Publications by authors named "Guangyi Fan"

The giant grouper (Epinephelus lanceolatus) is a large coral reef fish distributed in the Indian Ocean and the Pacific Ocean. With a high market value, this species can grow up to approximately 2.7 meters in length and weigh 440 kilograms.

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Sediment plays a pivotal role in deep-sea ecosystems by providing habitats for a diverse range of microorganisms and facilitates the cycling processes of carbon, sulfur and nitrogen. Beyond the normal seafloor (NS), distinctive geographical features such as cold seeps (CS) and hydrothermal vent (HV) are recognized as life oases harboring highly diverse microbial communities. A global atlas of microorganisms can reveal the notable association between geological processes and microbial colonization.

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Bats possess a range of distinctive characteristics, including flight, echolocation, impressive longevity, and the ability to harbor various zoonotic pathogens. Additionally, they account for the second-highest species diversity among mammalian orders, yet their phylogenetic relationships and demographic history remain underexplored. Here, we generated de novo assembled genomes for 17 bat species and 2 of their mammalian relatives (the Amur hedgehog and Chinese mole shrew), with 12 genomes reaching chromosome-level assembly.

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  • Algae can be unicellular (microalgae) or multicellular (macroalgae), with some unique cases of multinucleate unicellular forms that impact coral reef health and biocalcification.
  • A study reported a genome analysis of a giant multinucleate unicellular chlorophyte, revealing its complex genetic structure and potential evolutionary adaptations related to environmental changes.
  • The research reveals insights into how this alga survives physical fragmentation, its calcification processes, and its ability to adapt to ocean acidification, providing essential information for reef conservation efforts and bioengineering applications.
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  • Scientists found a lot of tiny living things called microbes in the ocean, gathering over 43,000 genomes to study.
  • They discovered new tools that could help fight bacteria, like a special CRISPR system and some substances that kill germs.
  • This research shows how the variety of microbes in the ocean can help us create new technology and medicine that can benefit us in the future.
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  • Lymphocyte receptors have evolved independently in both jawed and jawless vertebrates, showing similar adaptive immune responses, though the diversity in jawless vertebrates like lampreys is less understood.
  • Researchers used single-cell RNA sequencing on lamprey tissues, revealing that T-like cells show more variety than B-like cells, with a unique T-like cell type identified that has a receptor homologous to MPL.
  • These MPL-L+ T-like cells are present in various lamprey tissues and can proliferate in response to specific stimuli, offering new insights into the adaptive immune system of jawless vertebrates and its evolutionary background.
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  • Understanding the cellular architecture and evolution of immune cells in different species helps reveal how immune systems function and their vulnerability to diseases.
  • A study using single-cell RNA sequencing was conducted on immune cells from two types of fish: cartilaginous (white-spotted bamboo shark) and bony fishes (zebrafish and Chinese tongue sole), showing that similar cell types across species have comparable gene expression profiles.
  • The research identified unique immune cell populations in the bamboo shark, suggesting a less specialized approach to immune function compared to the more functionally distinct lymphocytes found in bony fishes, providing insights into the evolution of immune systems in jawed vertebrates.
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With climate change and anthropic influence on the coastal ecosystems, mangrove ecosystems are disappearing at an alarming rate. Accordingly, it becomes important to track, study, record and store the mangrove microbial community considering their ecological importance and potential for biotechnological applications. Here, we provide information on mangrove fungal community composition and diversity in mangrove ecosystems with different plant species and from various locations differing in relation to anthropic influences.

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Introduction: Citrus is one of the most important fruit crops worldwide, and the root-associated microbiota can have a profound impact on tree health and growth.

Methods: In a collaborative effort, the International Citrus Microbiome Consortium investigated the global citrus root microbiota with samples collected from nine citrus-producing countries across six continents. We analyzed 16S rDNA and ITS2 amplicon sequencing data to identify predominant prokaryotic and fungal taxa in citrus root samples.

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Intertidal algae may adapt to environmental challenges by acquiring genes from other organisms and relying on symbiotic microorganisms. Here, we obtained a symbiont-free and chromosome-level genome of Pyropia haitanensis (47.2 Mb), a type of intertidal algae, by using multiple symbiont screening methods.

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  • - Teleosts are highly successful vertebrates, and studying early teleosts like the Clown featherback can reveal important information about the evolution of their pectoral fins.
  • - This study offers the highest quality genome assembly for Osteoglossiformes, identifying the divergence of the Clown featherback around 202-203 million years ago, coinciding with major geological events.
  • - Key findings include a unique deletion of regulatory elements near a specific gene in teleosts, likely linked to pectoral fin adaptations, alongside significant changes in transposable elements that may influence their evolutionary path.
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Background: Cobia (Rachycentron canadum) is the only member of the Rachycentridae family and exhibits considerable sexual dimorphism in growth rate. Sex determination in teleosts has been a long-standing basic biological question, and the molecular mechanisms of sex determination/differentiation in cobia are completely unknown.

Results: Here, we reported 2 high-quality, chromosome-level annotated male and female cobia genomes with assembly sizes of 586.

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Sirenians of the superorder Afrotheria were the first mammals to transition from land to water and are the only herbivorous marine mammals. Here, we generated a chromosome-level dugong (Dugong dugon) genome. A comparison of our assembly with other afrotherian genomes reveals possible molecular adaptations to aquatic life by sirenians, including a shift in daily activity patterns (circadian clock) and tolerance to a high-iodine plant diet mediated through changes in the iodide transporter NIS (SLC5A5) and its co-transporters.

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  • * By utilizing metaproteomic and 16 rRNA amplicon sequencing methods, researchers found that microbial communities showed clear vertical connectivity in composition and function from the surface to depths of 3000 meters.
  • * Key microbial groups like Oceanospirillales, Alteromonadales, and Rhodobacterales were identified, with findings indicating that surface microbes influence deep-sea biochemistry by enhancing protein expression related to metabolism and environmental stress.
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Our recent multi-omics studies have revealed rich sources of novel bioactive proteins and polypeptides from marine organisms including cnidarians. In the present study, we initially conducted a transcriptomic analysis to review the composition profile of polypeptides from Zoanthus sociatus. Then, a newly discovered NPY-like polypeptide-ZoaNPY was selected for further in silico structural, binding and virtually pharmacological studies.

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The pharyngeal endoderm, an innovation of deuterostome ancestors, contributes to pharyngeal development by influencing the patterning and differentiation of pharyngeal structures in vertebrates; however, the evolutionary origin of the pharyngeal organs in vertebrates is largely unknown. The endostyle, a distinct pharyngeal organ exclusively present in basal chordates, represents a good model for understanding pharyngeal organ origins. Using Stereo-seq and single-cell RNA sequencing, we constructed aspatially resolved single-cell atlas for the endostyle of the ascidian .

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Unlabelled: The electric catfish (), belonging to the family Malapteruridae, order Siluriformes (Actinopterygii: Ostariophysi), is one of the six branches that has independently evolved electrical organs. We assembled a 796.75 Mb genome and anchored 88.

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Populations and species are threatened by human pressure, but their fate is variable. Some depleted populations, such as that of the northern elephant seal (Mirounga angustirostris), recover rapidly even when the surviving population was small. The northern elephant seal was hunted extensively and taken by collectors between the early 1800s and 1892, suffering an extreme population bottleneck as a consequence.

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Nonalcoholic fatty liver disease (NAFLD) is becoming the most common chronic liver disease in the world. Immunity is the major contributing factor in NAFLD; however, the interaction of immune cells and hepatocytes in disease progression has not been fully elucidated. As a popular species for studying NAFLD, zebrafish, whose liver is a complex immune system mediated by immune cells and non-immune cells in maintaining immune tolerance and homeostasis.

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Lineage-wise physiological activities of plankton communities in the ocean are important but challenging to characterize. Here, we conducted whole-assemblage metatranscriptomic profiling at continental shelf and slope sites in the South China Sea to investigate carbon fixation potential in different lineages. expression, the proxy of Calvin carbon fixation (CCF) potential, was mainly contributed by Bacillariophyta, Chlorophyta, Cyanobacteria, and Haptophyta, which was differentially affected by environmental factors among lineages.

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Glycogen serves as the principal energy reserve for metabolic processes in aquatic shellfish and substantially contributes to the flavor and quality of oysters. The Jinjiang oyster ( ) is an economically and ecologically important species in China. In the present study, RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) were performed to investigate gene expression and chromatin accessibility variations in oysters with different glycogen contents.

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Characiformes is a diverse and evolutionarily significant order of freshwater fish encompassing over 2,300 species. Despite its diversity, our understanding of Characiformes' evolutionary relationships and adaptive mechanisms is limited due to insufficient genome sequences. In this study, we sequenced and assembled the genomes of four Characiformes species, three of which were chromosome-level assemblies.

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The six species of lungfish possess both lungs and gills and are the closest extant relatives of tetrapods. Here, we report a single-cell transcriptome atlas of the West African lungfish (Protopterus annectens). This species manifests the most extreme form of terrestrialization, a life history strategy to survive dry periods that can last for years, characterized by dormancy and reversible adaptive changes of the gills and lungs.

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