Starr RC. The culture collection of algae at Indiana University. Amer J Bot. 1964;9:1013–44.
Article
Google Scholar
Ott FD. A review of the synonyms and the taxonomic positions of the red algal genus Porphyridium Naegeli 1849. Nova Hedwigia. 1972;23:237–89.
Google Scholar
Anderson DB, Eakin DE. A process for the production of polysaccharides from microalgae. Biotechnol Bioeng Symp. 1985;15:532–47.
Google Scholar
Surendra S, Arad S, Richmond A. Exotracellular polysaccharide production in outdoor mass cultures of Porphyridium sp. in flat glass reactors. J Appl Phycol. 2000;12:269–75.
Article
Google Scholar
Murphy JT, Lanagarias JC. The phytofluors: a new class of fluorescent protein probes. Curr Biol. 1997;11:870–6.
Article
Google Scholar
Khozin-Goldberg I, Cohen Z. Differential response of microalgae to the substituted pyridazinone, Sandoz 9785, reveal different pathways in the biosynthesis of eicosapentaenoic acid. Phytochemistry. 1996;4:1025–9.
Article
Google Scholar
Minkova K, Michailov Y, Toncheva-Panova T, Houbavenska N. Antiviral activity of Porphyridium cruentum polysaccharide. Pharmazie. 1996;51:194.
CAS
Google Scholar
Heheihel M, Ishanu V, Tal J, Arad SM. Activity of Porphyridium sp. polysaccharide against herpes simplex virus es in vitro and in vivo. J Biochem Biophys Methods. 2002;50:189–200.
Article
Google Scholar
Huleihel M, Ishanu V, Tal J, Arad S. Antiviral effect of red microalgal polysaccharides on Herpes simplex and Varicella zoster viruses. J Appl Phycol. 2001;13:127–34.
Article
CAS
Google Scholar
Liu S, Wei D, Wang Y. Antiviral activity of extracellular polysaccharide from Porphyridium sp. against respiratory syncytial virus (RSV). Nat Prod Res Dev. 2007;19:401–4.
Google Scholar
Jirovetz L, Buchbauer G, Stoyanova AS, Georgiev EV, Damianova ST. Composition quality control and antnicrobal activity of the essential oil of longtime dill seeds from Bulgaria. Chem Nat Compounds. 2003;51:3854–7.
CAS
Google Scholar
Yu J, Tang X, Li Y, Wang C, Liu W. The effect of UV-B radiation on the antioxidant system of marine microalgae. Mar Sci. 2002;12:53–6.
Google Scholar
Sun L. Preparation of polysaceharide from Porphyridium cruentum and its biologlcal activities. Dalian University of Technology, Doctoral dissertation. 2009
Dufosséa L, Galaupa P, Yaronb A, Aradb SM, Blancc P, Murthyd KC, Ravishankard GA. Microorganisms and microalgae as sources of pigments for food use: a scientific oddity or an industrial reality. Trends Food Sci Tech. 2005;389:389–406.
Article
Google Scholar
Dvir I, Chayoth R, Sod-Moriha U, Shany S, Nyska A, Stark AH, Madar Z, Arad SM. Soluble polysaccharide and biomass red mieroalga Porphyridium sp. alter intestinal morphology and reduce serum cholesterol in rats. Br J Nutr. 2000;84:469–76.
CAS
Google Scholar
Fuentes-Grünewald C, Bayliss C, Zanain M, Pooley C, Scolamacchia M, Silkina A. Evaluation of batch and semi-continuous culture of Porphyridium purpureum in a photo bioreactor in high latitudes using Fourier Transform Infrared spectroscopy for monitoring biomass composition and metabolites production. Bioresour Technol. 2015;189:357–63.
Article
Google Scholar
Morineau-Thomas O, Jaouen P, Legentilhomme P. The role of exopolysaccharides in fouling phenomenon during ultrafiltration of microalgae (Chlorella sp. and Porphyridium purpureum): advantage of a swirling decaying flow. Bioprocess Biosyst Eng. 2002;25:35–42.
Article
CAS
PubMed
Google Scholar
Gu N, Liu Y. Bioactive substances of Porphyridium and their applications. Chin J Marine Drugs. 2001;6:43–8.
Google Scholar
Scherer S, Lechner S, Böger P. psbD sequences of Bumilleriopsis filiformis (Heterokontophyta, Xanthophyceae) and Porphyridium purpureum (Rhodophyta, Bangiophycidae): evidence for polyphyletic origins of plastids. Curr Genet. 1993;23:437–42.
Article
Google Scholar
Tajima N, Sato S, Maruyama F, Kurokawa K, Ohta H, Tabata S, Sekine K, Moriyama T, Sato N. Analysis of the complete plastid genome of the unicellular red alga Porphyridium purpureum. J Plant Res. 2014;127:389–97.
Article
CAS
Google Scholar
Shen E, Liu Y, Ye C, Fang L. Recent studies on non-coding small RNAs in plants. J Zhejiang Univ. 2014;40:370–8.
CAS
Google Scholar
Ghildiyal M, Zamore PD. Small silencing RNAs: an expanding universe. Nat Rev Genet. 2009;10:94–108.
Article
CAS
PubMed Central
Google Scholar
Lee RC, Feinbaum RL, Ambros V. The C. elegans hetero chronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell. 1993;75:843–54.
Article
CAS
PubMed
Google Scholar
Wu L, Belasco JG. Let me count the way: mechanisms of gene regulation by miRNAs and siRNAs. Mol Cell. 2008;29:1–7.
Article
PubMed
Google Scholar
Long R, Li Y, Xu Q. Biogenesis, mechanism, function of microRNAs in animals and plants. Chin Bull Life Sci. 2007;19:127–30.
Google Scholar
Yoon S, De Micheli G. Computational identification of microRNAs and their targets. Birth Defects Res. 2006;78:118–28.
Article
CAS
Google Scholar
Zhang W, Luo Y, Gong X, Zeng W, Li S. Computational identification of 48 potato microRNAs and their targets. Comput Biol Chem. 2009;33:84–93.
Article
CAS
PubMed
Google Scholar
Jiao Y, Song W, Zhang M, Lai J. Identification of novel maize miRNAs by measuring the precision of precursor processing. BMC Plant Biol. 2011;11:141.
Article
CAS
PubMed
PubMed Central
Google Scholar
Guo Y, Liu H, Yang Z, Chen J, Sun Y, Ren X. Identification and characterization of miRNAome in tobacco (Nicotiana tabacum) by deep sequencing combined with microarry. Gene. 2012;501:24–32.
Article
CAS
PubMed
Google Scholar
Carnavale-Bottino M, Rosario S, Grativol C, Thiebaut F, Rojas CA, Farrineli L, Hemerly AS, Ferreira PC. High-throughput sequencing of small RNA transcriptome reveals salt stress regulated microRNAs in sugarcane. PLoS ONE. 2013;3:e59423.
Article
Google Scholar
Krishna S, Nair A, Cheedipudi S, Poduval D, Dhawan J, Palakodeti D, Ghanekar Y. Deep sequencing reveals unique small RNA repertoire that is regulated during head regeneration in Hydra magnipapillata. Nucl Acids Res. 2013;41:599–616.
Article
CAS
PubMed
Google Scholar
Su C, Yang X, Gao S, Tang Y, Zhao C, Li L. Identification and characterization of a subset of microRNAs in wheat (Triticum aestivum L.). Genomics. 2014;103:298–307.
Article
CAS
PubMed
Google Scholar
Jones-Rhoades MW, Bartel DP, Bartel B. MicroRNAs and their regulatory roles in plants. Ann Rev Plant Biol. 2006;57:19–53.
Article
CAS
Google Scholar
Moxon S, Jing R, Szittya G, Schwach F, Rusholme-Pilcher RL, Moulton V, Dalmay T. Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Res. 2008;18:1602–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang R, Marshall D, Bryan GJ, Hornyik C. Identification and characterization of miRNA transcriptome in potato by high-throughput sequencing. PLoS ONE. 2013;8:e57233.
Article
CAS
PubMed
PubMed Central
Google Scholar
Martinez G, Forment J, Llave C, Pallás V, Gómez G. High-throughput sequencing, characterization and detection of new and conserved cucumber miRNAs. PLoS ONE. 2011;6:e19523.
Article
CAS
PubMed
PubMed Central
Google Scholar
Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucl Acids Res. 2007;36:D154–8.
Article
PubMed
PubMed Central
Google Scholar
Bhattacharya D, Price DC, Chan C, Qiu H, Rose N, Ball S, Weber AP, Arias MC, Henrissat B, Coutinho PM, Krishnan A, Zäuner S, Morath S, Hilliou F, Egizi A, Perrineau MM, Yoon HS. Genome of the red alga Porphyridium purpureum. Nat Commun. 2013;4:1941.
Article
PubMed
PubMed Central
Google Scholar
Chellappan P, Jin H. Discovery of plant microRNAs and short-interfering RNAs by deep parallel sequencing. Methods Mol Biol. 2009;495:121–32.
Article
CAS
PubMed
Google Scholar
Vaucheret H. Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes Dev. 2006;20:759–71.
Article
CAS
PubMed
Google Scholar
Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu N, Mahuvakar VR, Andersen MR, Lao K, Livak KJ, Guegler KJ. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucl Acids Res. 2005;33:e179.
Article
PubMed
PubMed Central
Google Scholar
Ghildiyal M, Seitz H, Horwich MD, Li C, Du T, Lee S, Xu J, Kittler EL, Zapp ML, Weng Z, Zamore PD. Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science. 2008;5879:1077–81.
Article
Google Scholar
Sempere LF, Freemantle S, Pitha-Rowe I, Moss E, Dmitrovsky E, Ambros V. Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation. Genome Biol. 2004;5:R13.
Article
PubMed
PubMed Central
Google Scholar
Selbach M, Schwanhäusser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N. Widespread changes in protein synthesis induced by microRNAs. Nature. 2008;455:58–63.
Article
CAS
PubMed
Google Scholar
Starega-Roslan J, Galka-Marciniak P, Krzyzosiak WJ. Nucleotide sequence of miRNA precursor contributes to cleavage site selection by Dicer. Nucl Acids Res. 2015;43:10939–51.
Article
PubMed
PubMed Central
Google Scholar
Kidner CA, Martienssen RA. Macro effects of microRNAs in plants. Trends Genet. 2003;19:13–6.
Article
CAS
PubMed
Google Scholar
Hunter C, Poethig RS. miSSing LINKS: miRNAs and plant development. Curr Opin Genet Dev. 2003;13:372–8.
Article
CAS
PubMed
Google Scholar
Sunkar R, Zhu J. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell. 2004;16:2001–19.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucl Acids Res. 2000;28:27–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kanehisa M. KEGG bioinformatics resource for plant genomics and metabolomics. Methods Mol Biol. 2016;1374:55–70.
Article
PubMed
Google Scholar
Praneenararat T, Takagi T, Iwasaki W. Integration of interactive, multi-scale network navigation approach with Cytoscape for functional genomics in the big data era. BMC Genomics. 2012;13 Suppl 7:S24.
Article
PubMed
PubMed Central
Google Scholar
Naumann I, Darsow KH, Walter C, Lange HA, Buchholz R. Identification of sulfoglycolipids from the alga Porphyridium purpureum by matrix-assisted laser desorption/ionisation quadrupole ion trap time-of-flight mass spectrometry. Rapid Commun Mass Sp. 2007;21:3185–92.
Article
CAS
Google Scholar
Hong H, Liu Y, Zhang H, Xiao J, Li X, Wang S. Small RNAs and gene network in a durable disease resistance gene—mediated defense responses in rice. PLoS ONE. 2015;9:e0137360.
Article
Google Scholar
Liu F, Wang W, Sun X, Liang Z, Wang F. Conserved and novel heat stress-responsive microRNAs were identified by deep sequencing in Saccharina japonica (Laminariales, Phaeophyta). Plant Cell Environ. 2015;38:1357–67.
Article
CAS
PubMed
Google Scholar
Luo X, Shi T, Cai B, Gao Z. Identification and bioinformatics prediction of putative microRNAs in Prunus genus. Scientia Silvae Sinicae. 2012;48:75–81.
CAS
Google Scholar
Wei Q, Liang Y, Li G. Evolution of miRNA in plants. Hereditas. 2013;35:315–23.
Article
CAS
PubMed
Google Scholar
Mallory AC, Elmayan T, Vaucheret H. MicroRNA maturation and action-the expanding roles of ARGONAUTEs. Curr Opin Plant Biol. 2008;11:560–6.
Article
CAS
PubMed
Google Scholar
Murchison EP, Hannon GJ. miRNAs on the move: miRNA biogenesis and the RNAi machinery. Curr Opin Plant Biol. 2004;16:223–9.
Article
CAS
Google Scholar
Young MD, Wakefield MJ, Smyth GK, Oshlack A. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol. 2010;11:R14.
Article
PubMed
PubMed Central
Google Scholar
Benavides J, Rito-Palomares M. Simplified two-stage method to β-phycoerythrin recovery from Porphyridium cruentum. J Chromatgr B: Analyt Technol Biomed Life Sci. 2006;844:39–44.
Article
CAS
Google Scholar
Robles A, Esteban L, Giménez-Giménez A, Camacho-Páez B, José-Ibáñez M, Molina-Grima E. Lipase-catalyzed esterification of glycerol and polyunsaturated fatty acids from fish and microalgae oils. J Biotechnol. 1999;123:379–91.
Article
Google Scholar
Zhang J, Xu Y, Huan Q, Chong K. Deep sequencing of Brachypodium small RNA at the global genome level identifies microRNAs involved in cold stress response. BMC Genomics. 2009;10:449.
Article
PubMed
PubMed Central
Google Scholar
Chan C, Yang E, Banerjee T, Yoon HS, Martone PT, Estevez JM, Bhattacharya D. Red and green algal monophyly and extensive gene sharing found in a rich repertoire of red algal genes. Curr Biol. 2011;21:328–33.
Article
CAS
PubMed
Google Scholar
Greuber EK, Pendergast AM. Abl family kinases regulate FcγR-mediated phagocytosis in murine macrophages. J Immunol. 2012;189:5382–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bournazos S, Ravetch JV. Fcγ receptor pathways during active and passive immunization. Immunol Rev. 2015;1:88–103.
Article
Google Scholar
Deger JM, Gerson JE, Kayed R. The interrelationship of proteasome impairment and oligomeric intermediates in neurodegeneration. Aging Cell. 2015;14:715–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kim M, Ahn JW, Jin UH, Choi D, Paek KH, Pai HS. Activation of the programmed cell death pathway by inhibition of proteasome function in plants. J Biol Chem. 2003;23(21):19406–15.
Article
Google Scholar
Li Z. Culture, polysaccharide extraction and RAPD analysis of three species Porphyridium. Shanghai Normal University. Master dissertation. 2004
Sun L. Research on culture condition and enhancing bioactive content of Porphyridium cruentum. Ocean University of China. Master dissertation. 2004
Jones RF, Speer HL, Kury W. Studies on the growth of the red alga Porphyridium cruentum. Physiol Plant. 1963;16:636–43.
Article
CAS
Google Scholar
Chen B, Huang J, Liang S, Wang M, Li M, Zhuang H. Culture of Porphyridium cruentum in photobioreactor and its effect on hypolipidemiac. Chin J Appl Environt Biol. 2004;10:432–6.
CAS
Google Scholar
Hafner M, Landgraf P, Ludwig J, Rice A, Ojo T, Lin C, Holoch D, Lim C, Tuschl T. Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. Methods. 2008;44:3–12.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wei R, Qiu D, Wilson IW, Zhao H, Lu S, Miao J, Feng S, Bai L, Wu Q, Tu D, Ma X, Tang Q. Identification of novel and conserved microRNAs in Panax notoginseng roots by high-throughput sequencing. BMC Genomics. 2015;16:835.
Article
PubMed
PubMed Central
Google Scholar
Huang A, He L, Wang G. Identification and characterization of microRNAs from Phaeodactylum tricornutum by high throughput sequencing and bioinformatics analysis. BMC Genomics. 2011;12:337.
Article
CAS
PubMed
PubMed Central
Google Scholar
Khraiwesh B, Pugalenthi G, Fedoroff NV. Identification and analysis of red sea mangrove (Avicennia marina) microRNAs by high-throughput sequencing and their association with stress responses. PLoS ONE. 2013;8:e60774.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li R, Li Y, Kristiansen K, Wang J. SOAP: Short oligo nucleotide alignment program. Bioinformatics. 2008;24:713–4.
Article
CAS
PubMed
Google Scholar
Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A. Rfam: annotating non-coding RNAs in complete genomes. Nucl Acids Res. 2005;33:D121–4.
Article
CAS
Google Scholar
Zhang Z, Song R, Peng H, Luo M, Shen Y, Liu L, Zhao M, Pan G. Bioinformatic prediction of microRNAs and their target genes in maize. Acta Agron Sin. 2010;36:1324–35.
Article
CAS
Google Scholar
Li Y, Zhang Z, Liu F, Vongsangnak W, Jing Q, Shen B. Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis. Nucl Acids Res. 2012;40:4298–305.
Article
CAS
PubMed Central
Google Scholar
Warris S, Boymans S, Muiser I, Noback M, Krijnen W, Nap JP. Fast selection of miRNA candidates based on large-scale pre-computed MFE sets of randomized sequences. BMC Res Notes. 2014;7:34.
Article
PubMed Central
Google Scholar
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. Clustal W and Clustal X version 2.0. Bioinformatics. 2007;23:2947–8.
Article
CAS
Google Scholar
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011;28:2731–9.
Article
CAS
PubMed Central
Google Scholar
Cuperus JT, Fahlgren N, Carrington JC. Evolution and functional diversification of MIRNA genes. Plant Cell. 2011;23:431–42.
Article
CAS
PubMed Central
Google Scholar
Várallyay É, Burgyán J, Havelda Z. MicroRNA detection by northern blotting using locked nucleic acid probes. Nat Protocols. 2008;3:190–6.
Article
Google Scholar
Jin W, Li N, Wu F, Kong D, Guo A. Prediction and Validation of microRNAs from rice genome using mature-SVM. Chin J Biochem Mol Biol. 2007;23:743–50.
CAS
Google Scholar
Varkonyi-Gasic E, Wu R, Wood M, Walton EF, Hellens RP. Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs. Plant Methods. 2007;3:12.
Article
PubMed Central
Google Scholar
Wu H, Ma Y, Chen T, Wang M, Wang X. PsRobot: a web-based plant small RNA meta-analysis toolbox. Nucl Acids Res. 2012;40:W22–8.
Article
CAS
PubMed Central
Google Scholar
Kiełbasa SM, Blüthgen N, Fähling M, Mrowka R. Targetfinder.org: a resource for systematic discovery of transcription factor target genes. Nucl Acids Res. 2010;38:W233–8.
Article
PubMed Central
Google Scholar
Xie F, Huang S, Guo K, Xiang A, Zhu Y, Nie L, Yang Z. Computational identification of novel microRNAs and targets in Brassica napus. FEBS Lett. 2007;581:1464–74.
Article
CAS
Google Scholar
Dai X, Zhao P. psRNATarget: a plant small RNA target analysis server. Nucl Acids Res. 2001;39:W155–9.
Article
Google Scholar
Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Conesa A. High-throughput functional annotation and data mining with the Blast2GO suite. Nucl Acids Res. 2008;36:3420–35.
Article
PubMed Central
Google Scholar
Zheng Q, Wang X. GOEAST: a web-based software toolkit for gene ontology enrichment analysis. Nucl Acid Res. 2008;36:W358–63.
Article
CAS
Google Scholar
Carlini DB, Makowski M. Codon bias and gene ontology in holometabolous and hemimetabolous insects. J Exp Zool B Mol Dev Evol. 2005;324:686–98.
Article
Google Scholar
Srivastava PK, Moturu TR, Pandey P, Baldwin IT, Pandey SP. A comparison of performance of plant miRNA target prediction tools and the characterization of features for genome-wide target prediction. BMC Genomics. 2014;15:348.
Article
PubMed Central
Google Scholar
Xie C, Mao X, Huang J, Ding Y, Wu J, Dong S. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucl Acids Res. 2011;39:W316–22.
Article
CAS
PubMed Central
Google Scholar
Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M. KEGG as a reference resource for gene and protein annotation. Nucl Acids Res. 2016;44:D457–62.
Article
Google Scholar
Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucl Acids Res. 2012;40:D109–14.
Article
CAS
Google Scholar
Storey JD, Tibshirani R. Statistical significance for genome wide studies. Proc Nat Acad Sci USA. 2003;100:9440–5.
Article
CAS
PubMed Central
Google Scholar
Wang J, Zhong J, Chen G, Li M, Wu F, Pan Y. ClusterViz: a cytoscape APP for cluster analysis of biological network. IEEE/ACM Trans Comput Biol Bioinform. 2015;12:815–22.
Article
Google Scholar