identify breaking points, pair them to indicate the real neighbor sites, verify the variation by phased SNPs and finally assemble the sequence blocks to recover the underlying genome. The analysis method outputed a result set revealing several interesting large SVs in the famous NA12878 samples which have not been reported so far.
Synthetic long reads (SLR) sequencing technologies have recently been developed and applied widely for genome assembly. Despite their advances in effectiveness for de novo genome assembly, the independent assembly modules were lacking, which can be applied for different kinds of synthetic long reads (especially for single-tube long fragment read, stLFR (Wang, et al., 2019)) and combining other datasets (third generation long reads, etc.). Here, we developed the stLFR scaffolder, an standalone scaffolding tool for (but not limited) stLFR co-barcode reads, with a top-to-bottom scheme where long fragment read(LFR) information is used in global scaffolding firstly and then the paired end (PE) information is used in local scaffolding later, to effectively use the synthetic long reads information. Furthermore, a screening algorithm for the input contigs with low quality have been firstly introduced to strengthen the robust of the tool. Comparing the scaffolding results with other available tools for several stLFR co-barcode reads datasets, we found that our tool can produce assemblies with the highest quality meaning with longer contiguity and less errors in the assembly. We provided the first scaffolding software for the stLFR data, which can also be used for other synthetic long reads data. Considering advantages of synthetic long reads, our assembler can be used widely in future genome studies.
Genomics is at the forefront of unraveling the biodiversity on earth. Large genomics initiatives including Bird 10K, Genome 10K, TARA Ocean, and Insect 5K, have been undertaken to understand the phylogeny and evolution of various clad of species. The Genome 10K estimated that we only know about 10% of the vertebrate species and the TARA Ocean have estimated that we only know 1/100 of the marine planktons. Marine genomes are often complex and presents a number of challenges. For example some dinoflagellate and algal genomes are extremely large at 50-100 Gb. Secondly, many algae such as Chlorella form symbiosis or other complex relationships with bacteria, complicating the process of genome assembly. Frasergen is developing techniques and tools to overcome these challenges and to further our understanding of biodiversity. We present a number of examples using long read sequencing and Hi-C to construct platinum-grade reference genomes and identifying important structural variations through pan-genome analysis. Additionally, with phasing information from Hi-C, we were also able to separate sub-genomes from polyploid genomes. Frasergen’s technology is well positioned and applicable to marine species as part of a large initiative such as the Fish 10K project as well as individual marine species genome projects.
Building a photosynthetic organelle: insights from genome analysis of Archaeplastida and the amoeba Paulinella
Glaucophyta are members of the Archaeplastida, the founding group of photosynthetic eukaryotes that also includes red algae, green algae, plants, and the recently discovered phagotrophic Rhodelphis species. I will discuss insights gained from analysis of a high-quality genome assembly of the glaucophyte Cyanophora paradoxa that was built using long-read sequences. This gene-rich species has complex gene structures and chimeric origin of some metabolic pathways. Gene expression analysis was used to study peptidoglycan biosynthesis and to understand the evolution of diurnal cycles in Archaeplastida. I will also discuss ongoing analyses of the genome of the photosynthetic amoeba, Paulinella whose plastid originated about 100 million years ago. Members of this genus contain a permanent photosynthetic organelle, referred to as a chromatophore that is derived from an alpha-cyanobacterial endosymbiont. I will present the results of our collaborative research on the behavior of Paulinella cultures and of genome and transcriptome data from two species, P. chromatophora and P. micropora. This information provides important insights into early events in organelle evolution.
The Mariana Trench is the deepest known site in the Earth's oceans, reaching a depth of ~11,000 m at the Challenger Deep. Recent studies reveal that hadal waters harbour distinctive microbial planktonic communities. However, the genetic potential of microbial communities within the hadal zone is poorly understood. Here, implementing both culture-dependent and culture-independent methods, we perform extensive analysis of microbial populations and their genetic potential at different depths in the Mariana Trench. Unexpectedly, we observed an abrupt increase in the abundance of hydrocarbon-degrading bacteria at depths >10,400 m in the Challenger Deep. Indeed, the proportion of hydrocarbon-degrading bacteria at > 10,400 m is the highest observed in any natural environment on Earth. These bacteria were mainly Oleibacter, Thalassolituus and Alcanivorax genera, all of which include species known to consume aliphatic hydrocarbons. This community shift towards hydrocarbon degraders was accompanied by increased abundance and transcription of genes involved in alkane degradation. Correspondingly, three Alcanivorax species that were isolated from 10,400 m water supplemented with hexadecane were able to efficiently degrade n-alkanes under conditions simulating the deep sea, as did a reference Oleibacter strain cultured at atmospheric pressure. Abundant n-alkanes were observed in sinking particles at 2,000, 4,000 and 6,000 m (averaged 23.5 μg/gdw) and hadal surface sediments at depths of 10,908, 10,909 and 10,911 m (averaged 2.3 μg/gdw). The δ2H values of n-C16/18 alkanes that dominated surface sediments at near 11,000 m depths ranged from -79 to -93‰, suggesting these alkanes may derive from an unknown biological source. These results reveal that hydrocarbon-degrading microorganisms are present in great abundance in the deepest seawater on Earth and shed a new light on potential biological processes in this extreme environment.
Diatoms are unicellular eukaryotic phytoplankton that play important ecological roles in the ocean on a global scale. Diatoms account for 20% of global carbon fixation and 40% of marine primary productivity, thus they drive global biogeochemical cycle and climate, and form a substantial basis of marine food web. The genomes of five diatom species have been sequenced, however, a high-quality map of diatom proteome is still not available. Here we present a draft map of the model diatom Thalassiosira pseudonana proteome using a combination of multiple protein extraction methods, the enrichment strategy and high-resolution mass spectrometry. In-depth proteomic profiling identified 9,594 proteins accounting for approximately 82% of the predicted coding protein genes. A newly developed proteogenomic strategy enabled us to discover 1,235 novel genes (30 of them were mapped in the region of pseudogene), 979 revised genes, 104 splice variants and 234 single amino acid variants. These findings complement the genome annotation of T. pseudonana and provide import resource and support for the study of diatom. This diatom proteome catalogue will complement available diatom genome and transcriptome data to accelerate the study of diatom biology and ecology in the ocean.
Environmental Impact Assessment of Harmful Marine Algae Bloom Species and the Relevant Biological Management as Ocean Ecological Environmental Improvement
Red tide is a common natural disaster caused by the explosive increase of red tide algae. It causes immeasurable losses to the marine environment and restricts the economic development of coastal areas. Biological control has been considered as one of the most used ways to control red tide. It has broader application prospects than physical and chemical methods since it has the advantages in selectivity, safety, long-term efficiency and economy. In the presented study, we screened a total of 6,730 bacterial strains from marine environment of seawater and sediment under both aerobic and anaerobic condition. Among the strains, R Jin 1-1 showed the highest algae-killing ability of 94% against C. polykrikoides, R Dol 0-4 of 68.27% to C. Marina, MS Yeon 1-1 of 51.57% against H. Triquetra, DZ Yeongu 1-4 of 17.54% against H. Akashiwo, M Yeonmyeong 2-22 of 24.86% against P. Minimum, ZB Yeonmyeong 1-13 of 84.03% against S. Trochoidea, and M Dol 1-8 of 68.07% against S. costatum. We further adsorbed the bacterial strains onto ceramic carriers in marine environment, and the results indicated that this technology can efficiently remove red tide-causing algae in saltwater. Chattonella marina, the main cause of red tide, were efficiently controlled in 24 hours. Red tide polluted seawater biological treatment technology in the experiment, has the characteristics of improving reaction efficiency, easy recycling, reusability, and low cost, and these will be the great advantages for a wide range of popularization and application.
Seaweed is becoming more attractive because of its rich content and remarkable industrial value. Agar, carrageenan, and alginate are the main components of marine algae. There are numbers of marine microbes involved in the degradation of seaweed polysaccharides through their glycoside hydrolase (GH) and glycoside lyase (PL). For example, it has been reported that some vibrios are capable of degrading alginates with a high efficiency and contain a unique and complete alginate degradation system. Therefore, vibrios are suggested to be an important microbial resource for industrial ethanol production. However, due to the restriction of microbial pure culture technology, only a few Vibrio species with high-efficiency alginate degradation are isolated. Bioinformatics, especially the rapid development of omics technology, supplies new fields of microbial research and provides new sights for the excavation of microbial resources. The combination of omics such as proteomics, metabolomes, and metagenomics can effectively screen the marine environment to obtain genetic resources for efficient degradation of seaweed polysaccharides. Based on this, structural bioinformatics is used to analyze the specificity and promiscuous patterns of algae polysaccharide degrading enzymes on substrate recognition, thus to understand the molecular mechanism of high-efficiency degradation of seaweed polysaccharides. In addition, the mechanism of algae polysaccharide degradation is also elucidated on the genetic level to achieve the construction of engineering strains with high-efficiency seaweed polysaccharide degradation.
Temperature drives the diversity of co-occurrence networks between micro-eukaryotes and prokaryotes in the surface ocean
Microbial eukaryotes and prokaryotes have co-occurred in the global surface ocean for more than 200 million years. Their interactions underpin marine food webs and global biogeochemical cycles on Earth. However, how the environment impacts their biotic interactions from pole to pole has barely been studied yet. Here we use >70 natural microbial communities from the Arctic to the Southern Ocean to show that temperature is the single most important environmental variable explaining the diversity and activity of their interacting co-occurrence subnetworks based on 16S and 18S amplicon, metatranscriptome and metagenome sequencing. We found two co-occurrence subnetworks, a polar and a non-polar subnetwork separated at annual average surface ocean temperatures between 10 and 15 degrees Celsius. This result suggests that there are breakpoints in the surface ocean driven by temperature, which impact the diversity and activity of microbial communities. If global warming impacts the latitudinal position of these breakpoints, microbial communities might change more rapidly over time where the breakpoints shift due to increasing surface ocean temperatures.
It is debated to what extent the course of evolution in certain directions rather than others. One contract can be made is ‘co-opting’ an existing gene to perform a new role versus ‘inventing’ a new gene. Investigation of oyster stress response adaptation to intertidal environment illustrates duplication of an existing gene followed by the divergence of the duplicated genes contributes to such adaptation. On the other hand, my research in butterfly wings suggests how co-option contributes to color pattern diversity. CRISPR/Cas9 genome editing leads to the discovery that the presence, absence, and shape of butterfly eyespots can be controlled by the activity of two co-opted transcription factors. Macroevolution study demonstrates the activity of a single locus optix could explain dramatic evolution shift in butterfly wing pattern features after co-option. My work leads a better understanding of how genetic novelty shape animal diversity and evolution.
ApeC: a novel protein domain mostly present in aquatic animals shows diverse functional implications
Apextrin C-terminal (ApeC) is a novel protein domain first discovered in amphioxus, a marine invertebrate. Though the functions of ApeC-containing proteins (ACP) remain mostly unknown, early studies suggest that some ACPs are capable of binding carbohydrates, and involved in development and immunity. Here we will discuss the taxonomic distribution, sequence diversification, preliminary functional information and origination of the ACPs in Metazoa.
Ascidian embryos highlight the importance of cell lineages in animal development. As simple proto-vertebrates, they also provide insights into the evolutionary origins of cell types such as cranial placodes and neural crest cells. Here we have determined single-cell transcriptomes for more than 90,000 cells that span the entirety of development—from the onset of gastrulation to swimming tadpoles—in Ciona intestinalis. Owing to the small numbers of cells in ascidian embryos, this represents an average of over 12-fold coverage for every cell at every stage of development. We used single-cell transcriptome trajectories to construct virtual cell-lineage maps and provisional gene networks for all major tissues and most neural subtypes that comprise the larval nervous system, which shear insights for the evolutionary origin of cell types such as chordate notochord and vertebrate telencephalon.
Direct full-length RNA sequencing reveals unexpected transcriptome complexity during C. elegans development
High throughput RNA sequencing (RNA-seq) using cDNA has played a key role in delineating transcriptome complexity, including alternative transcription initiation, splicing, polyadenylation and base modification. However, the reads derived from current RNA-seq technologies are usually short and deprived of information on modification during reverse transcription, compromising their potential in defining transcriptome complexity. Here we applied a direct RNA sequencing method with ultra-long reads from Oxford Nanopore Technologies (ONT) to study the transcriptome complexity in C. elegans. We sequenced native poly-A tailed mRNAs by generating approximately six million reads from embryos, L1 larvae and young adult animals, with average read lengths ranging from 900 to 1,100 bps across stages. Around half of the reads represent full-length transcripts, judged by the presence of a splicing-leader or their full coverage of an existing transcript. To take advantage of the full-length transcripts in defining transcriptome complexity, we devised a novel algorithm to predict novel isoforms or group them with exiting isoforms using their mapping tracks rather than the existing intron/exon structures, which allowed us to identify roughly 57,000 novel isoforms and recover at least 26,000 out of the 33,500 existing isoforms. Intriguingly, stage-specific expression at the level of gene and isoform demonstrates little correlation. Finally, we observed an elevated level of modification in all bases in the coding region relative to the UTR. Taken together, the ONT long reads are expected to deliver new insights into RNA processing and modification and their underlying biology.
Evolution of Anterior-Posterior Axis Specification and Patterning: Insights from the Sea Urchin Embryo
The early specification and patterning of cell fates along the primary body axis of many metazoan embryos relies on a gradient of Wnt signaling. In most embryos this patterning mechanism depends primarily on high levels of localized canonical Wnt/Beta-catenin signaling around one pole of this embryonic axis, which will form endoderm/endomesoderm, and localized Wnt signaling antagonists around the opposite pole that typically aid in specifying the ectodermal and neuroectodermal territories. We have recently shown for the first time in any embryo that the deuterostome sea urchin integrates information from three different Wnt signaling branches (the canonical Wnt/Beta-catenin as well as non-canonical Wnt/JNK and Wnt/PKC pathways) to specify and pattern early regulatory states along the embryonic anterior-posterior (AP) axis. Our functional evidence indicate that these pathways interact at through several extracellular Wnt signaling modulators (e.g. Wnt1, Wnt8, Wnt16, and Dkk1), receptors (Fzl5/8 and Fzl1/2/7), intracellular transduction molecules (e.g. PKC, NFAT, and ATF2) and the transcriptional gene regulatory networks they activate. Here, we present new evidence that the transcription factor Sp5 is activated by the non-canonical Wnt1/Wnt8-Fzl5/8-JNK signaling pathway that is essential to position the anterior neuroectoderm (ANE) gene regulatory network (GRN) around the anterior pole of the embryo. Our functional data indicate that SP5 acts downstream of Wnt1/Wnt8-Fzl5/8-JNK to downregulate the ANE GRN from more posterior equatorial ectoderm cells. Importantly, evidence from vertebrate studies indicates that Sp5 also works downstream of early AP Wnt signaling to position the ANE GRN around the anterior pole. Together with our results, these data suggest that the Wnt/Sp5 regulatory cassette represents a fundamental AP patterning mechanism conserved among deuterostome embryos.
Notochord is the typical organ exclusively exists in chordate animals, playing structurally important and regulatory roles in early embryogenesis and organ function maintenance. In this presentation, I will talk distinct cellular elongation strategies and the underlying molecular mechanisms utilized in notochord elongation based on our recently published papers and the current ongoing projects. Especially, I will discuss our findings that how the cytokinetic-like actomyosin rings drive the cell elongation but not cell division; how the contractile rings form and organize; and how the ring position is maintained at cell equatorial region by the tug-of-war between actomyosin contractility and planar cell polarity. I will also present our recent finding regarding how the ventral actomyosin contractility in notochord coordinated with the faster dorsal epithelial cell proliferation to drive tail bending in Ciona embryo. This work provides an insight on how the different tissues coordinate to determine the embryo morphogenesis.
Common carp (Cyprinus carpio) is an allotetraploid Cyprinid species derived from recent whole genome duplication and provides an excellent model system for studying polyploid genome evolution in vertebrates. To explore the origins and consequences of tetraploidy in C. carpio, we generated chromosome-level reference genomes of C. carpio and compared them to the related diploid Cyprinid genome sequences. We identified a progenitor-like diploid Barbinae lineage by analysing the phylogenetic relationship of the homoeologous genes of C. carpio and their orthologues in closely related diploid Cyprinids. We then characterized the allotetraploid origin of C. carpio and divided its genome into two homoeologous subgenomes that are marked by a distinct genome similarity to their diploid progenitor. On the basis of the divergence rates of homoeologous genes and transposable elements in two subgenomes, we estimated that the two diploid progenitor species diverged approximately 23 million years ago (Mya) and merged to form the allotetraploid C. carpio approximately 12.4 Mya, which likely correlated with environmental upheavals caused by the extensive uplift of the Qinghai-Tibetan Plateau. No large-scale gene losses or rediploidization were observed in the two subgenomes. Instead, we found extensive homoeologous gene expression bias across twelve surveyed tissues, which indicates that one subgenome is dominant in homoeologous expression. DNA methylation analysis suggested that CG methylation in promoter regions plays an important role in altering the expression of these homoeologous genes in allotetraploid C. carpio. This study provides an essential genome resource and insights for extending further investigation on the evolutionary consequences of vertebrate polyploidy.
The present paper reviews the process of fish genomic researches in China, which started with nothing and then developed from small to large. The important progress regarding BAC library construction, high-density genetic linkage map construction, genome sequencing and fine mapping, genome selection and genome editing by Chinese scientists were introduced. Based on the comparison with the international progress in this field, it was pointed that Chinese scientists followed the international research from 2008 to 2013. While from 2014 to 2018, China's fish genomic study has accelerated development and been catching up. Just during the past five years, the top journals like Nature and Nature Genetics have published several papers of genome sequencing and fine mapping in important aquatic fish from China, such as half-smooth tongue sole, common carp, grass carp, Japanese flounder and sea horse. The progress has brought China's fish genomic research from full-scale following in the past to the present coexistence of following, running side-by-side, and even leading in a few fish species. In the meanwhile, we summarized the current shortcomings and problems in fish genomic research and application field, and prospected the future development direction of fish genomic research in China.
Genomic and transcriptomic investigations reveal the adaptation of black rockfish (Sebastes schlegelii) to viviparity
Black rockfish (Sebastes schlegelii) is a teleost species where eggs are fertilized internally and retained in the maternal reproductive system, where they undergo development until live birth (termed viviparity). In the present study, we report a chromosome-level black rockfish genome assembly. High-throughput transcriptome analysis, coupled with in situ hybridization (ISH) and immunofluorescence, identify several adaptation characteristics of black rockfish to viviparity. First, in terms of sperm storage, we propose that zona pellucida (ZP) proteins retain sperm at the oocyte envelope, while genes in two distinct astacin metalloproteinase subfamilies serve to release sperm from the ZP and free the embryo from chorion at pre-hatching stage. Secondly, we obtain the evidence of maternal preparation for embryo attachment and placenta formation. Thirdly, a distinct placenta structure was found in the ovarian system to supply nutrients to the developing embryos. Finally, we present a model of black rockfish reproduction, and propose that the rockfish has evolved a primitive placenta, through which the mother provides nutrients to the embryo during gestation, a pattern known as “matrotrophy”. In addition, rockfish ovarian wall has a similar function to the uterus of mammals. Taken together, these genomic data reveal unprecedented insights into the evolution of an unusual teleost life history strategy, and provide a sound foundation for studying viviparity in non-mammalian vertebrates and an invaluable resource for rockfish ecological and evolutionary research.
Microorganisms derived from the deep-sea (depth > 1000 m) are a promising resource for natural products with novel chemical structures and specific bioactivities. According to our literature reviews and statistics, nearly 60% of the natural products from deep-sea-sample-derived microorganisms were reported to possess bioactivity with more than 30% demonstrating beneficial cytotoxicity. Although many attentions have been attracted, only about 400 deep-sea derived new secondary metabolites have been reported in the past decades, among the over 30,000 marine natural products. Moreover, most of the gene clusters encoding bioactive molecules are silent. For exploring the bioactive secondary metabolites from deep-sea derived microorganisms, we collected over 100 deep-sea samples with the depth from 1000 to 10,000 meters and over 1500 strains were isolated from them. Employing modern natural products strategies and the silent gene activation methods (OSMAC, epigenetic modification, co-cultivation, genome manipulation, etc), we have reported over 80 new deep-sea derived compounds and some of them showed promising cytotoxic, antibacterial, antiviral, lipid-lowering activities, in the past 15 years.
The ocean covers 71% of the earth's surface. The complex and diverse marine environment fosters a rich world of marine life, as well as a large number of marine natural products that are widely used in many fields. Globally, more than 30,000 marine natural products have been discovered in approximately 40 years. These natural products have a wide range of uses in pharmaceutical research, biomedical material preparation, food and cosmetics industries. However, due to the bottleneck problems of difficult resource acquisition, complex structure and low content of compounds, marine drug research and development is still restricted to the production of marine innovative drugs. Innovation Center for Marine drug screening combined with the Center for Intelligent Supercomputers of Qingdao Pilot National Laboratory for Marine Science and Technology (QNLM), built the intelligent supercomputers coupled biological measurement system of marine drug screening technology. Through the establishment of the world's first three-dimensional database of more than 30,000 marine natural products and a database containing thousands of innovative drug target structures, we simulate the virtual drug screening, and then form a molecular library of virtual marine innovative drugs. Subsequently, organic synthesis and derivative synthesis of key marine drug precursor molecules were carried out by organic synthesis and medicinal chemistry experts, and then biological activity and pharmacological and pharmacodynamic studies were carried out. Through computer drug screening, organic synthesis, biological measurement and artificial big data mining technology, we have built a complete chain of marine drug research and development technology system for super-pharmaceutical drug screening and drug-making research. Based on intelligent supercomputer and artificial big data technology, hundreds of developmental marine drug precursor molecules or drug lead compounds have been discovered.
Natural products – small, naturally-produced molecules – are central to a number of human activities, most notably to medicine, where they have contributed with ca. 40% of approved drugs. Plants, fungi and bacteria are the sources of most natural products known to date. While the natural products chemistry field has been dealing with increasing re-discovery rates, in particular for plants, bacterial genome data tells us that the large majority of natural products from this domain are yet to be uncovered. In cyanobacterial genomes, for example, between 80-90% of the secondary metabolite biosynthetic gene clusters have no associated known compound. In this talk, I will discuss recent trends in natural product discovery in this group of chemically-rich photosynthetic bacteria. I will provide examples from our own work of how genomic information can be used to guide or assist natural products discovery.
Plants, fungi, insects, marine organisms and bacteria are important sources of biologically active substances, and most drugs in clinical use are either of natural origin or were developed by chemical synthesis from natural products. Although there are several strategies and methodologies available today to synthesize and discover new drugs, chemistry of natural product represents one of these successful alternatives, historically privileged. Many secondary or special metabolites have emerged as valuable raw materials for the production of numerous contemporary medicines, proving that the partnership between medicinal chemists and natural product chemists is a strategy for the discovery of innovative drugs.
Seas and oceans occupy more than 2/3 of the Earth's surface and house almost all groups of living organisms, including representatives of 35 of the 36 phyla described. Thus, marine ecosystems can be considered to have the largest animal biodiversity, with virtually unlimited associated biotechnological potential. Despite its immense, not all the surface of the seas and oceans are apt for the development of biodiversity. Most marine organisms need hard bottoms to develop, and if we consider that only 1% of the seabed is made up of consolidated substrates such as rocks, canyons and reefs, we have a space problem for just enough biodiversity. Reef environments have great biodiversity, but they need strict conditions for survival (temperatures higher than 20ºC, good light, clear water and shallow areas). Knowing that only 15% of the seabed is between 0-30 meters, coral reefs account for only 0.2% of the world's ocean area (6,000,000 km2). Few space for so much biodiversity. Most reef organisms are sessile or sedentary like algae, sponges, cnidarians, bryozoans and ascidians or with reduced mobility like mollusks and polychaetes. Sessile or fixed organisms use a chemical arsenal to fight for space and to survive against predators, as well as to assist in biological activities such as feeding and reproduction. These organisms use water as a vehicle to carry out their activities, releasing chemicals directly into the seawater. These chemicals are primary and secondary metabolites such as terpenes, steroids, alkaloids, etc. Allelopathy is one of the phenomena that these organisms use to successfully fight for space.
Organisms with such diverse and developed chemical arsenals were promptly targeted for biotechnological studies. Natural products have been a major source of inspiration for many areas of chemistry and science in general. Using, copying or modifying molecules synthesized by living organisms, humans have obtained innovations for their benefit in several areas and, among them, the production of drugs. From the analgesic morphine to the antibiotic penicillin to paclitaxel anticancer (Taxol®), it is estimated that 80% of the drugs in use are natural products or were inspired by nature. In this context, terrestrial organisms (mainly microorganisms and plants) are responsible for almost all of these substances, while marine organisms, although promising, have been systematically investigated only recently.
Until the 1950s, the marine ecosystem escaped from the interest of natural product scientists, mainly due to the difficult access to its depths. With the advancement of techniques and the advent of safe diving equipment, in the 1970s, seaweed and marine invertebrates were able to begin their stories in chemistry and pharmacology laboratories. However, it was not until the discovery of large quantities of prostaglandins in the octocoral Plexaura homomalla in 1978 by Alfred J. Weinheimer and Robert L. Spraggins of the University of Oklahoma that the interest and investment of pharmaceutical industries in laboratory´s research on marine natural products were awakened. Advances in isolation and chemical characterization techniques, progress and sophistication of bioassays, which are becoming increasingly specific and accurate, have also been reinforced by another important group of fruitful producers of interesting molecules: marine microorganisms. Almost half (45%) of natural products of marine microorganisms were isolated after the year 2000, demonstrating recent interest in this area. Marine microorganisms have had revolutionary implications in studies with natural products, not only for chemical diversity, but mainly for the prospect of sustainability, associated with the possibility of fermentation to produce sufficient material for preclinical and clinical stages of drug development. Despite about 18,500 isolated substances between 1965 and 2006, it is estimated that less than 3% of the estimated total marine organisms have been studied. In addition to their peculiar structures, marine natural products have an extraordinary diversity of molecular targets with remarkable selectivity, which greatly increases the pharmacological and therapeutic potential of these molecules. Considering only prototypes in clinical trials, we can recognize some therapeutic targets: ion channels, enzymes, microtubules, DNA, lysosomes, calmodulin, proteasomes, besides the induction of oxidative stress and modulation of the immune system. Most of the identified targets are relevant in cancer treatment and it is precisely in the study and treatment of this disease that we can see the greatest impact of substances of marine origin.
The major drawbacks of marine biotechnology are the high costs and the lengthy process. The costs involved in this process are extremely high and may involve costs of around R 900 million) for anticancer drugs. In addition, the process takes a long time, taking about 15 years from the discovery of the molecule to the pharmacy counter. This has caused large pharmaceutical companies to lose interest in natural marine products, but since 2000 they have begun to regain it through collaborations with small businesses or institutional laboratories. It is worth mentioning that 13 new drugs related to natural products were approved between 2005 and 2007. There are currently four marine drugs in clinical use – such as anticancer [ara-C (Citarabi¬na®) and trabectedin (Yondelis®)], antiviral [ara-A (Vidarabina®)] and neuropathic analgesic [ziconotide Prialt®)]. During the drug research and development process, of every 5000 substances that go into preclinical testing phase only five passed into clinical studies and only one molecule resulted in one drug. Although the major bottleneck in the evolution of studies on marine substances has been the provision of adequate human testing quantities, the limiting factor for therapeutic use lies in the toxicity associated with use.
Indeed, the ecological function of pharmacologically active molecules isolated from marine sources seems to be to ensure the success of the host in competing for space or in defense against predators or pathogenic microorganisms. Whether they were sessile or low-mobility animals, soft-bodied and lacking physical defense structures such as non-calcareous sponges, sea squirts, soft corals, algae, and some groups of Shell-less molluscs, which have yielded most of the molecules that are currently in preclinical studies. The bioactivity of molecules of marine origin is often extremely potent, which reinforces the hypothesis of their protective function, as they must overcome the incredible diluent ability of seawater to reach its target and take effect. However, in the process of transforming the “chemical weapons” of marine organisms into drugs for human use, this particularity impacts on the high toxicity of these molecules or on intolerable side-effects. The low material yield, the frequent structural complexity of natural products and their consequent difficulty of the synthesis, point to improve and optimize the development of medicines of marine origin.
The achievements and progress of research into marine natural products already have their place in the pharmaceutical industry, and the promise of marine drugs has become a reality. Clearly, there is a considerable number of substances with pharmaceutical potential, translating into new therapeutic alternatives, mainly for cancer treatment. However, this area is still far from maturity, and the search for new sources and large-scale production strategies continues. Bacteria, fungi and cyanobacteria are also emerging as new sources, challenge microbiologists, and the possibility of using metagenomics to make the study of their metabolites feasible in molecular biology. The use of screening in silico techniques and the creation of targeted libraries are strategies to accelerate the process of discovery of new molecules using automated systems (high-throughput screening). Gene cloning and expression in heterologous bacteria has been already a viable alternative for the synthesis of some polyketides. Finally, synthesis methodologies that incorporate complex enzymatic reactions will be strong allies in obtaining sufficient quantities of molecules of marine origin for clinical studies and eventual commercialization.
Coral reefs are one of the most productive ecosystems on the planet that host a high marine biodiversity that forms an intricate web of ecological interrelationships. Complex relationships involving morphological and chemical complexities, producing substances to ensure their survival, and giving humanity new chemical tools to fight countless diseases and pathogens, forming a true living pharmacy.
Next-generation diagnostic monoclonal antibody development based on cartilaginous fish genomes and phage display technology
Cartilaginous fish (Chondrichthyes) is one of the oldest extant jawed vertebrate groups, with an adaptive immune system based on Ig superfamily receptors, including sharks, rays, skates, sawfish, and chimaeras. They produce the immunoglobulin new antigen receptor (IgNAR), a homodimeric heavy chain-only antibody. Antigen binding of IgNAR is mediated exclusively by a small and highly stable domain, called vNAR. With a molecular weight of approximately 12 kDa, the vNAR domain is the smallest antibody-like antigen binding domain in the animal kingdom known to date. However, lack of the chondrichthyes genomes limits the study and industrial application of vNAR. In this project, we establish a route for vNAR development based on chondrichthyes genomes and phage display technology. Through assembling the chromesome level genome of bamboo shark, we identified IgNAR gene and designed the primer special to vNAR. Using phage display technology, we constructed the vNAR-phage antibody library of bamboo shark, and are screening monoclonal vNAR antibodies to marker of diseases. Next, we plan to assemble 30 representative cartilage fish genomes and construct a higher diversity vNAR library by synthetic biology methods and oligonucleotide mutation technology, which is a useful source for isolating vNAR antibodies to a wide range of antigens. This platform may be applicable to the diagnostic antibody development.