Advertisement

Journal of Applied Phycology

, Volume 25, Issue 4, pp 1237–1246 | Cite as

Transcriptome sequencing and comparative analysis of the gametophyte thalli of Pyropia tenera under normal and high temperature conditions

  • San Choi
  • Mi Sook Hwang
  • Sungoh Im
  • Namju Kim
  • Won-Joong Jeong
  • Eun-Jeong Park
  • Yong-Gun Gong
  • Dong-Woog ChoiEmail author
Article

Abstract

The marine red alga Pyropia tenera grows on intertidal rocks, where it undergoes dynamic environmental changes including temperature, desiccation, osmotic shock, and changes in light intensity. Therefore, Pyropia have developed a variety of strategies and mechanisms to overcome those environmental stressors. In an effort to identify the genes involved in the high-temperature tolerance of P. tenera, we generated 368,334 expression sequence tags (ESTs) using 454 sequencing technology and 3,331 ESTs using the Sanger method. Among the total ESTs, 222,024 reads were generated from gametophyte thalli under control condition and 149,641 reads were generated under high temperature condition. These ESTs were assembled into 17,870 contigs consisting of 336,016 reads, whereas 35,924 sequences remained as unassembled ESTs. Only 16.5 % of contigs shared significant similarity with an E value of ≤1E− 10 with UniProt sequence. The 95 different SSR motifs were discovered in 1,586 contigs. Trinucleotide repeat was absolutely predominant (90.2 %) SSR, and GGC was the most common motif. A comparison of the ESTs from gametophyte thalli under normal and heat stress conditions enabled us to identify the transcripts that were up or downregulated by high temperature. Most of transcripts produced under the high temperature condition belong to heat shock protein family and novel transcripts not matched to known genes in current public databases. These ESTs will provide valuable information to identify the DNA markers for the Pyropia species and the genes involved in the molecular mechanism of thermotolerance in red algae.

Keywords

Pyropia tenera Rhodophyta ESTs Heat temperature response (HTR) gene Transcriptome 

Notes

Acknowledgments

This research was supported by a grant (RP-2011-BT-058) from National Fisheries Research and Development Institute, South Korea.

Supplementary material

10811_2012_9921_MOESM1_ESM.doc (122 kb)
ESM 1 (DOC 121 kb)

References

  1. Asamizu E, Nakajima M, Kitade Y, Saga N, Nakamura Y, Tabata S (2003) Comparison of RNA expression profiles between the two generations of Porphyra yezoensis (Rhodophyta), based on expressed sequence tag frequency analysis. J Phycol 39:923–30CrossRefGoogle Scholar
  2. Bloom JS, Khan Z, Kryglyak L, Singh M, Cauday AA (2009) Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays. BMC Genomics 10:221PubMedCrossRefGoogle Scholar
  3. Blouin NA, Brodie JA, Grossman AC, Xu P, Brawley SH (2011) Porphyra: a marine crop shaped by stress. Trends Plant Sci 16:29–37PubMedCrossRefGoogle Scholar
  4. Boston RS, Viitanen PV, Vierling E (1996) Molecular chaperones and protein folding in plants. Plant Mol Biol 32:191–222PubMedCrossRefGoogle Scholar
  5. Bowman JL, Floyd SK, Sakakibara K (2007) Green genes-comparative genomics of the green branch life. Cell 129:229–234PubMedCrossRefGoogle Scholar
  6. Brautigam M, Lindlof A, Zakhrabekova S, Gharti-Chhetri G, Olsson B, Olsson O (2005) Generation and analysis of 9,792 EST sequences from cold acclimated oat, Avena sativa. BMC Plant Biol 5:18PubMedCrossRefGoogle Scholar
  7. Bray EA, Bailey-Serres J, Weretilnyk E (2000) Responses to abiotic stresses. In: Buchanan B, Gruissem W, Jones R (eds) Biochemistry and molecular biology of plants. American Society of Plant Biologists, Rockville, pp 1158–1203Google Scholar
  8. Busch W, Wunderlich M, Schoffl F (2005) Identification of novel heat shock factor-dependent genes and biochemical pathways in Arabidopsis thaliana. Plant J 41:1–14PubMedCrossRefGoogle Scholar
  9. Chan CX, Yang EC, Banerjee T, Yoon HS, Martone PT, Estevez JM, Bhattacharya D (2011) Red and green algal monophyly and extensive gene sharing found in a rich repertoire of red algal genes. Curr Biol 21:328–333PubMedCrossRefGoogle Scholar
  10. Cheung F, Hass BJ, Goldberg SMD, May GD, Xiao Y, Town CD (2006) Sequencing Medicago truncatula expressed sequenced tags using 454 Life Science technology. BMC Genomics 7:272PubMedCrossRefGoogle Scholar
  11. Cheung F, Win J, Lang JM, Hamilton J, Vuong H, Leach JE, Kamoun S, Levesque A, Tisserat N, Buell CR (2008) Analysis of the Pythium ultimum transcriptome using Sanger and pyrosequencing approaches. BMC Genomics 9:542PubMedCrossRefGoogle Scholar
  12. Choi DW, Jung JD, Ha YI, Park HW, In DS, Chung HJ, Liu JR (2005) Analysis of transcripts in methyl jasmonate-treated ginseng hairy roots to identify genes involved in the biosynthesis of ginsenosides and other secondary metabolites. Plant Cell Rep 23:557–566PubMedCrossRefGoogle Scholar
  13. Cock JM, Coelho SM (2011) Algal models in plant biology. J Exp Bot 62:2425–2430PubMedCrossRefGoogle Scholar
  14. Feder ME, Hofmann GE (1999) Heat-shock proteins, molecular chaperones, and the stress response: evolutionary and ecological physiology. Annu Rev Physiol 61:243–282PubMedCrossRefGoogle Scholar
  15. Guo S, Zheng Y, Joung JG, Liu S, Zhang Z, Crasta OR, Sobral BW, Xu Y, Huang S, Fei Z (2010) Transcriptome sequencing and comparative analysis of cucumber flower with different sex types. BMC Genomics 11:384PubMedCrossRefGoogle Scholar
  16. Houde M, Belcaid M, Ouellet F, Danyluk J, Monroy AF, Dryanova A, Gulick P, Bergeron A, Laroche A, Links MG, MacCarthy L, Crosby WL, Sarhan F (2006) Wheat EST resources for functional genomics of abiotic stress. BMC Genomics 7:149PubMedCrossRefGoogle Scholar
  17. Huan P, Wang H, Liu B (2012) Transcriptomic analysis of the clam Meretrix meretrix on different larval stages. Mar Biotechnol 14:69–78PubMedCrossRefGoogle Scholar
  18. Huang J, Lu X, Yan H, Chen S, Zhang W, Huang R (2012) Transcriptome characterization and sequencing-based identification of salt-responsive genes in Millettia pinnata, a semi-mangove plant. DNA Res 19:195–207PubMedCrossRefGoogle Scholar
  19. Hwang MS, Chung IK, Oh YS (1997) Temperature responses of Porphyra tenera Kjellman and P. yezoensis Ueda (Bangiales, Rhodophyta) from Korea. Algae 12:207–213Google Scholar
  20. Hwang MS, Kim SM, Ha DS, Baek JM, Kim HS, Choi HG (2005) DNA sequences and identification of Porphyra cultivated by natural seeding on the southwest coast of Korea. Algae 20:183–196CrossRefGoogle Scholar
  21. Ireland HE, Harding SJ, Bonwick GA, Jones M, Smith CJ, Williams JHH (2004) Evaluation of heat shock protein 70 as a biomarker of environmental stress in Fucus serratus and Lemna minor. Biomarkers 9:139–155CrossRefGoogle Scholar
  22. Karlin S, Brocchieri L (1998) Heat shock protein 70 family: multiple sequence comparisons, function, and evolution. J Mol Evol 47:565–577PubMedCrossRefGoogle Scholar
  23. Kim E, Park HS, Jung YJ, Jeong WJ, Park HS, Hwang MS, Park EJ, Gong YG, Choi DW (2011) Identification of the high-temperature response genes from Porphyra seriata (Rhodophyta) ESTs and enhancement of heat tolerance of Chlamydomonas (Chlorophyta) by expression of the Porphyra HTR2 gene. J Phycol 47:821–828CrossRefGoogle Scholar
  24. Kitade Y, Asamizu E, Satoru F, Nakajima M, Ootsuka S, Endo H, Tabata S, Saga N (2008) Identification of genes preferentially expressed during asexual sporulation in Porphyra yezoensis gametophytes (Bangiales, Rhodophyta). J Phycol 44:113–123CrossRefGoogle Scholar
  25. Lister R, Gregory BD, Ecker JR (2008) Next is now: new technologies for sequencing of genomes, transcriptomes and beyond. Curr Opin Plant Biol 12:107–118CrossRefGoogle Scholar
  26. Lluisma A, Ragan MA (1997) Expressed sequence tags (ESTs) from the marine red alga Gracilaria gracilis. J Appl Phycol 9:287–293CrossRefGoogle Scholar
  27. Mayer MP, Bukau B (2005) HSP70 chaperones: cellular functions and molecular mechanism. Cell Mol Life Sci 62:670–684PubMedCrossRefGoogle Scholar
  28. McLachlan J (1973) Growth media-marine. In: Stein JR (ed) Handbook of phycological methods. Cambridge Univ. Press, New York, pp 25–51Google Scholar
  29. Miura A (1988) Taxonomic studies of Porphyra species cultivated in Japan, referring to their transition to the cultivated variety. J Tokyo Univ Fish 75:311–325Google Scholar
  30. Nelson RJ, Ziegelhoffer T, Nicolet C, Werner-Washburne M, Craig EA (1992) The translation machinery and 70 kD heat shock protein cooperate in protein synthesis. Cell 71:97–105PubMedCrossRefGoogle Scholar
  31. Nikaido I, Asamizu E, Nakajima M, Nakamura Y, Saga N, Tabata S (2000) Generation of 10,154 expressed sequence tags from a leafy gametophyte of a marine red alga, Porphyra yezoensis. DNA Res 7:223–227PubMedCrossRefGoogle Scholar
  32. Nover L, Bharti K, Koskull-Döring P, Mishra SK, Ganguli A, Scharf KD (2001) Arabidopsis and the heat stress transcription factor world: how many heat stress transcription factors do we need? Cell Stress Chaperon 6:177–189CrossRefGoogle Scholar
  33. Park HS, Jeong WJ, Kim EC, Jung YJ, Lim JM, Hwang MS, Park EJ, Ha DS, Choi DW (2011) Heat shock protein gene family of the Porphyra seriata and enhancement of heat stress tolerance by PsHSP70 in Chlamydomonas. Mar Biotech 14:332–342CrossRefGoogle Scholar
  34. Pearson GA, Hoarau G, Lago-Leston A, Coyer JA, Kube M, Reinhardt R, Henckel K, Serrao ETA, Corre E, Olsen JL (2010) An expressed sequence tag analysis of the intertidal brown seaweeds Fucus serratus (L.) and F. vesiculsus (L.) (Heterokontophyta, Phaeophyceae) in response to abiotic stressors. Mar Biotech 12:195–213CrossRefGoogle Scholar
  35. Qin D, Wu H, Peng H, Yao Y, Ni Z, Li Z, Zhou C, Sun Q (2008) Heat stress-responsive trancriptome analysis in heat susceptible and tolerant wheat (Triticum aestivum L.) by using Wheat Genome Array. BMC Genomics 9:432PubMedCrossRefGoogle Scholar
  36. Renner T, Waters ER (2007) Comparative genomic analysis of the HSP70s from five diverse photosynthetic eukaryotes. Cell Stress Chaperones 12:172–185PubMedCrossRefGoogle Scholar
  37. Roeder V, Collén J, Rousvoal S, Corre E, Leblanc C, Boyen C (2005) Identification of stress gene transcripts in Laminaria digitata (Phaeophyceae) protoplast cultures by expressed sequence tag analysis. J Phycol 41:1227–1235CrossRefGoogle Scholar
  38. Sahoo D, Tang X, Yarish C (2002) Porphyra—the economic seaweed as a new experimental system. Curr Sci 83:1313–1316Google Scholar
  39. Schroda M, Vallon O (2009) Chaperones and proteases. In: Stern DB (ed) Chlamydomonas source book, volume 2, 2nd edn. Elsevier, San Diego, pp 671–729Google Scholar
  40. Tanaka KI, Namba T, Arai Y, Fujimoto M, Adachi H, Sobue G, Takeuchi K, Nakai A, Mizushima T (2007) Genetic evidence for a protective role for heat shock factor 1 and heat shock protein 70 against colitis. J Biol Chem 282:23240–23252PubMedCrossRefGoogle Scholar
  41. Thiel T, Michalek Wm Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422PubMedGoogle Scholar
  42. Wang W, Vinocur B, Shoseyov O, Altman A (2004) Role of plant heat-shock proteins and molecular chaperons in the abiotic stress response. Trends Plant Sci 9:244–252PubMedCrossRefGoogle Scholar
  43. Xiaolei F, Yongjun F, Songnian H, Guangce W (2007) Generation and analysis of 5318 expressed sequence tags from the filamentous sporophyte of Porphyra haitanensis (Rhodophyta). J Phycol 43:1287–1294CrossRefGoogle Scholar
  44. Yang H, Mao YX, Kong FN, Yang GP, Ma Fm Wang L (2011) Profiling of the transcriptome of Porphyra yezoenesis with Solexa sequencing technology. Chinese Sci Bull 56:2119–2130CrossRefGoogle Scholar
  45. Zhang Y, Mian MA, Chekhovskiy K, So S, Kupfer D, Lai H, Roe BA (2005) Differential gene expression in Festuca under heat stress conditions. J Exp Bot 56:897–907PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2012

Authors and Affiliations

  • San Choi
    • 1
  • Mi Sook Hwang
    • 2
  • Sungoh Im
    • 1
  • Namju Kim
    • 1
  • Won-Joong Jeong
    • 3
  • Eun-Jeong Park
    • 2
  • Yong-Gun Gong
    • 2
  • Dong-Woog Choi
    • 1
    Email author
  1. 1.Department of Biology EducationChonnam National University and KhumHo Research InstituteGwangjuSouth Korea
  2. 2.Seaweed Research CenterNational Fisheries Research and Development InstituteMokpoSouth Korea
  3. 3.Plant Systems Engineering Research CenterKorea Research Institute of Bioscience and BiotechnologyDaejeonSouth Korea

Personalised recommendations