Blouin NA, Brodie JA, Grossma AC, Xu P, Brawley SH: Porphyra: a marine crop shaped by stress. Trends Plant Sci. 2010, 16: 29-37.
Article
PubMed
Google Scholar
Sutherland J, Lindstrom S, Nelson W, Brodie J, Lynch M, Hwang M, Choi H, Miyata M, Kikuchi N, Oliveira MC, Farr T, Neefus C, Mols-Mortensen A, Milstein J, Miller K: A new look at an ancient order: generic revision of the Bangiales. J Phycol. 2011, 47: 1131-1151. 10.1111/j.1529-8817.2011.01052.x.
Article
Google Scholar
Sahoo D, Tang XR, Yarish C: Porphyra-the economic seaweed as a new experimental system. Curr Sci. 2002, 83: 1313-16.
Google Scholar
Zhang XC, Qin S, Ma JH, Xu P: The genetics of marine algae. 2005, Beijing: China agriculture press
Google Scholar
Xie CT, Chen CS, Xu Y, Ji DH: Construction of a genetic linkage map for Porphyra haitanensis (Bangiales, Rhodophyta) Based on sequence-related amplified polymorphism and simple sequence repeat markers. J Phycol. 2010, 46: 780-787. 10.1111/j.1529-8817.2010.00855.x.
Article
CAS
Google Scholar
Waaland JR, Stiller JW, Cheney DP: Macroalgal candidates for genomics. J Phycol. 2004, 40: 26-33. 10.1111/j.0022-3646.2003.03-148.x.
Article
Google Scholar
Nikaido I, Asamizu E, Nakajima M, Nakamura Y, Saga N, et al: Generation of 10,154 expressed sequence tags from a leafy gametophyte of a marine red alga,Porphyra yezoensis. DNA Res. 2000, 7: 223-227. 10.1093/dnares/7.3.223.
Article
PubMed
Google Scholar
Asamizu E, Nakajima M, Kitade Y, Saga N, Nakamura Y, et al: Comparison of RNA expression profiles between the two generations of Porphyra yezoensis (Rhodophyta), based on expressed sequence tag frequency analysis. J Phycol. 2003, 39: 923-930. 10.1046/j.1529-8817.2003.03003.x.
Article
Google Scholar
Kakinuma M, Coury DA, Nakamoto C, Sakaguchi K, Amano H: Molecular analysis of physiological responses to changes in nitrogen in a marine macroalga, Porphyra yezoensis (Rhodophyta). Cell Biol Toxicol. 2008, 24: 629-639. 10.1007/s10565-007-9053-7.
Article
CAS
PubMed
Google Scholar
Liang CW, Zhang XW, Zou J, Xu D, Su F, Ye NH: Identification of miRNA from Porphyra yezoensis by high-throughput sequencing and bioinformatics analysis. PLoS One. 2010, 5: e10698-10.1371/journal.pone.0010698.
Article
PubMed Central
PubMed
Google Scholar
Yang H, Mao YX, Kong FN, Yang GP, Ma F, Wang L: Profiling of the transcriptome of Porphyra yezoensis with Solexa sequencing technology. Chin Sci Bull. 2011, 56: 2119-2130. 10.1007/s11434-011-4546-4.
Article
CAS
Google Scholar
Shen SD, Zhang GC, Li YY, Wang L, Xu P, Yi LF: Comparison of RNA expression profiles on generations of Porphyra yezoensis (Rhodophyta), based on suppression subtractive hybridization (SSH). BMC Res Notes. 2011, 4: 428-10.1186/1756-0500-4-428.
Article
PubMed Central
CAS
PubMed
Google Scholar
Fan XL, Fang YJ, Hu SN, Wang GC: Generation and analysis of 5318 expressed sequence tags from the filamentous sporophyte of Porphyra haitanensis (Rhodophyta). J Phycol. 2007, 43: 1287-1294. 10.1111/j.1529-8817.2007.00415.x.
Article
CAS
Google Scholar
Mao YX, Zhang BL, Kong FN, Wang L: The complete mitochondrial genome of Pyropia haitanensis Chang et Zheng. Mitochondrial DNA. 2012, 23: 344-346. 10.3109/19401736.2012.690751.
Article
CAS
PubMed
Google Scholar
Wang Z, Gerstein M, Snyder M: RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009, 10: 57-63. 10.1038/nrg2484.
Article
PubMed Central
CAS
PubMed
Google Scholar
Muers M: Gene expression: Transcriptome to proteome and back to genome. Nat Rev Genet. 2011, 12: 518-
Article
CAS
PubMed
Google Scholar
Flintoft L: Transcriptomics: Measuring gene expression in non-model organisms. Nat Rev Genet. 2011, 12: 742-742.
Google Scholar
Michael LM: Sequencing technologies-the next generation. Nat Rev Genet. 2010, 11: 31-46. 10.1038/nrg2626.
Article
Google Scholar
Wang X: A Review on the processing and analysis of next-generation RNA-seq Data. Prog Biochem Biophys. 2010, 5: 834-846.
Article
Google Scholar
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, et al: Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011, 29: 644-652. 10.1038/nbt.1883.
Article
PubMed Central
CAS
PubMed
Google Scholar
Martin JA, Wang Z: Next-generation transcriptome assembly. Nat Rev Genet. 2011, 12: 671-82. 10.1038/nrg3068.
Article
CAS
PubMed
Google Scholar
Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M: Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005, 21: 3674-3676. 10.1093/bioinformatics/bti610.
Article
CAS
PubMed
Google Scholar
Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L: WEGO: a web tool for plotting GO annotations. Nucleic Acids Res. 2006, 34: W293-297. 10.1093/nar/gkl031.
Article
PubMed Central
CAS
PubMed
Google Scholar
Luo QJ, Pei LQ, Pan SY: Utilization of inorganic carbon in free-living conchocelis of Porphyra haitanensis. J Fish. 2002, 26: 477-480. in Chinese with English abstract
CAS
Google Scholar
Zhang BY, Yang F, Wang GC, Peng G: Cloning and quantitative analysis of the carbonic anhydrase gene from Porphyra yezoensis. J Phycol. 2010, 46: 290-296. 10.1111/j.1529-8817.2009.00801.x.
Article
CAS
Google Scholar
Matsuoka M, Furbank RT, Fukayama H, Miyao M: Molecular engineering of C4 photosynthesis. Annu Rev Plant Physiol Plant Mol Biol. 2001, 52: 297-314. 10.1146/annurev.arplant.52.1.297.
Article
CAS
PubMed
Google Scholar
Samuel M, Jürg B: RNA-seq: from technology to biology. Cell Mol Life Sci. 2009, 67: 569-579.
Google Scholar
Maher CA, Palanisamy N, Brenner JC, Cao X, Kalyana-Sundaram S, Luo S, Khrebtukova I, Barrette TR, Grasso C, Yu JD, Lonigro RJ, Schroth G, Kumar-Sinha C, Chinnaiyan AM: Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Natl Acad Sci USA. 2009, 106: 12353-12358. 10.1073/pnas.0904720106.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wu T, Qin Z, Zhou X, Feng Z, Du Y: Transcriptome profile analysis of floral sex determination in cucumber. J Plant Physiol. 2010, 167: 905-913. 10.1016/j.jplph.2010.02.004.
Article
CAS
PubMed
Google Scholar
Wang XW, Luan JB, Li JM, Bao YY, Zhang CX, Liu SS: De novo characterization of a whitefly transcriptome and analysis of its gene expression during development. BMC Genomics. 2010, 11 (1): 400-10.1186/1471-2164-11-400.
Article
PubMed Central
PubMed
Google Scholar
Shen GM, Dou W, Niu JZ, Jiang HB, Yang WJ, Jia FX, Hu F, Cong L, Wang JJ: Transcriptome Analysis of the Oriental Fruit Fly (Bactrocera dorsalis). PLoS One. 2011, 6: e29127-10.1371/journal.pone.0029127.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wang ZY, Fang BP, Chen JY, Zhang XJ, Luo ZX, Huang LF, Chen XL, Li YJ: De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas). BMC Genomics. 2010, 11: 726-10.1186/1471-2164-11-726.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zhang JN, Liang S, Duan JL, Wang J, Chen SL, Cheng ZS, Zhang Q, Liang XQ, Li YR: De novo assembly and Characterisation of the Transcriptome during seed development, and generation of genic-SSR markers in Peanut (Arachis hypogaea L.). BMC Genomics. 2012, 13: 90-10.1186/1471-2164-13-90.
Article
PubMed Central
CAS
PubMed
Google Scholar
Li DJ, Deng Z, Qin B, Liu XH, Men ZH: De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.). BMC Genomics. 2012, 13: 192-10.1186/1471-2164-13-192.
Article
PubMed Central
CAS
PubMed
Google Scholar
Li CY, Deng GM, Yang J, Viljoen A, Jin Y, Kuang RB, Zuo CW, Lv ZC, Yang QS, Sheng O, Wei YR, Hu CH, Dong T, Yi GJ: Transcriptome profiling of resistant and susceptible Cavendish banana roots following inoculation with Fusarium oxysporum f. sp. cubense tropical race 4. BMC Genomics. 2012, 13: 374-10.1186/1471-2164-13-374.
Article
PubMed Central
CAS
PubMed
Google Scholar
Victoria FC, Maia LC, Oliveira AC: In silico comparative analysis of SSR markers in plants. BMC Plant Biol. 2011, 11: 15-10.1186/1471-2229-11-15.
Article
PubMed Central
PubMed
Google Scholar
Von Stackelberg MV, Rensing SA, Reski R: Identification of genic moss SSR markers and a comparative analysis of twnty-four algal and plant gene indices reveal species-specific rather than group-specific characteristics of microsatellites. BMC Plant Biol. 2006, 6: 9-10.1186/1471-2229-6-9.
Article
PubMed Central
PubMed
Google Scholar
Taiz L, Zeiger E: Plant Physiology. Photosynthesis: The carbon reactions. 2010, Sunderland: Sinauer Assoc, Inc, 5
Google Scholar
Hibberd JM, Covshoff S: The Regulation of Gene Expression Required for C4 Photosynthesis. Annu Rev Plant Biol. 2010, 61: 181-207. 10.1146/annurev-arplant-042809-112238.
Article
CAS
PubMed
Google Scholar
Langdale JA: C4 Cycles: Past, Present, and Future Research on C4 Photosynthesis. Plant Cell. 2011, 23: 3879-3892. 10.1105/tpc.111.092098.
Article
PubMed Central
CAS
PubMed
Google Scholar
Reinfelder JR, Kraepiel AML, Morel FMM: Unicellular C4 photosynthesis in a marine diatom. Nature. 2000, 407: 996-999. 10.1038/35039612.
Article
CAS
PubMed
Google Scholar
Reinfelder JR, Milligan AJ, Morel FMM: The role of the C4 pathway in carbon accumulation and fixation in a marine diatom. Plant Physiol. 2004, 135: 2106-2111. 10.1104/pp.104.041319.
Article
PubMed Central
CAS
PubMed
Google Scholar
Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, Zhou S, Allen AE, et al: The genome of the diatom Thalassiosira pseudonana: Ecology, evolution, and metabolism. Science. 2004, 306: 79-86. 10.1126/science.1101156.
Article
CAS
PubMed
Google Scholar
Roberts K, Granum E, Leegood RC, Raven JA: C3 and C4 pathways of photosynthetic carbon assimilation in marine diatoms are under genetic, not environmental, control. Plant Physiol. 2007, 145: 230-235. 10.1104/pp.107.102616.
Article
PubMed Central
CAS
PubMed
Google Scholar
Holdsworth ES, Bruck K: Enzymes concerned with betacarboxylation in marine phytoplankter: purification and properties of phosphoenolpyruvate carboxykinase. Arch Biochem Biophys. 1977, 182: 87-94. 10.1016/0003-9861(77)90286-7.
Article
CAS
PubMed
Google Scholar
Kerby NW, Evans LV: Phosphoenolpyruvate carboxykinase activity in Ascophyllum nodosum (Phaeophyceae). J Phycol. 1983, 19: 1-3. 10.1111/j.0022-3646.1983.00001.x.
Article
CAS
Google Scholar
Kerby NW, Raven JA: Transport and fixation of inorganic carbon by marine algae. Advance Botany Research. 1985, 11: 71-123.
Article
CAS
Google Scholar
Lucas WJ, Berry JA: Inorganic carbon transport in aquatic photosynthetic organisms. Physiol Plant. 1985, 65: 539-543. 10.1111/j.1399-3054.1985.tb08687.x.
Article
CAS
Google Scholar
Pônsgen-Schmidt E, Schneider T, Hammer U, Betz A: Comparison of phosphoenolpyruvate-carboxykinase from autotrophically and heterotrophically grown Euglena and its role during dark anaerobiosis. Plant Physiol. 1988, 86: 457-462. 10.1104/pp.86.2.457.
Article
PubMed Central
PubMed
Google Scholar
Reiskind JB, Bowes G: The role of phosphoenolpyruvate carboxykinase in a marine macroalga with C4-like photosynthetic characteristics. Proc Natl Acad Sci USA. 1991, 88: 2883-2887. 10.1073/pnas.88.7.2883.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ellis JR, Burke JM: EST-SSRs as a resource for population genetic analyses. Heredity. 2007, 99: 125-132. 10.1038/sj.hdy.6801001.
Article
CAS
PubMed
Google Scholar
Zuo ZH, Wang CG, Cao XH, Su Y, Liao LJ, Chen YX: Isolation and characterization of microsatellite loci from a commercial cultivar ofPorphyra haitanensis. Mol Ecol Notes. 2006, 7: 522-524. 10.1111/j.1471-8286.2006.01642.x.
Article
Google Scholar
Liu BQ, Zeng QG, Luo QJ, Wang YJ, Li SH: Isolation of microsafellite loci from dbEST of algae Porphyra yezoensis and primer amplification of interspecies transfer. Oceanologia et limnologia sinica. 2005, 36: 248-254.
CAS
Google Scholar
Sun JW, Liu T, Guo BT, Jin DM, Weng ML, Feng YB, Xu P, Duan DL, Wang B: Development of SSR primers from EST sequences and their application in germplasm identification of Porphyra lines (Rhodophyta). Eur. J. Phycol. 2006, 41: 329-336. 10.1080/09670260600740906.
Article
CAS
Google Scholar
Wang MQ, Hu JJ, Zhuang YY, Zhang L, Liu W, Mao YX: In Silico screening for microsatellite markers from expressed sequence tags of Porphyra yezoensis (Bangiales, Rhodophyta). Journal of Ocean University of China (Oceanic and Coastal Sea Research). 2007, 6: 161-166. 10.1007/s11802-007-0161-z.
Article
Google Scholar
Xie CT, Chen CS, Ji DH, Xu Y: Characterization, development and exploitation of EST-derived microsatellites in Porphyra haitanensis Chang et Zheng (Bangiales, Rhodophyta). J Appl Phycol. 2009, 21: 367-374. 10.1007/s10811-008-9379-4.
Article
CAS
Google Scholar
Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch SR: Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 2001, 11: 1441-1452. 10.1101/gr.184001.
Article
PubMed Central
CAS
PubMed
Google Scholar
Rajeev KV, Andreas G, Mark ES: Genic microsatellite markers in plants: features and applications. Trends Biotechnol. 2005, 23: 48-55. 10.1016/j.tibtech.2004.11.005.
Article
Google Scholar
Cardle L, Ratnsay L, Milbourne D, Macaulay M, Marshall D, Waugh R: Computational and ex-perimental characterization of physically clustered simple sequence repeats in plants. Genetics. 2000, 156: 847-854.
PubMed Central
CAS
PubMed
Google Scholar
Varshney RK, Graner A, Sorrells ME: Genic microsatellite markers in plants: features and applications. Trends Biotechnol. 2005, 23 (1): 48-55. 10.1016/j.tibtech.2004.11.005.
Article
CAS
PubMed
Google Scholar
Iseli C, Jongeneel CV, Bucher P: ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol. 1999, 138-148.
Google Scholar
Kanehisa M, Goto S: KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000, 28: 27-30. 10.1093/nar/28.1.27.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wu XJ, Niu JF, Huang AY, Xu ML, Wang GC: Selection of internal control gene for expression studies in Porphyra haitanensis (Rhodophyta) at different life-history stages. J Phycol. 2012, 48: 1040-1044. 10.1111/j.1529-8817.2012.01188.x.
Article
CAS
Google Scholar