Abstract
With high-throughput Solexa sequencing technology, we profiled Porphyra yezoensis transcriptomes from 8 different samples. More than 1200 megabases from 13333334 quality paired-end reads were generated, which were assembled into 31538 unigenes. Blast analysis showed that 56.7% unigenes were novel, which represented the specific genes of Porphyra and/or rhodophytes. Several hundreds of unigenes related to stress tolerance were discovered, including genes related to desiccation-(211) and high light-tolerance (31), flavonoid biosynthesis (10), reactive oxygen scavenging (48) and other stress-tolerance processes (208), which indicated there existed complex and diversity modes of stress tolerance in this species. A complete set of essential genes involved in the C3-(57) and C4-(44) carbon fixation pathway (except pyruvate phosphate dikinase) were discovered, which not only proved that they were actively transcribed but also clearly outlined the panoptic view of carbon fixation in Porphyra. Moreover, by statistically analyzing the types, proportions and frequencies of the interspersed repeats (TEs) and simple sequence repeats (SSRs), we discovered that the top three types of TEs were all retrotransposons and the trinucleotide was the absolute predominant type among SSRs, promoting our understanding of structural characteristics of the transcriptome. This study substantially improved the global view of the Porphyra genome and provided a valuable resource for future research.
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References
Mumford T F, Miura A. Porphyra as food: Cultivation and economics. In: Lemby C A, Walland J R, eds. Algae and Human Affairs. Cambridge: Cambridge University Press, 1988. 87–117
Kuwano K, Aruga Y, Saga N. Cryopreservation and clonal gametophytic thalli of Porphyra (Rhodophyta). Plant Sci, 1996, 116: 117–124
Sahoo D, Tang X R, Yarish C. Porphyra-the economic seaweed as a new experimental system. Curr Sci India, 2002, 83: 1313–1316
Le Gall Y, Brown S, Marie D, et al. Quantification of nuclear DNA and GC content in marine macroalgae by flow cytometry of isolated nuclei. Protoplasma, 1993, 173: 123–132
Davison I R, Pearson G A. Stress tolerance in intertidal seaweeds. J Phycol, 1996, 32: 197–211
Guo S, Zheng Y, Joung J G, et al. Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. BMC Genomics, 2010, 11: 384
Nikaido I, Asamizu E, Nakajima M, 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
Asamizu E, Nakajima M, Kitade 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
Xu M J, Mao Y X, Zhang X C, et al. Bioinformatic analysis of expressed sequence tags from sporophyte of Porphyra yezoensis (Bagiaceae, Rhodophyta). Prog Nat Sci, 2006, 16: 39–49
Morozova O, Hirst M, Marra M A. Applications of new sequencing technologies for transcriptome analysis. Annu Rev Genom Hum G, 2009, 10: 135–151
Mu Y, Ding F, Cui P, et al. Transcriptome and expression profiling analysis revealed changes of multiple signaling pathways involved in the large yellow croaker during Aeromonas hydrophila infection. BMC Genomics, 2010, 11: 506
Hegedűs Z, Zakrzewska A, Agoston V C, et al. Deep sequencing of the zebrafish transcriptome response to mycobacterium infection. Mol Immunol, 2009, 46: 2918–2930
Wang B, Guo G, Wang C, et al. Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing. Nucleic Acids Res, 2010, 15: 5075–5087
Zhang G, Guo G, Hu X, et al. Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res, 2010, 20: 646–654
Rosenkranz R, Borodina T, Lehrach H, et al. Characterizing the mouse ES cell transcriptome with Illumina sequencing. Genomics, 2008, 92: 187–194
Montgomery S B, Sammeth M, Gutierrez-Arcelus M, et al. Transcriptome genetics using second generation sequencing in a Caucasian population. Nature, 2010, 464: 773–777
Morozova O, Marra M A. Applications of next-generation sequencing technologies in functional genomics. Genomics, 2008, 92: 255–264
Li R, Zhu H, Ruan J, et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res, 2010, 20: 265–272
Conesa A, Götz S, García-Gómez J M, et al. Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 2005, 21: 3674–3676
Ye J, Fang L, Zheng H, et al. WEGO: A web tool for plotting GO annotations. Nucleic Acids Res, 2006, 34: W293–297
Iseli C, Jongeneel C V, Bucher P. ESTScan: A program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol, 1999, 7: 138–148
Altschul S F, Madden T L, Schäffer A A, et al. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res, 1997, 25: 3389–3402
Thiel T, Michalek W, Varshney R K, et al. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet, 2003, 106: 411–422
Cardle L, Ramsay L, Milbourne D, et al. Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics, 2000, 156: 847–854
Wang C B, Guo W Z, Cai C P, et al. Characterization, development and exploitation of EST-derived microsatellites in Gossypium raimondii Ulbrich. Chinese Sci Bull, 2006, 51: 557–561
Teich R, Zauner S, Baurain D, et al. Origin and distribution of Calvin cycle fructose and sedoheptulose bisphosphatases in plantae and complex algae: A single secondary origin of complex red plastids and subsequent propagation via tertiary endosymbioses. Protist, 2006, 158: 263–276
Kitade Y, Asamizu E, Fukuda S, et al. Identification of genes preferentially expressed during asexual sporulation in Porphyra yezoensis gametophytes (Bangiales, Rhodophyta). J Phycol, 2008, 44: 113–123
Derelle E, Ferraz C, Rombauts S, et al. Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proc Natl Acad Sci USA, 2006, 103: 11647–11652
Fan X L, Fang Y J, Hu S N, et al. Generation and analysis of 5,318 expressed sequence tags from the filamentous sporophyte of Porphyra haitanensis (Phodophyta). J Phycol, 2007, 43: 1287–1294
Blouin N A, Brodie J A, Grossman A C, et al. Porphyra: A marine crop shaped by stress. Trends Plant Sci, 2011, 16: 29–37
Gao K S, Ji Y, Aruga Y, et al. Relationship of CO2 concentrations to photosynthesis of intertidal macroalgae during emersion. Hydrobiologia, 1999, 398/399: 355–359
Herbert S K. Photoinhibition resistance in the red alga Porphyra perforata: The role of photoinhibition repair. Plant Physiol, 1990, 92: 514–519
Collén J, Davison I R. Stress tolerance and reactive oxygen metabolism in the intertidal red seaweeds Mastocarpus stellatus and Chondrus crispus. Plant Cell Environ, 1999, 22: 1143–1151
Wolfe-Simon F, Grzebyk D, Schofield O, et al. The role and evolution of superoxide dismutases in algae. J Phycol, 2005, 41: 453–465
Korbee N, Huovinen P, Figueroa F L, et al. Availability of ammonium influences photosynthesis and the accumulation of mycosporine-like amino acids in two Porphyra species (Bangiales, Rhodophyta). Mar Biol, 2005, 146: 645–654
Singh S P, Klisch M, Sinha R P, et al. Genome mining of mycosporine-like amino acid (MAA) synthesizing and non-synthesizing cyanobacteria: A bioinformatics study. Genomics, 2010, 95: 120–128
Rozema J, Björn L O, Bornman J F, et al. The role of UV-B radiation in aquatic and terrestrial ecosystems-an experimental and functional analysis of the evolution of UV-absorbing compounds. J Photochem Photobiol B, 2002, 66: 2–12
Cock J M, Sterck L, Rouze P, et al. The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature, 2010, 465: 617–621
Dittami S M, Michel G, Collén J, et al. Chlorophyll-binding proteins revisited—amultigenic family of light-harvesting and stress proteins from a brown algal perspective. BMC Evol Biol, 2010, 10: 365
Llorca O, Martín-Benito J, Ritco-Vonsovici M, et al. Eukaryotic chaperonin CCT stabilizes actin and tubulin folding intermediates in open quasi-native conformations. EMBO J, 2000, 19: 5971–5979
Oliver M J, Dowd S E, Zaragoza J, et al. The rehydration transcriptome of the desiccation-tolerant bryophyte Tortula ruralis: Transcript classification and analysis. BMC Genomics, 2004, 5: 89
Bartels D. Desiccation tolerance studied in the resurrection plant Craterostigma plantagineum. Integr Comp Biol, 2005, 45: 696–701
Bennetzen J L. Transposable element contributions to plant gene and genome evolution. Plant Mol Biol, 2000, 42: 251–269
Nigumann P, Redik K, Mätlik K, et al. Many human genes are transcribed from the antisense promoter of L1 retrotransposon. Genomics, 2002, 79: 628–634
Miyao A, Tanaka K, Murata K, et al. Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon rich regions of the genome. Plant Cell, 2003, 15: 1771–1780
Le Q, Melayah D, Bonnivard E, et al. Distribution dynamics of the Tnt1 retrotransposon in tobacco. Mol Genet Genomics, 2007, 278: 639–651
Sin H S, Huh J W, Kim D S, et al. Transcriptional control of the HERV-HLTR element of the GSDML gene in human tissues and cancer cells. Arch Virol, 2006, 151: 1985–1994
Faulkner G J, Kimura Y, Daub C O, et al. The regulated retrotransposon transcriptome of mammalian cells. Nat Genet, 2009, 41: 563–571
Gupta P K, Rustgi S. Molecular markers from the transcribed/expressed region of the genome in higher plants. Funct Integr Genomic, 2004, 4: 139–162
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Yang, H., Mao, Y., Kong, F. et al. Profiling of the transcriptome of Porphyra yezoensis with Solexa sequencing technology. Chin. Sci. Bull. 56, 2119–2130 (2011). https://doi.org/10.1007/s11434-011-4546-4
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DOI: https://doi.org/10.1007/s11434-011-4546-4