Description of nitrogen metabolism pathway based on Skeletonema marinoi transcriptome
JING Xiao-li1,2, MI Tie-zhu2,3, ZHEN Yu2,3, FU Bao-zhong1,2, LI Cheng-feng4, YU Zhi-gang5
1. College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China;
2. China Ministry of Education Key Laboratory of Marine Environment and Ecology, Ocean University of China, Qingdao 266100, China;
3. College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China;
4. East China Sea Environmental Monitoring Center, State Oceanic Administration, Shanghai 200137, China;
5. Ministry of Education Key Laboratory of Marine Chemistry Theory and Technology, Ocean University of China, Qingdao 266100, China
Abstract：The transcriptomeof Skeletonema marinoi at different growth stages,different temperatures and low silicon concentration was analyzed with Illumina Hiseq 2000 platform sequencing technology,producing and identifying 39,098 transcripts totally.Assembled sequences were subjected to NR BLAST similarity searches and annotated with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes orthology (KO) identifiers.These analyses identified the important metabolic pathways and genes of S.marinoi,especially the nitrogen metabolism pathway involving 20 enzymes and proteins.Comparative analysis of enzyme-coding genes among S.marinoi,Thalassiosira pseudonana and Phaeodactylum tricornutum using BLASTx revealed relatively high homologous genes between S.marinoi and T.pseudonana.Using the Digital Gene Expression Profiling,we also found different gene expression in the pathway.Compared to exponential growth phase (EP),three genes coding nitrate reductase or nitrite reductase which were involved in nitrate assimilation process showed significantly increasing expression in stationary phase (SP),as well as carbamoyl-phosphate synthase-coding and carbamate kinase-coding genes.The results indicated the molecular responses of S.marinoi on the nitrogen changes in different growth phases.Our study will contribute to analyze gene regulation of key enzymes involved in nitrogen metabolism of S.marinoi,providing a basis to enhance our knowledge about gene expression and regulation patterns in nitrogen limitation,which will be beneficial to in-depth understand the nutrients utilization in harmful algae bloom species.
LAVERY P,PATTIARATCHI C,WYLLIE A.Water quality monitoring in estuarine waters using the Landsat Thematic Mapper[J].Remote Sensing of Environment,1993,46 (3):268-280.
GRABHERR M G,HAAS B J,YASSOUR M,et al.Full-length transcriptome assembly from RNA-Seq data without a reference genome [J].Nature Biotechnolgy,2011,29(7):644-652.
WANG P,EBERSOLE B A,SMITH E R,et al.Temporal and spatial variations of surf-zone currents and suspended sediment concentration[J].Coastal Engineering,2002,46(3):175-211.
[13]
PRINCE R C.Crude oil biodegradation.The encyclopedia of environmental analysis and remediation[M].New York:Wiley,1998,2:1327-1342.
DEKKER A,PETERS S.The use of the Thematic Mapper for the analysis of eutrophic lakes:a case study in the Netherlands[J].International Journal of Remote Sensing,1993,14 (5):799-821.
[23]
DEGROOTR S,WILSON M A,BOUMANS R M J.A typology for the classification,description and valuation of ecosystem functions,goods and services[J].Ecological Economics,2002,41(3):393-408.
[24]
CAMACHO C,COULOURIS G,AVAGYAN V,et al.BLAST+:architecture and applications [J].BMC Bioinformatics,2009,10(1):421.
[25]
EMADIAN S M,HOSSEINI M,RAHIMNEJAD M,et al.Treatment of a low-strength bilge water of Caspian Sea ships by HUASB technique[J].Ecological Engineering,2015,82:272-275.
[26]
VOULGARIS G,MEYERS S T.Temporal variability of hydrodynamics,sediment concentration and sediment settling velocity in a tidal creek[J].Continental Shelf Research,2004,24(15):1659-1683.
[27]
FREEMAN K H,HAYES J M,TRENDEL J M,et al.Evidence from carbon isotope measurements for diverse origins of sedimentary hydrocarbons[J].Nature,1990,343(6255):254-256.
[28]
HALLEGRAEFF G M.A review of harmful algal blooms and their apparent global increase[J].Phycologia,1993,32(2):79-99.
[29]
OLMANSON L G,BAUER M E,BREZONIK P L.A 20-year Landsat water clarity census of Minnesota's 10,000 lakes[J].Remote Sensing of Environment,2008,112 (11):4086-4097.
[30]
COSTANZA R,GROOT R,SUTTON P,et al.Changes in the global value of ecosystem services[J].Global Environmental Change,2014,26:152-158.
[31]
Millennium Ecosystem Assessment.Ecosystems and human well-being:synthesis[R].Washington,DC:Island Press,2005.
GÖTZ S,GARCÍA-GÓMEZ J M,TEROL J,et al.High-throughput functional annotation and data mining with the Blast2GO suite [J].Nucleic Acids Research,2008,36(10):3420-3435.
[37]
CARLESI C,RAMÍREZ N G,CARVAJAL D.Electrochemical treatment of bilge wastewater[J].Desalination and Water Treatment,2015,54(6):1556-1562.
CERUSSI A E,BERGER A J,BEVILACQUA F,et al.Sources of absorption and scattering contrast for near-infrared optical mammography[J].Academic Radiology,2001,8(3):211-218.
[42]
HAYES J M,FREEMAN K H,POPP B N,et al.Compound-specific isotopic analyses:a novel tool for reconstruction of ancient biogeochemical processes[J].Organic Geochemistry,1990,16(4/5/6):1115-1128.
[43]
AZANZA R V,TAYLOR F J R M.Are Pyrodinium blooms in the southeast Asian region recurring and spreading? A view at the end of the millennium[J].Ambio,2001,30(6):356-364.
BAILEY S W,FRANZ B A.WERDELL P J.Estimation of near-infrared water-leaving reflectance for satellite ocean color data processing[J].Optics Express,2010,18 (7):7521-7527.
[48]
KANEHISA M,GOTO S.KEGG:Kyoto encyclopedia of genes and genomes [J].Nucleic Acids Research,2000,28(1):27-30.
[49]
WINK D A,NIMS R W,SAAVEDRA J E,et al.The Fenton oxidation mechanism:reactivities of biologically relevant substrates with two oxidizing intermediates differ from those predicted for the hydroxyl radical[J].Proceedings of the National Academy of Sciences of the United States of America,1994,91(14):6604-6608.
GITELSON A,GARBUZOV G,SZILAGYI F,et al.Quantitative remote sensing methods for real-time monitoring of inland waters quality[J].International Journal of Remote Sensing,1993,14(7):1269-1295.
[56]
BJORØY M,HALL K,MOE R P.Stable carbon isotope variation ofn-alkanes in Central Graben oils[J].Organic Geochemistry,1994,22(3/4/5):355-381.
[57]
SIRINGAN F P,AZANZA R V,MACALALAD N J H,et al.Temporal changes in the cyst densities ofPyrodinium bahamense var.compressum and other dinoflagellates in Manila Bay,Philippines[J].Harmful Algae,2008,7(4):523-531.
GOYENS C,JAMET C,SCHROEDER T.Evaluation of four atmospheric correction algorithms for MODIS-Aqua images over contrasted coastal waters[J].Remote Sensing of Environment,2013,131:63-75.
[66]
MORIYA Y,ITOH M,OKUDA S,et al.KAAS:An automatic genome annotation and pathway reconstruction server [J].Nucleic Acids Research,2007,35(Suppl.2):W182-W185.
LI Y,XIONG Y Q,YANG W Y,et al.Compound-specific stable carbon isotopic composition of petroleum hydrocarbons as a tool for tracing the source of oil spills[J].Marine Pollution Bulletin,2009,58(1):114-117.
TODD E C D.Domoic acid and amnesic shellfish poisoning-a review[J].Journal of Food Protection,1993,56(1):69-83.
[71]
SON S,WANG M.Water properties in Chesapeake Bay from MODIS-Aqua measurements[J].Remote Sensing of Environment,2012,123:163-174.
[72]
LI B,DEWEY C N.RSEM:accurate transcript quantification from RNA-Seq data with or without a reference genome [J].BMC Bioinformatics,2011,12:323.
[73]
MOORE G F,AIK/EN J,LAVENDER S J.The atmospheric correction of water colour and the quantitative retrieval of suspended particulate matter in case Ⅱ waters:application to MERIS[J].International Journal of Remote Sensing,1999,20(9):1713-1733.
[74]
WANG Z D,FINGAS M,PAGE D S.Oil spill identification[J].Journal of Chromatography A,1999,843(1/2):369-411.
DICKEY R W,FRYXELL G A,GRANADE H R,et al.Detection of the marine toxins okadaic acid and domoic acid in shellfish and phytoplankton in the Gulf of Mexico[J].Toxicon,1992,30(3):355-359.
ANDERS S,HUBER W.Differential expression analysis for sequence count data [J].Genome Biology,2010,11:R106.
[80]
DEKKER A G,VOS R J,PETERS S W M.Analytical algorithms for lake water TSM estimation for retrospective analyses of TM and SPOT sensor data[J].International Journal of Remote Sensing,2002,23(1):15-35.
TRAINER V L,BATES S S,LUNDHOLM N,et al.Pseudo-nitzschia physiological ecology,phylogeny,toxicity,monitoring and impacts on ecosystem health[J].Harmful Algae,2012,14:271-300.
[84]
FLEMING-LEHTINEN V,LAAMANEN M.Long-term changes in Secchi depth and the role of phytoplankton in explaining light attenuation in the Baltic Sea[J].Estuarine,Coastal and Shelf Science,2012,102-103:1-10.
TRAPNELL C,WILLIAMS B A,PERTERA G,et al.Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation [J].Nature Biotechnology,2010,28:511-515.
[88]
BINDING C E,BOWERS D G,MITCHELSON-JACOB E G.An algorithm for the retrieval of suspended sediment concentrations in the Irish Sea from SeaWiFS ocean colour satellite imagery[J].International Journal of Remote Sensing,2003,24(19):3791-3806.
[89]
STEWART I.Environmental risk factors for temporal lobe epilepsy-Is prenatal exposure to the marine algal neurotoxin domoic acid a potentially preventable cause?[J].Medical Hypotheses,2010,74(3):466-481.
[90]
杨军霞.中国东南沿海四种拟菱形藻生长特性与毒素检测研究[D].厦门:厦门大学,2007.
[91]
YANG Z B,HODGKISS I J.Potentially harmful Pseudo-nitzschia species in Hong Kong[C]//HO K C,LAM H Y I,YU Y S.Prevention and toxicity management of harmful algal blooms in the South China Sea.Hong Kong:The Association on Harmful Algal Blooms in the South China Sea,2002:123-128.
[92]
KOPONEN S,PULLIAINEN J,KALLIO K.Lake water quality classification with airborne hyperspectral spectrometer and simulated MERIS data[J].Remote Sensing of Environment,2002,79 (1):51-59.
[93]
DILLIES M A,RAU A,AUBERT J,et al.A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis [J].Brief in Bioinformatics,2013,14(6):671-683.
[94]
TEODORO A C,VELOSO-GOMES F,GONCALVES H.Retrieving TSM concentration from multispectral satellite data by multiple regression and artificial neural networks[J].IEEE Transactions on Geoscience and Remote Sensing,2007,45(5):1342-1350.
LI A F,YU R C,WANG Y F,et al.Morphological and toxicity characteristics of Pseudo-nitzschia pungens strain PP0201-01 isolated from the East China Sea[J].Chinese Journal of Oceanology and Limnology,2005,23(4):418-426.
TASSAN S.Local algorithms using SeaWiFS data for the retrieval of phytoplankton,pigments,suspended sediment,and yellow substance in coastal waters[J].Applied optics,1994,33 (12):2369-2378.
[104]
RIEGMAN R,VAN BOEKEL W.The ecophysiology of Phaeocystis globosa:A review [J].Journal of Sea Research,1996,35(4):235-242.
[105]
AHN Y H,MOON J E,GALLEGOS S.Development of suspended particulate matter algorithms for ocean colour remote sensing[J].Korean Journal of Remote Sensing,2001,17(4):285-295.
LEWIS R J,JONES A,VERNOUX J P.HPLC/Tandem electrospray mass spectrometry for the determination of sub-ppb levels of pacific and Caribbean ciguatoxins in crude extracts of fish[J].Analytical Chemistry,1999,71(1):247-250.
DORON M,BABIN M,MANGIN A.Estimation of light penetration,and horizontal and vertical visibility in oceanic and coastal waters from surface reflectance[J].Journal of Geophysical Research,2007,112(C6):C06003.
[118]
JOSEPH L,VILLAREAL T A.Nitrate reductase activity as a measure of nitrogen incorporation in Rhizosolenia formosa (H.Peragallo):Internal nitrate and diel effects [J].Journal of Experimental Marine Biology and Ecology,1998,229(2):159-176.
LIU R Y,LIANG Y B,WU X L,et al.First report on the detection of pectenotoxin groups in Chinese shellfish by LC-MS/MS[J].Toxicon,2011,57(7/8):1000-1007.
TYLER J E.The Secchi disc[J].Limnology and Oceanography,1968,VⅢ (1):1-6.
[125]
DONG H P,HUANG K X,WANG H L,et al.Understanding strategy of nitrate and urea assimilation in a Chinese strain of Aureococcus anophagefferens through RNA-Seq analysis [J].PLoS One,2014,9(10):e111069.
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