Comparison of transcriptome under red and blue light culture of Saccharina japonica (Phaeophyceae)

Planta

Volumn 237, Issue 4, 2013, Pages 1123-1133

  Wang, Wen Jun ^a   Wang, Fei Jiu ^a   Sun, Xiu Tao ^a   Liu, Fu Li ^a   Liang, Zhou Rui ^a  

^a YELLOW SEA FISHERIES RESEARCH INSTITUTE   (China)

Author keywords

Carbon fixation; Differential gene expression; High throughput sequencing; Photoreceptor; Photosynthesis; Pigment biosynthesis

Indexed keywords

LAMINARIA JAPONICA; LAMINARIALES; PHAEOPHYCEAE; SACCHARINA;

EID: 84875427776     PISSN: 00320935     EISSN: 14322048     Source Type: Journal    
DOI: 10.1007/s00425-012-1831-7     Document Type: Article

References (48)

1. Ahmad M, Cashmore AR (1993) HY4 gene of Arabidopsis thaliana encodes a protein with characteristics of a blue-light photoreceptor. Nature 366: 162-166.
2. Armbrust EV, Berges JA, Bowler C et al (2004) The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science 306: 79-86.
3. Audic S, Claverie JM (1997) The significance of digital gene expression profiles. Genome Res 7: 986-995.
4. Benjamini Y, Yekutieli D (2001) The control of the false discovery rate in multiple testing under dependency. Ann Stat 29: 1165-1188.
5. Busch S, Schmid R (2001) Enzymes associated with β-carboxylation in Ectocarpus siliculosus (Phaeophyceae): are they involved in net carbon acquisition? Eur J Phycol 36: 61-70.
6. Butler WL, Norris KH, Siegelman HW, Hendricks SB (1959) Detection, assay, and preliminary purification of the pigment controlling photoresponsive development of plants. Proc Natl Acad Sci USA 45: 1703-1708.
7. Cock JM, Sterck L, Rouzé P et al (2010) The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature 465: 617-621.
8. Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676.
9. Deng Y, Yao J, Wang X, Guo H, Duan D (2012) Transcriptome sequencing and comparative analysis of Saccharina japonica (Laminariales, Phaeophyceae) under blue light induction. PLoS ONE 7(6): e39704. doi: 10. 1371/journal. pone. 0039704.
10. Dionisio-Sese ML, Fukuzawa H, Miyachi S (1990) Light-induced carbonic anhydrase expression in Chlamydomonas reinhardtii. Plant Physiol 94: 1103-1110.
11. Dring MJ (1981) Chromatic adaptation of photosynthesis in benthic marine algae: an examination of its ecological significance using a theoretical model. Limnol Oceanogr 26: 271-284.
12. Dring MJ (1989) Stimulation of light-saturated photosynthesis in Laminaria (Phaeophyta) by blue light. J Phycol 25: 254-258.
13. Figueroa FL, Aguilera J, Niell FX (1995) Red and blue light regulation of growth and photosynthetic metabolism in Porphyra umbiliculis (Bangiales, Rhodophyta). Eur J Phycol 30: 11-18.
14. Forster RM, Dring MJ (1994) Influence of blue light on the photosynthetic capacity of marine plants from different taxonomic, ecological and morphological groups. Eur J Phycol 29: 21-27.
15. Garg R, Patel RK, Jhanwar S, Priya P, Bhattacharjee A, Yadav G, Bhatia S, Chattopadhyay D, Tyagi AK, Jain M (2011) Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development. Plant Physiol 156: 1661-1678.
16. Grabherr MG, Haas BJ, Yassour M et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotech 29: 644-652.
17. Ishikawa M, Takahashi F, Nozaki H, Nagasato C, Motomura T, Kataoka H (2009) Distribution and phylogeny of the blue light receptors aureochromes in eukaryotes. Planta 230: 543-552.
18. Kanehisa M, Araki M, Goto S et al (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36(database issue): D480-D484.
19. Kim JH, Glick RE, Melis A (1993) Dynamics of photosystem stoichiometry adjustment by light quality in chloroplasts. Plant Physiol 102: 181-190.
20. +-ATPase in the blue-light enhancement of photosynthesis in Laminaria digitata (Phaeophyta). J Phycol 38: 1143-1149.
21. Lane CE, Mayes CM, Druehl LG, Saunders GW (2006) A multi-gene molecular investigation of the kelp (Laminariales, Phaeophyceae) resolves competing phylogenetic hypotheses and supports substantial taxonomic reorganization. J Phycol 42: 493-512.
22. Li R, Yu C, Li Y, Lam T, Yiu S, Kristiansen K, Wang J (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966-1967.
23. Li R, Zhu H, Ruan J et al (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20: 265-272.
24. Ma L, Li J, Qu L, Hager J, Chen Z, Zhao H, Deng XW (2001) Light control of Arabidopsis development entails coordinated regulation of genome expression and cellular pathways. Plant Cell 13: 2589-2608.
25. Marrs KA, Kaufman LS (1991) Rapid transcriptional regulation of the Cab and pEA207 gene family in peas by blue light in the absence of cytoplasmic protein synthesis. Planta 183: 327-333.
26. Mizuta H, Kai T, Tabuchi K, Yasui H (2007) Effects of light quality on the reproduction and morphology of sporophytes of Laminaria japonica (Phaeophyceae). Aquac Res 38: 1323-1329.
27. Möglich A, Yang X, Ayers RA, Keith M (2010) Structure and function of plant photoreceptors. Annu Rev Plant Biol 61: 21-47.
28. Mortazavi A, Williams BA, McCue K, SchaeVer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628.
29. Paraskevopoulou TB, Anastassiou R, Akoyunoglou JA (1995) Circadian expression of the light-harvesting protein of photosystem II in etiolated bean leaves following a single red light pulse: coordination with the capacity of the plant to form chlorophyll and the thylakoid-bound protease. Photosynth Res 44: 93-106.
30. Pertea G, Huang X, Liang F et al (2003) TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19: 651-652.
31. Quiñlones MA, Zeiger E (1994) A putative role of the xanthophylls, zeaxanthin, in blue light photoreception of corn coleoptiles. Science 264: 558-561.
32. Réka T (2003) Analysis of regulatory function of circadian clock on photoreceptor gene expression. Ph. D thesis. Biological Research Center of the Hungarian Academy Sciences, Hungary.
33. Schmid R, Dring MJ (1993) Evidence for two different blue-light-receptor systems for the fast responses of stimulation of photosynthetic capacity and acidification of the plant surface in brown algae. Planta 191: 489-495.
34. Schmid R, Mills JA, Dring MJ (1996) Influence of carbon supply on the stimulation of light-saturated photosynthesis by blue light in Laminaria saccharina: implications for the mechanism of carbon acquisition in higher brown algae. Plant Cell Environ 19: 383-391.
35. Schmittgen TD, Zakrajsek BA, Mills AG, Corn V, Singer MJ, Reed MW (2000) Quantitative reverse transcription-polymerase chain reaction to study mRNA decay: comparison of endpoint and real-time methods. Anal Biochem 285: 194-204.
36. Suetsugu N, Mittmann F, Wagner G, Hughes J, Wada M (2005) A chimeric photoreceptor gene, NEOCHROME, has arisen twice during plant evolution. Proc Natl Acad Sci USA 102: 13705-13709.
37. Takahashi F, Yamagata D, Ishikawa M, Fukamatsu Y, Ogura Y, Kasahara M, Klyosue T, Klkuyama M, Wada M, Kataoka H (2007) AUREOCHROME, a photoreceptor required for photomorphogenesis in stramenopiles. Proc Natl Acad Sci USA 104: 19625-19630.
38. Tlalka M, Runguist M, Fricker M (1999) Light perception and the role of the xanthophylls cycle in blue-light dependent chloroplast movements in Lemna trisulca L. Plant J 20: 447-459.
39. Tsinoremas NF, Schaefer MR, Golden SS (1994) Blue and red light reversibly control psbA expression in the cyanobacterium Synechococcus sp. strain PCC 7942. J Biol Chem 269: 16143-16147.
40. Vijaya V, Anand N (2009) Blue light enhances the pigment synthesis in cyanobacterium Anabaena ambigua Rao (Nostacales). ARPN J Agric Biol Sci 4: 36-43.
41. Wang WJ, Wang GC, Zhang M, Tseng CK (2005) Isolation of fucoxanthin from the rhizoid of Laminaria japonica Aresch. J Integr Plant Biol 47: 1009-1015.
42. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63.
43. Wang W, Sun X, Wang G, Xu P, Wang X, Lin Z, Wang F (2010a) Effect of blue light on indoor seedling culture of Saccharina japonica (Phaeophyta). J Appl Phycol 22: 737-744.
44. Wang WJ, Sun XT, Wang FJ (2010b) Effect of blue light on early sporophyte development of Saccharina japonica (Phaeophyta). Mar Biol 157: 1811-1817.
45. Wang C, Fan X, Wang G, Niu J, Zhou B (2011) Differential expression of Rubisco in sporophytes and gametophytes of some marine macroalgae. PLoS ONE 6(1): e16351. doi: 10. 1371/journal. pone. 0016351.
46. Yang H, Mao YX, Kong FN, Yang GP, Ma F, Wang L (2011) Profiling of the transcriptome of Porphyra yezoensis with Solexa sequencing technology. Chin Sci Bull 20: 2119-2130.
47. Ye J, Ye J, Fang L, Zheng H, Zheng H et al (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34(web server issue): W293-W297.
48. Zhao X, Wang Q, Jiao Y, Huang R, Deng Y, Wang H, Du X (2012) Identification of genes potentially related to biomineralization and immunity by transcriptome analysis of pearl sac in pearl oyster Pinctada martensii. Mar Biotechnol. doi: 10. 1007/s10126-012-9438-3.