Biology subjects

Qian, P.-Y.

Publications and source records attributed to Qian, P.-Y..

13 recordsLinked to original sources

bioRxiv2026

CnidoSite: A Multi-Omics Database for Cnidarians

The phylum Cnidaria, encompassing reef-building corals, sea anemones, hydroids, and jellyfish, includes both ecological keystones of the marine biosphere and indispensable models for reconstructing early animal evolution. However, escalating ocean warming, recurrent mass coral bleaching events, and intensifying jellyfish blooms have underscored the urgent need to dissect the molecular underpinnings of cnidarian thermal tolerance, symbiosis, and environmental adaptation. Progress in cnidarian research is hindered by the lack of centralized, high-quality multi-omics resources. To address this, we present CnidoSite (https://CnidoSite.org), a comprehensive, analysis-ready multi-omics platform dedicated to Cnidaria. Spanning 327 species across 120 families, 23 orders, and 7 classes, it integrates 147 full-annotated genomes, 15,642 bulk transcriptomes, 50 single-cell datasets, 46 proteomes, 723 epigenomes, 1,650 metagenomic samples, and 180,652 phenotype records. Complemented by advanced toolkits for multidimensional functional and comparative analyses, CnidoSite provides extensive functional genomic resources, including genome assemblies, phylogenies, fossil entries, functional annotations, BUSCO assessments, and mitochondrial annotations. Key features include 29 co-expression networks with cross-tissue visualization and single-cell atlases to map developmental trajectories and stress responses. In summary, CnidoSite serves as a centralized platform that bridges cnidarian biology, marine conservation, and evolutionary genomics to investigate coral bleaching, symbiosis breakdown, jellyfish blooms, and the mechanisms driving environmental adaptation.

bioinformatics↗

bioRxiv2025

Population genomics of the endangered scaly-foot snail defines conservation units amid deep-sea mining threats in Indian Ocean vents

Hydrothermal vents in the Indian Ocean face imminent deep-sea mining, yet lack baseline high-resolution connectivity data for their endemic fauna. We present the first population genomic study of the endangered scaly-foot snail (Chrysomallon squamiferum), an iconic species distributed across three vent biogeographic provinces. Analysing 125 individuals from eight vent fields using 14 million single-nucleotide polymorphisms, we identify five genetic groups that warrant recognition as evolutionarily significant units. Demographic modelling reveals critical contributions from extinct or unsampled phantom populations to the contemporary genetic structure. Together with physical ocean modelling, we show that the deep currents drive asymmetric south-to-north gene flows, while transform faults act as dispersal barriers. We propose Longqi-Duanqiao fields on the Southwest Indian Ridge and Wocan field on the Carlsberg Ridge as two isolated populations prioritised for protection. Given its exceptional adaptations, wide distribution, and public recognition, the scaly-foot snail is well-positioned to serve as both a flagship and umbrella species to ensure the survival of a broader suite of vent biodiversity. As the International Seabed Authority finalises its Mining Code in 2025, our findings provide essential genomic evidence to mitigate the impacts of mining on genetic diversity and inform transboundary conservation strategies for this vulnerable ecosystem.

ecology↗

bioRxiv2025

A multilamellar organelle for chemosymbiosis in an aplacophoran mollusc adapted to anoxic cold seep sediment

Symbiosis with chemoautotrophic bacteria has evolved in many animal lineages inhabiting reducing habitats such as hydrothermal vents, allowing these holobionts to thrive in dark biospheres1. In certain instances, the symbionts have become intracellular, residing within specialised bacteriocytes2. The integration of microbial symbionts with eukaryotic cells vary across known animals; however, no specialised organelle dedicated to chemosynthesis has been identified yet2. Here, we report a mode of symbiosis where sulphur-oxidising bacteria cultured within spherical multilamellar compartments (~12 m) in the cold-seep aplacophoran mollusc Chaetoderma shenloong. This organelle, which we name dracosphera, is ubiquitous within the hypertrophied and intricately reticulate digestive gland of C. shenloong, which has otherwise lost most of its gut. Given that the symbionts are strictly anaerobic and the host resides in anoxic sediments tens of centimetres below the surface, the dracosphera may serve to minimise oxygen diffusion to the bacteria, akin to mechanisms observed in microbial diazotrophs3 or termite hindguts4, as supported by our genomic and spatial transcriptomic analyses. Hypoxic conditions have been known to induce radical adaptations in meiofauna, exemplified by the acquisition of hydrogenosomes5. Our discovery of similarly exceptional adaptations in C. shenloong provides new insights into the evolution of such organelles also in larger animals.

microbiology↗

bioRxiv2024

Circatidal control of gene expression in the deep-sea hot vent shrimp Shinkaicaris leurokolos

Biological clocks are a ubiquitous feature of all life, enabling the use of natural environmental cycles to track time. Although studies on circadian rhythms have contributed greatly to the knowledge of chronobiology, biological rhythms in dark biospheres such as the deep sea remain poorly understood. Here, based on a laboratory free-running experiment, we reveal potentially endogenous rhythms in gene expression of the deep-sea hydrothermal vent shrimp Rimicaris leurokolos. Oscillations with [~]12-hour periods, likely reflecting tidal influence, greatly prevail over others in the temporal transcriptome, indicating R. leurokolos likely depends on a circatidal clock consisting of at least some components independent of the circadian clocks. The tidal transcripts exhibit an antiphased expression pattern divided into two internally synchronized clusters, correlated with wide-ranging biological processes that occur in the nucleus and cytoplasm, respectively. In addition, comparing the tidal transcripts with the [~]12-hour ultradian rhythms genes in fruit flies and mice shows large similarity, indicating the likely scenario of broad impact of the tide on the [~]12-hour oscillations across the metazoan. These findings not only provide new insights into the temporal adaptations in deep-sea organisms but also highlight deep-sea hydrothermal vent organisms as intriguing models for chronobiological, particularly 12-hour ultradian rhythms, studies.

ecology↗

bioRxiv2023

Deciphering deep-sea chemosynthetic symbiosis by single-nucleus RNA-sequencing

Bathymodioline mussels dominate deep-sea methane seep and hydrothermal vent habitats and obtain nutrients and energy primarily through chemosynthetic endosymbiotic bacteria in the bacteriocytes of their gill. However, the molecular mechanisms that orchestrate mussel host-symbiont interactions remain unclear. Here, we constructed a comprehensive cell atlas of the gill in the mussel Gigantidas platifrons from the South China Sea methane seeps (1100m depth) using single-nucleus RNA sequencing (snRNA-seq) and whole-mount in situ hybridisation. We identified 13 types of cells, including three previously unknown ones, and uncovered unknown tissue heterogeneity. Every cell type has a designated function in supporting the gills structure and function, creating an optimal environment for chemosynthesis, and effectively acquiring nutrients from the endosymbiotic bacteria. Analysis of snRNA-seq of in situ transplanted mussels clearly showed the shifts in cell state in response to environmental oscillations. Our findings provide insight into principles of host-symbiont interaction and the bivalves environmental adaption mechanisms.

ecology↗

bioRxiv2022

Host mixotrophy, habitat stability and recombination may all decrease geographic differentiation between symbiont populations in Western Pacific deep-sea mussels

The intra-host composition of horizontally transmitted microbial symbionts can vary across host populations due to interactive effects of host genetics, environmental and geographic factors. While adaptation to local habitat conditions can drive geographic subdivision of symbiont strains, it is unknown whether these patterns are universal and how differences in ecological characteristics among host-symbiont associations influence the genomic structure of symbiont populations. To address this question, we sequenced metagenomes of different populations of the deep-sea mussel Bathymodiolus septemdierum, which are common at Western Pacific deep-sea hydrothermal vents and show characteristic patterns of niche partitioning with sympatric gastropod symbioses. Bathymodiolus septemdierum lives in close symbiotic relationship with sulfur-oxidizing chemosynthetic bacteria but supplements its symbiotrophic diet through filter-feeding, enabling it to occupy ecological niches with less exposure to geochemical reductants. Our analyses indicate that symbiont populations associated with B. septemdierum show structuring by geographic location, but that the dominant symbiont strain is uncorrelated with vent site. These patterns are in contrast to co-occurring Alviniconcha and Ifremeria symbioses that exhibit greater symbiont nutritional dependence and occupy habitats with higher spatial variability in environmental conditions. Our results suggest that relative habitat homogeneity combined with sufficient symbiont dispersal and genomic mixing might promote persistence of similar symbiont strains across geographic locations, while mixotrophy might decrease selective pressures on the host to affiliate with locally adapted symbiont strains. Overall, these data contribute to our understanding of the potential mechanisms influencing symbiont population structure across a spectrum of marine microbial symbioses that vary in ecological niche and relative host dependency.

evolutionary biology↗

bioRxiv2022

The hologenome of Osedax frankpressi reveals the genetic interplay for the symbiotic digestion of vertebrate bone

The marine annelid Osedax has evolved a unique heterotrophic symbiosis that allows it to feed exclusively on sunken bones. Yet, the genetic and physiological principles sustaining this symbiosis are poorly understood. Here we show that Osedax frankpressi has a small, AT-rich genome shaped by extensive gene loss. While the Oceanospirillales endosymbiont of Osedax is enriched in genes for carbohydrate and nitrogen metabolism, O. frankpressi has undergone genetic changes to accommodate bone digestion, including the expansion of matrix metalloproteases, and a loss of pathways to synthesize amino acids that are abundant in collagen. Unlike other symbioses, however, innate immunity genes required to acquire and control the endosymbionts are reduced in O. frankpressi. These findings reveal Osedax has evolved an alternative genomic toolkit to bacterial symbiosis where host-symbiont co-dependence has favoured genome simplicity in the host to exploit the nutritionally unbalanced diet of bones. TeaserGenome reduction and adaptations for collagen digestion underpin the symbiosis of Osedax worms to exploit decaying bones.

genomics↗

bioRxiv2020

Dual symbiosis in the deep-sea hydrothermal vent snail Gigantopelta aegis revealed by its hologenome

Animals endemic to deep-sea hydrothermal vents often form obligatory relationships with bacterial symbionts, maintained by intricate host-symbiont interactions. Endosymbiosis with more than one symbiont is uncommon, and most genomic studies focusing on such dual symbiosis systems have not investigated the host and the symbionts to a similar depth simultaneously. Here, we report a novel dual symbiosis among the peltospirid snail Gigantopelta aegis and its two Gammaproteobacteria endosymbionts - one being a sulphur oxidiser and the other a methane oxidiser. We assembled high-quality genomes for all three parties of this holobiont, with a chromosome-level assembly for the snail host (1.15 Gb, N50 = 82 Mb, 15 pseudo-chromosomes). In-depth analyses of these genomes reveal an intimate mutualistic relationship with complementarity in nutrition and metabolic codependency, resulting in a system highly versatile in transportation and utilisation of chemical energy. Moreover, G. aegis has an enhanced immune capability that likely facilitates the possession of more than one type of symbiont. Comparisons with Chrysomallon squamiferum, another chemosymbiotic snail in the same family but only with one sulphur-oxidising endosymbiont, show that the two snails sulphur-oxidising endosymbionts are phylogenetically distant, agreeing with previous results that the two snails have evolved endosymbiosis independently and convergently. Notably, the same capabilities of biosynthesis of specific nutrition lacking in the host genome are shared by the two sulphur-oxidising endosymbionts of the two snail genera, which may be a key criterion in the selection of symbionts by the hosts.

genomics↗

bioRxiv2020

Tripartite holobiont system in a vent snail broadens the concept of chemosymbiosis

Many animals inhabiting deep-sea vents are energetically dependent on chemosynthetic endosymbionts, but how such symbiont community interacts with host, and whether other nutritional sources are available to such animals remain unclear. To reveal the genomic basis of symbiosis in the vent snail Alviniconcha marisindica, we sequenced high-quality genomes of the host and gill campylobacterial endosymbionts, as well as metagenome of the gut microbiome. The gill endosymbiont has a streamlined genome for efficient chemoautotrophy, but also shows metabolic heterogeneity among populations. Inter- and intra-host variabilities among endosymbiont populations indicate the host poses low selection on gill endosymbionts. Virulence factors and genomic plasticity of the endosymbiont provide advantages for cooperating with host immunity to maintain mutualism and thriving in changing environments. In addition to endosymbiosis, the gut and its microbiome expand the holobionts utilisation of energy sources. Host-microbiota mutualism contributes to a highly flexible holobiont that can excel in various extreme environments.

ecology↗

bioRxiv2020

Mutanofactin promotes bacterial adhesion and biofilm formation of cariogenic Streptococcus mutans

Cariogenic Streptococcus mutans is known as a predominant etiological agent of dental caries due to its exceptional capacity in forming biofilms. From strains of S. mutans isolated from dental plaque, we here discover a polyketide/non-ribosomal peptide biosynthetic gene cluster, muf, which directly correlates with a strong biofilm-forming capability. We then identify the muf-associated bioactive product, mutanofactin-697 that contains a novel molecular scaffold, along with its biosynthetic logic. Further mode-of-action studies reveal mutanofactin-697 binds to S. mutans cells nonspecifically, increases bacterial hydrophobicity, and promotes bacterial adhesion and subsequent biofilm formation. Our findings provide the first example of a microbial secondary metabolite promoting biofilm formation via a physicochemical approach, highlighting the significance of secondary metabolism in mediating critical processes related to the development of dental caries.

microbiology↗

bioRxiv2020

Horseshoe crab genomes reveal the evolutionary fates of genes and microRNAs after three rounds (3R) of whole genome duplication

Whole genome duplication (WGD) has occurred in relatively few sexually reproducing invertebrates. Consequently, the WGD that occurred in the common ancestor of horseshoe crabs ~135 million years ago provides a rare opportunity to decipher the evolutionary consequences of a duplicated invertebrate genome. Here, we present a high-quality genome assembly for the mangrove horseshoe crab Carcinoscorpius rotundicauda (1.7Gb, N50 = 90.2Mb, with 89.8% sequences anchored to 16 pseudomolecules, 2n = 32), and a resequenced genome of the tri-spine horseshoe crab Tachypleus tridentatus (1.7Gb, N50 = 109.7Mb). Analyses of gene families, microRNAs, and synteny show that horseshoe crabs have undergone three rounds (3R) of WGD, and that these WGD events are shared with spiders. Comparison of the genomes of C. rotundicauda and T. tridentatus populations from several geographic locations further elucidates the diverse fates of both coding and noncoding genes. Together, the present study represents a cornerstone for a better understanding of the consequences of invertebrate WGD events on evolutionary fates of genes and microRNAs at individual and population levels, and highlights the genetic diversity with practical values for breeding programs and conservation of horseshoe crabs.

evolutionary biology↗

bioRxiv2020

A potent antibiofilm agent inhibits and eradicates mono- and multi-species biofilms

Biofilms are surface-attached multicellular communities that create many problems in human health and various industries. Given the prominence of biofilms in biofouling and infectious diseases, antibiofilm control approaches are highly sought after. In the present study, we identified elasnin as a potent antibiofilm agent through a bioassay-guided approach. Elasnin specifically inhibited the biofilm formation of bacterial mono-species and eradicated the mature biofilm of Gram-positive bacteria at concentrations below 2.5 g/mL with a low toxic effect on cells and a low resistance risk. Confocal observations illustrated that elasnin decreased cell aggregations and destroyed the biofilm matrix. Furthermore, elasnin-based antibiofilm coatings were prepared and inhibited the formation of multi-species biofilms and the attachment of large biofouling organisms in the field test. These findings suggest that elasnin is a promising antibiofilm agent for future applications in biofilm control. ImportanceDue to the increased diversity of biofilm-associated infections and the failure of conventional antimicrobial treatment, new and effective biofilm-specific pharmacologic strategies are urgently needed. Elasnin is a new antibiofilm natural product produced by Streptomyces with high efficiency and low toxicity. Elasnin effectively destroyed the biofilm matrix of Gram-positive bacteria, thus making them more susceptible to antibiotics. Unlike currently deployed antibiotic vancomycin, which exclusively targets essential life processes and kills the pathogen, elasnin did not exhibit bactericidal effect and thus held great potential in delaying resistance. With high yield, elasnin-based coatings were easily prepared with low expenditures and exhibited favorable performance in field test. Collectively, the antibiofilm properties of elasnin, combined with the low cost of supply and the low risk of resistance, could provide the basis for the development of a novel antibiofilm agent that could help fight to antibiotics resistance.

microbiology↗

bioRxiv2019

Macrocyclic colibactin induces DNA double-strand breaks via copper-mediated oxidative cleavage

Colibactin is an as-yet-uncharacterized human gut bacterial genotoxin, whose biosynthesis is linked to clb genomic island that distributes widespread in pathogenic and commensal human enterobacteria. Colibactin-producing gut microbes promote colon tumor formation and enhance progression of colorectal cancer (CRC) via DNA double-strand breaks (DSBs)-induced cellular senescence and death; however, the chemical basis contributing to the pathogenesis at the molecular level remains elusive. Here we report the discovery and the mechanism of action of colibactin-645 as the highly sought final colibactin metabolite with a novel molecular scaffold. Colibactin-645 recapitulates its previously assumed genotoxicity and cytotoxicity, exhibiting a strong DNA DSBs activity in vitro and in human cell cultures via a unique copper-mediated oxidative mechanism. We also present a complete model for colibactin biosynthesis, revealing an unprecedented dual function of the aminomalonate-utilizing polyketide synthases. This work thus provides the first molecular basis for colibactins genotoxic activity and facilitates further mechanistic study of colibactin-related CRC incidence and prevention.

microbiology↗