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Combined ATAC-seq,RNA-seq,and GWAs analysis reveals glycogen metabolism regulatory network in Jinjiang oyster(Crassostrea ariakensis)

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Zoological research 2024年第1期45卷 201-214页

作者： Biao Wu Xi Chen Jie Hu Zhen-Yuan Wang Yan Wang Da-You Xu Hao-Bing Guo Chang-Wei shao Li-Qing Zhou Xiu-Jun sun Tao Yu Xiao-Mei Wang Yan-Xin Zheng Guang-Yi Fan Zhi-Hong Liu state Key Laboratory of Mariculture Biobreeding and sustainable Goods Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdaoShandong 266071China Laboratory for marine Fisheries science and Food Production Processes Laoshan LaboratoryQingdaoShandong 266071China BGI-Qingdao BGI-ShenzhenQingdaoShandong 266426China National Demonstration Center for Experimental Fisheries science Education Shanghai Ocean UniversityShanghai 201306China Changdao Enhancement and Experiment station Chinese Academy of Fishery SciencesYantaiShandong 265800China state Key Laboratory of Agricultural Genomics BGI-ShenzhenShenzhenGuangdong 518083China

Glycogen serves as the principal energy reserve for metabolic processes in aquatic shellfish and substantially contributes to the flavor and quality of *** Jinjiang oyster(Crassostrea ariakensis)is an economically and ecologically important species 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 *** identified 9483 differentially expressed genes(DEGs)and 7215 genes with significantly differential chromatin accessibility(DCAGs)were obtained,with an overlap of 2600 genes between ***,a significant proportion of these genes were enriched in pathways related to glycogen metabolism,including“Glycogen metabolic process”and“starch and sucrose metabolism”.In addition,genome-wide association study(GWAs)identified 526 single nucleotide polymorphism(sNP)loci associated with glycogen *** loci corresponded to 241 genes,63 of which were categorized as both DEGs and *** study enriches basic research data and provides insights into the molecular mechanisms underlying the regulation of glycogen metabolism in ***.

关键词： Crassostrea ariakensis Glycogen Transcriptome ATAC GWAs

Dinophysis caudata generated lipophilic shellfish toxins in bivalves from the Nanji Islands, East china sea

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Chinese Journal of Oceanology and Limnology 2014年第1期32卷 130-139页

作者：江涛徐轶肖李扬齐雨藻江天久吴锋张帆 research Center for Harmful Algae and marine Biology Jinan University school of Geographical and Oceanographic sciences Nanjing University College of Life science South China Normal University

A 12-month program of monitoring potentially toxic microalgae(that produce lipophilic shellfi sh toxins; LsTs) and their toxins in bivalves was conducted from April 2006 to March 2007 in the Nanji Islands, East china sea. Two Dinophysis species, D. caudata and D. acuminata, were identifi ed, and D. caudat a was found to be the dominant species. D. caudata was detected in water samples between April and June 2006, and between February and March 2007. It reached its highest abundances in May, with a mean abundance of 1.38×10 2 cells/L in surface water and 1.25×10 2 cells/L in bottom water(stribution of D. caudata was associated with the occurrence of LsTs in bivalve samples, which mostly occurred at the same time as D. caudata blooms, between April and July 2006. All of the cultured bivalves sampled between April and June were contaminated with LsTs, with an average toxicity of 85 μg okadaic acid(OA) eq./100 g meat, which was four times higher than the Chinese regulatory limit(20 μg OA eq./100 g meat). Ten out of fi fteen wild samples(66.7%) collected during the same period were positive for LsTs, and contained an average LsT toxicity of 45 μg OA eq./100 g meat(more than twice the regulatory value). Cultured Patinopecten yessoensis collected on 15 May 2006 had the highest toxicity, 320 μg OA eq./100 g meat, and relatively high toxicities(80 to 160 μg OA eq./100 g meat) were found in bivalves until the end of July.

关键词： Dinophysis lipophilic shellfish toxins D. caudate East china sea Nanji Islands

spatial and seasonal variability of global ocean diapycnal transport inferred from Argo profiles

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Journal of Oceanology and Limnology 2019年第2期37卷 498-512页

作者： HUANG Chao XU Yongsheng Key Laboratory of Ocean Circulation and Waves Institute of Oceanology Chinese Academy of Sciences Qingdao 266071China Function Laboratory for Ocean Dynamics and Climate Qingdao National Laboratory for Marine Science and TechnologyQingdao 266000 China University of Chinese Academy of sciences Beijing 100049 China Center for Ocean Mega-science Chinese Academy of Sciences Qingdao 266071 China

The global diapycnal transport in the ocean interior is one of the significant branches to return the deep water back toward near-surface. However, the amount of the diapycnal transport and the seasonal variations are not determined yet. This paper estimates the dissipation rate and the associated diapycnal transports at 500 m, 750 m and 1 000 m depth throughout the global ocean from the wide-spread Argo profiles, using the finescale parameterizations and classic advection-diff usion balance. The net upwelling is ~5.2±0.81 sv (sverdrup) which is approximately one fifth in magnitude of the formation of the deep water. The southern Ocean is the major region with the upward diapycnal transport, while the downwelling emerges mainly in the northern North Atlantic. The upwelling in the southern Ocean accounts for over 50% of the amount of the global summation. The seasonal cycle is obvious at 500 m and vanishes with depth, indicating the energy source at surface. The enhancement of diapycnal transport occurs at 1000min the southern Ocean, which is pertinent with the internal wave generation due to the interaction between the robust deep-reaching flows and the rough topography. Our estimates of the diapycnal transport in the ocean interior have implications for the closure of the oceanic energy budget and the understanding of global Meridional Overturning Circulation.

关键词： dissipation rate diapycnal transport upwelling meridional overturning circulation

Adaptive Bird-like Genome Miniaturization During the Evolution of scallop swimming Lifestyle

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Genomics, Proteomics & Bioinformatics 2022年第6期20卷 1066-1077页

作者： Yuli Li Yaran Liu Hongwei Yu Fuyun Liu Wentao Han Qifan Zeng Yuehuan Zhang Lingling Zhang Jingjie Hu Zhenmin Bao shi Wang sars-Fang Centre&MOE Key Laboratory of marine Genetics and Breeding College of Marine Life SciencesOcean University of ChinaQingdao 266003China Laboratory for marine Biology and Biotechnology Pilot Qingdao National Laboratory for Marine Science and TechnologyQingdao 266237China Laboratory for marine Fisheries science and Food Production Processes Pilot Qingdao National Laboratory for Marine Science and TechnologyQingdao 266237China Key Laboratory of Tropical Aquatic Germplasm of Hainan Province Sanya Oceanographic InstitutionOcean University of ChinaSanya 572000China CAs Key Laboratory of Tropical marine Bio-resources and Ecology South China Sea Institute of OceanologyChinese Academy of SciencesGuangzhou 510301China

Genome miniaturization drives key evolutionary innovations of adaptive traits in vertebrates,such as the flight evolution of ***,whether similar evolutionary processes exist in invertebrates remains poorly *** from the second-largest animal phylum,scallops are a special group of bivalve molluscs and acquire the evolutionary novelty of the swimming lifestyle,providing excellent models for investigating the coordinated genome and lifestyle ***,we show for the first time that genome sizes of scallops exhibit a generally negative correlation with locomotion *** elucidate the co-evolution of genome size and swimming lifestyle,we focus on the Asian moon scallop(Amusium pleuronectes)that possesses the smallest known scallop genome while being among scallops with the highest swimming ***-genome sequencing of *** reveals highly conserved chromosomal macrosynteny and microsynteny,suggestive of a highly contracted but not degenerated *** reduction of *** is facilitated by significant inactivation of transposable elements,leading to reduced gene length,elevated expression of genes involved in energy-producing pathways,and decreased copy numbers and expression levels of biomineralization-related *** evolutionary changes of relevant pathways are also observed for bird genome reduction with flight *** striking mimicry of genome miniaturization underlying the evolution of bird flight and scallop swimming unveils the potentially common,pivotal role of genome size fluctuation in the evolution of novel lifestyles in the animal kingdom.

关键词： Genome size Lifestyle evolution Genome sequencing scallop Bird

Cytological and transcriptional analysis reveal phosphatidylinositol signaling pathway plays key role in mitotic division of Pyropia yezoensis

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Journal of Oceanology and Limnology 2022年第3期40卷 1148-1159页

作者： Yunke ZHU Xinran WANG Bin sUN Xianghai TANG Yunxiang MAO Key Laboratory of marine Genetics and Breeding(Ministry of Education) College of Marine Life SciencesOcean University of ChinaQingdao 266003China MOE Key Laboratory of Utilization and Conservation for Tropical marine Bioresources College of Fisheries and Life ScienceHainan Tropical Ocean UniversitySanya 572022China Laboratory for marine Biology and Biotechnology Pilot National Laboratory for Marine Science and Technology(Qingdao)Qingdao 266237China

The phosphatidylinositol(PI)signaling system,a central regulator of eukaryotic metabolism,is widely found in eukaryotes for regulating a variety of cell *** of the genes in the PI signaling system were found conserved in Pyropia *** this experiment,wortmannin was used as an inhibitor to inhibit the activity of phosphatidylinositol-3 kinase(PI3K),an important regulator of the PI signaling *** wortmannin treatment,the mitotic division of *** was signifi cantly inhibited in a dose-dependent manner,and the mitotic division percentage was reduced by 68.1%and 91.9%in the 5-and 10-μmol/L groups,*** thalli were treated with wortmannin,the levels of reactive oxygen species(ROs)were signifi cantly ***,the expression level of PI3K was inhibited and the expression levels of downstream genes regulated by PI3K was signifi cantly *** the PI3K-AGC signaling pathway,the expression levels of serine/threonine protein kinase(AGC)and cyclindependent kinases A(CDKA)were downregulated,while WEE1 kinase gene(WEE1)was *** nicotinamide adenine dinucleotide phosphate(NADPH)oxidase genes were downregulated after wortmannin *** results indicate that the PI signaling system plays an important role in the regulation of cell activity in *** was speculated that the growth and development of *** might be regulated by *** PI3K,which promoted the expression of the AGC gene and further regulates the expression of downstream WEE1 and CDKA genes to advance mitotic division,and also promoted the expression level of NADPH oxidase that regulates ROs homeostasis.

关键词： Pyropia yezoensis phosphatidylinositol signaling system reactive oxygen species mitotic division

studies on marine dynamic disasters

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Journal of Oceanology and Limnology 2019年第6期37卷 1791-1794页

作者： HU Po LIU Yahao HOU Yijun Key Laboratory of Ocean Circulation and Waves Institute of OceanologyChinese Academy of SciencesQingdao 266071China Center for Ocean Mega-science Chinese Academy of SciencesQingdao 266071China University of Chinese Academy of sciences Beijing 100049China Laboratory for Ocean and Climate Dynamics Qingdao National Laboratory for Marine Science and TechnologyQingdao 266237China

marine dynamic disasters,including storm surges,huge waves,and sea ice,are the most harmful natural disasters aff ecting coastal countries in the *** the infl uence of global climate change,the mechanisms,frequencies,and damage severity of marine dynamic disasters are exhibiting new *** enormity,unpredictability,and chain eff ects of these disasters have become increasingly prominent,and the losses endured by coastal countries around the world have been increasing year by ***,the prediction of,risk assessment for,and emergency response to marine dynamic disasters are important issues for disaster prevention and mitigation worldwide.

关键词： marine dynamic disasters storm surges huge waves

Purification and Characterization of a Novel Lipase from Antarctic Krill

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Journal of Ocean University of china 2020年第1期19卷 209-215页

作者： CHEN Xin WANG Chunlan XU Jiakun WANG Fang JIANG Yihui CHEN Yixuan and ZHAO Xianyong College of Food science and Technology Shanghai Ocean UniversityShanghai 201306China Yellow sea Fisheries research Institute Chinese Academy of Fishery SciencesKey Laboratory of Sustainable Development of Polar FisheryMinistry of Agriculture and Rural Affairs of PRCQingdao 266071China Laboratory for marine Drugs and Bioproducts of Qingdao National Laboratory for marine science and Technology Qingdao 266237China Laboratory for marine Fisheries science and Food Production Processes Qingdao National Laboratory for Marine Science and TechnologyQingdao 266071China College of Chemistry and Chemical Engineering Ocean University of ChinaQingdao 266100China

Lipase from Antarctic krill,with a molecular weight of 71.27kDa,was purified with ammonium sulfate precipitation and a series of chromatographic separations over ion exchange(DEAE)and gel filtration columns(sephacryl s-100),resulting in 5.2%recovery with a 22.4-fold purification *** optimal pH and temperature for enzyme activity were 8.0 and 45℃,*** lipase had Km and Vmax values of 3.27mmolL−1 and 2.4Umg−1,respectively,using p-nitrophenyl laurate as the *** activity was enhanced by adding Ca2+and Mg2+ions in the concentration ranges of 0–0.5mmolL−1 and 0–0.3mmolL−1,respectively,while the activity was inhibited by a further increase in these ion ***3+and Cu2+ions showed obvious inhibitory effects on enzyme activity,and the inhibition rates were 71.8%and 53.3%when the ion concentrations were 0.5mmolL−1.

关键词： Antarctic krill lipase isolation and purification enzymology properties

Decadal characteristics of the floating Ulva and sargassum in the subei shoal,Yellow sea

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Acta Oceanologica sinica 2020年第10期39卷 1-10页

作者： Jie Xiao shiliang Fan Zongling Wang Mingzhu Fu Hongjun song Xiao Wang Chao Yuan Min Pang Xiaoxiang Miao Xuelei Zhang Key Laboratory of marine Eco-Environmental science and Technology First Institute of OceanographyMinistry of Natural ResourcesQingdao 266061China Laboratory of marine Ecology and Environmental science Pilot National Laboratory for Marine Science and Technology(Qingdao)Qingdao 266237China College of Environmental science and Engineering Ocean University of ChinaQingdao 266100China

The data of field surveys during 2009 to 2018 was analyzed to understand the seasonality and inter-annual variability of the floating Ulva and sargassum in the subei shoal,the southwestern Yellow sea of china on decadal *** floating Ulva biomass was consistently originated from the central region of the subei shoal in middle to late April,increased rapidly,drifted and extended into the offshore water in May and *** average floating Ulva biomass in the shoal generally increased over the years with evident inter-annual *** contrast,pelagic sargassum was accumulated in the subei shoal and formed the spring bloom only in 2013,2017 and 2018,and the biomass was higher than the co-occurring Ulva during the survey in these three *** to the raft-origin floating Ulva,genesis and development of the pelagic sargassum was *** on the current research,the sargassum biomass was exotic and often initiated in the offshore water in March,and intruded into the shoal in April and *** analysis on the environmental parameters was inconclusive since multiple anthropogenic and non-indigenous factors could influence the green tides in this *** research covering both the East china sea and the Yellow sea is needed to trace the origin of the floating sargassum and to understand the interactions between these two co-occurring seaweeds.

关键词： seaweed bloom green tide golden tide Ulva sargassum Yellow sea

A simple guideline to apply excitation-emission matrix spectroscopy(EEMs)for the characterization of dissolved organic matter(DOM)in anoxic marine sediments

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Acta Oceanologica sinica 2023年第1期42卷 109-119页

作者： shuchai Gan Verena BHeuer Frauke schmidt Lars Wörmer Kai-Uwe Hinrichs MARUM—Center for marine Environmental sciences University of BremenBremenD-28359Germany

marine sediments represent a major carbon reservoir on *** organic matter(DOM)in pore waters accumulates products and intermediates of carbon cycling in *** application of excitation-emission matrix spectroscopy(EEMs)in the analysis of subseafloor DOM samples is largely unexplored due to the redox-sensitive matrix of anoxic pore ***,this study aims to investigate the interference caused by the matrix on EEMs and propose a guideline to prepare pore water samples from anoxic marine *** parameters determined by fluorescence spectra include 3D-index derived from EEMs after parallel factor analysis(PARAFAC),fluorescence index(FI)(contribution of terrigenous DOM),biological index(BIX)and humification index(HIX)derived from 2D emission ***,we investigated the impacts of extensively-presented ions as typical electron acceptors,which are utilized by anaerobic microbes and stratified in marine sediments:Fe(II),Fe(III),Mn(II)and sulfide in anoxic pore water resulted in biases of fluorescent *** proposed threshold concentrations of these ions when the interference on EEMs *** removal of sulfide from sulfide-rich samples could be achieved by flushing with N_(2)for 2 ***,the tests based on DOM standard were further verified using pristine samples from marine *** was a significant change in the fluorescence spectra of DOM in anoxic sediments from the Rhône *** study demonstrated that the change was caused by oxidation of the matrix rather than the intrinsic alteration of *** was confirmed by extracted DOM via both EEMs analysis and Fourier transform ion cyclotron resonance mass spectrometry(FT-ICR-Ms).slight oxidation of sulfur-containing compounds(e.g.,sulfhydryl)and polyphenol-like compounds ***,a sample preparation sequence is proposed for pore water from anoxic *** method enables measurement with small volumes of the sample(e.g.,50µL in this study)an

关键词： marine subsurface sediment EEMs PARAFAC FT-ICR-Ms anaerobic pore water