A5088264016- Invertebrate Immune Response Mechanisms
- interferon and immune responses
- Immune Response and Inflammation
- Aquaculture disease management and microbiota
- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- NF-κB Signaling Pathways
- RNA and protein synthesis mechanisms
- Antimicrobial Peptides and Activities
- Neutrophil, Myeloperoxidase and Oxidative Mechanisms
- Enzyme-mediated dye degradation
- Complement system in diseases
- RNA modifications and cancer
- RNA Interference and Gene Delivery
- Environmental Toxicology and Ecotoxicology
- Cell Adhesion Molecules Research
- Oxidative Organic Chemistry Reactions
- RNA Research and Splicing
- Ubiquitin and proteasome pathways
- Studies on Chitinases and Chitosanases
- Proteoglycans and glycosaminoglycans research
- Coral and Marine Ecosystems Studies
- Aquaculture Nutrition and Growth
- T-cell and B-cell Immunology
- Cell death mechanisms and regulation
Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)
2020-2025
Sun Yat-sen University
2016-2025
Qingdao National Laboratory for Marine Science and Technology
2019-2024
Wuhan Children's Hospital
2024
Huazhong University of Science and Technology
2024
Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)
2020-2021
Chinese Academy of Fishery Sciences
2017-2018
Shanghai Ocean University
2018
Biocontrol (Brazil)
2017
Zero to Three
2012
It has been speculated that before vertebrates evolved somatic diversity-based adaptive immunity, the germline-encoded diversity of innate immunity may have more developed. Amphioxus occupies basal position chordate phylum and hence is an important reference to evolution vertebrate immunity. Here we report first comprehensive genomic survey immune gene repertoire amphioxus Branchiostoma floridae . reported purple sea urchin a vastly expanded receptor not previously seen in other species,...
Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that been sculpted by two whole-genome duplications. Here we sequence genome of Mediterranean amphioxus (Branchiostoma lanceolatum) characterize DNA methylation, chromatin accessibility, histone modifications transcriptomes across multiple developmental stages adult tissues to investigate evolution regulation genome. Comparisons with vertebrates identify an intermediate stage in...
De novo assembly is a difficult issue for heterozygous diploid genomes. The advent of high-throughput short-read and long-read sequencing technologies provides both new challenges potential solutions to the issue. Here, we present HaploMerger2 (HM2), an automated pipeline rebuilding haploid sub-assemblies from polymorphic genome assembly. It designed work on pre-existing assemblies, which are typically created by using de assemblers. HM2 can process any but it especially suitable assemblies...
Abstract To investigate the evolution and immune function of C-type lectin in amphioxus, primitive representative chordate phylum, we identified three lectins consisting solely a carbohydrate recognition domain N-terminal signal peptide found that they had distinct express patterns special tissues response to stimulations analyzed by quantitative real-time PCR. We characterized biochemical biological properties AmphiCTL1, which was dramatically up-regulated amphioxus challenged with...
Abstract Vertebrates diverged from other chordates ~500 Myr ago and experienced successful innovations adaptations, but the genomic basis underlying vertebrate origins are not fully understood. Here we suggest, through comparison with multiple lancelet (amphioxus) genomes, that ancient vertebrates high rates of protein evolution, genome rearrangement domain shuffling these greatly slowed down after divergence jawed jawless vertebrates. Compared lancelets, modern retain, at least relatively,...
Whole-genome shotgun assembly has been a long-standing issue for highly polymorphic genomes, and the advent of next-generation sequencing technologies made more challenging than ever. Here we present an automated pipeline, HaploMerger, reconstructing allelic relationships in diploid assembly. HaploMerger combines LASTZ-ChainNet alignment approach with novel graph-based structure, which helps to untangle between two haplotypes guides subsequent creation reference haploid assemblies. The...
Increasing amounts of genes have been shown to utilize alternative polyadenylation (APA) 3′-processing sites depending on the cell and tissue type and/or physiological pathological conditions at time processing, construction genome-wide database regarding APA is urgently needed for better understanding poly(A) site selection APA-directed gene expression regulation a given biology. Here we present web-accessible database, named APASdb (http://mosas.sysu.edu.cn/utr), which can visualize...
Abstract The antiviral immune responses were triggered by the innate recognition of viral infection. type I IFNs (IFN-β and IFN-α) are key cytokines produced upon infection consequently link immunity with adaptive immunity. A main system in mammals is TRIF-dependent TLRs pathway, but TRIF-independent RIG-I has also been discovered recently. In this manuscript, our study focuses on functional characterization zebrafish TRIF based comparison its sequence evolution from to mammals. Our...
Tandem 3′ untranslated regions (UTRs), produced by alternative polyadenylation (APA) in the terminal exon of a gene, could have critical roles regulating gene networks. Here we profiled tandem poly(A) events on genome-wide scale during embryonic development zebrafish ( Danio rerio ) using recently developed SAPAS method. We showed that 43% expressed protein-coding genes UTRs. The average UTR length follows V-shaped dynamic pattern early embryogenesis, which UTRs are first shortened at...
Unspecific peroxygenases (UPO) (EC 1.11.2.1) represent an intriguing oxidoreductase sub-subclass of heme proteins with peroxygenase and peroxidase activity. With over 300 identified substrates, UPOs catalyze numerous oxidations including 1- or 2- electron oxygenation, selective oxyfunctionalizations, which make them most significant in organic syntheses potentially attractive as industrial biocatalysts. There are very few available distinct properties, notably, MroUPO shows behavior ranging...
Abstract Both amphioxus and the sea urchin encode a complex innate immune gene repertoire in their genomes, but composition mechanisms of systems, as well fundamental differences between two remain largely unexplored. In this study, we dissect mucosal complexity into different evolutionary-functional modes regulatory patterns by integrating information from phylogenetic inferences, genome-wide digital expression profiles, time course dynamics, functional analyses. With these rich data,...
IL-1R-associated kinases (IRAKs) are signal transducers of the TLR/IL-1R-MyD88-TRAF6 pathways. Vertebrates possess two IRAK lineages, IRAK1/2/3 and IRAK4. In mammals, IRAK4/IRAK1 IRAK4/IRAK2 pathway enhancers, whereas IRAK3 is a repressor. However, in bony fish, IRAK2 absent, it remains elusive how fish IRAK1/3/4 functionally differ from their mammalian counterparts. this study, we explored using zebrafish model. First, showed that human 293T cells, IRAK1 IRAK4 were components Myddosome...
Abstract Among five Toll/IL-1R resistance adaptors, sterile α and motif containing protein (SARM) is the only one conserved from Caenorhabditis elegans to human. However, its physiologic roles are hardly understood, involvement in TLR signaling remains debatable. In this study, we first demonstrated a predominant expression of amphioxus SARM (Branchiostoma belcheri tsingtauense SARM) neural cells during embryogenesis digestive system larva adult, suggesting primitive role development...
The TNF-associated factor (TRAF) family, the crucial adaptor group in innate immune signaling, increased to 24 amphioxus, oldest lineage of Chordata. To address how these expanded molecules evolved adapt changing TRAF mediated signaling pathways, here we conducted genomic and functional comparisons four distinct amphioxus groups with their human counterparts. We showed that lineage-specific duplication rearrangement were responsible for expansion TRAF1/2 3 lineages, whereas TRAF4 6...
Abstract In seeking evidence of the existence adaptive immune system (AIS) in ancient chordate, cDNA clones six libraries from a protochordate, Chinese amphioxus, were sequenced. Although key molecules such as TCR, MHC, Ig, and RAG AIS have not been identified our database, we demonstrated this study extensive molecular for presence genes homologous to many that are involved directly or indirectly, including some which may represent putative precursors vertebrate AIS-related genes. The...
Abstract C1q is the target recognition protein of classical complement pathway and a major connecting link between innate adaptive immunities. Its globular signature domain also found in variety noncomplement that can be grouped together as family. In this study, we have cloned identified novel family member cephalochordate amphioxus named it AmphiC1q1. The high transcriptional levels gene were detected during all stages embryonic development, section situ hybridization demonstrated...
The ficolin-mediated complement pathway plays an important role in vertebrate immunity, but it is not clear whether this exists invertebrates. Here we identified homologs of ficolin components from the cephalochordate amphioxus and investigated they had been co-opted into a functional pathway. Four these homologs, FCN1, serine protease MASP1 MASP3, component C3, were highly expressed mucosal tissues gonads, significantly up-regulated following bacterial infection. Recombinant FCN1 could...
Significance Microbial specific pathogen-associated molecular patterns (PAMPs) constitute a key feature by which host organism detects the presence of microbes and mounts immune responses. Here, we report discovery two proteins (bjALP1 2) that interact with muramyl dipeptide, pan-bacterial PAMP via novel pattern recognition domain ApeC. Our studies have revealed bjALP1 is secreted effector, whereas bjALP2 functions as an intracellular receptor (PRR), both having important role in protecting...