Validation of housekeeping genes for gene expression studies in an ice alga Chlamydomonas during freezing acclimation

Extremophiles

Volumn 16, Issue 3, 2012, Pages 419-425

  Liu, Chenlin ^a   Wu, Guangting ^a   Huang, Xiaohang ^a   Liu, Shenghao ^a   Cong, Bailin ^a  

^a FIRST INSTITUTE OF OCEANOGRAPHY   (China)

Author keywords

Chlamydomonas sp. ICE L; FAD3; Freezing acclimation; Normalization; Real time RT PCR; Reference genes

Indexed keywords

ACCLIMATIZATION; ARTICLE; CHLAMYDOMONAS; ESSENTIAL GENE; FREEZING; PHYSIOLOGY; PLANT GENE;

ACCLIMATIZATION; CHLAMYDOMONAS; FREEZING; GENES, ESSENTIAL; GENES, PLANT;

ALGAE; CHLAMYDOMONAS; CHLAMYDOMONAS SP. ICE-L;

EID: 84860839197     PISSN: 14310651     EISSN: 14334909     Source Type: Journal    
DOI: 10.1007/s00792-012-0441-4     Document Type: Article

References (35)

1. Andersen CL, Jensen JL, Ørntoft TF (2004) Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res 64: 5245-5250.
2. Barsalobres-Cavallari C, Severino F, Maluf M, Maia I (2009) Identification of suitable internal control genes for expression studies in Coffea arabica under different experimental conditions. BMC Mol Biol 10(1): 1.
3. Cuevas JC, Lo'pez-Cobollo R, Alca'zar R, Zarza X, Koncz C, Altabella T, Salinas J, Tiburcio AF, Ferrando A (2008) Putrescine is involved in Arabidopsis freezing tolerance and cold acclimation by regulating abscisic acid levels in response to low temperature. Plant Physiol 148: 1094-1105.
4. Czechowski T, Stitt M, Altmann T, Udvardi MK, Scheible WR (2005) Genome-wide identification and testing of superior reference genes for transcript normalisation in Arabidopsis. Plant Physiol 139(1): 5-17.
5. De Jonge HJ, Fehrmann RS, de Bont ES, Hofstra RM, Gerbens F (2007) Evidence based selection of housekeeping genes. PLoS ONE 2: e898.
6. Dombrowski JE, Martin RC (2009) Evaluation of reference genes for quantitative RT-PCR in Lolium temulentum under abiotic stress. Plant Sci 176: 390-396.
7. Exposito-Rodriguez M, Borges AA, Borges-Perez A, Perez JA (2008) Selection of internal control genes for quantitative real-time RT-PCR studies during tomato development process. BMC Plant Biol 8: 131.
8. Gradinger RR (2001) Adaptation of Arctic and Antarctic ice metazoa to their habitat. Zoology 104: 339-345.
9. Guenin S, Mauriat M, Pelloux J, Van WO, Bellini C, Gutierrez L (2009) Normalization of qRT-PCR data: the necessity of adopting a systematic, experimental conditions-specific, validation of references. J Exp Bot 60: 487-493.
10. Hicks GR, Hironaka CM, Dauvilee D, Funke RP, D'Hulst C, Waffenschmidt S, Ball SG (2001) When simpler is better. Unicellular green algae for discovering new genes and functions in carbohydrate metabolism. Plant Physiol 127: 1334-1338.
11. Hong SY, Seo PJ, Yang MS, Xiang F, Park CM (2008) Exploring valid reference genes for gene expression studies in Brachypodium distachyon by real-time PCR. BMC Plant Biol 8: 112-123.
12. Hou X, Jiang Y, Li G (2002) Relations of total lipid content and fatty acid composition of Antarctic ice-microalgae to its low temperature adaptability. J Oceanogr Huang Hai Bo Hai Seas 20(1): 1-10.
13. Hsiao LL, Dangond F, Yoshida T, Hong R, Jensen RV (2001) A compendium of gene expression in normal human tissues. Physiol Genomics 7: 97-104.
14. Huggett J, Dheda K, Bustin S, Zumla A (2005) Real-time RT-PCR normalisation; strategies and considerations. Genes Immun 6: 279-284.
15. Iskandar HM, Simpson RS, Casu RE, Bonnett GD, Maclean DJ, Manners JM (2004) Comparison of reference genes for quantitative real-time polymerase chain reaction analysis of gene expression. Plant Mol Biol Rep 22: 325-337.
16. Jian B, Liu B, Bi Y, Hou W, Wu C, Han T (2008) Validation of internal control for gene expression study in soybean by quantitative real-time PCR. BMC Mol Biol 9: 59.
17. Kan G, Zheng Z, Jiang Y, Miao J, Zhang B, Li G (2006) Salt resistance of Antarctic ice microalga Chlamydomonas sp. J Fishery Sci China 13: 73-78.
18. Le Bail A, Dittami S, de Franco PO, Rousvoal S, Cock M, Tonon T, Charrier B (2008) Normalisation genes for expression analyses in the brown alga model Ectocarpus siliculosus. BMC Mol Biol 9: 1-75.
19. Liu C, Huang X, Wang X, Zhang X, Li G (2006) Phylogenetic studies on two strains of Antarctic ice algae based on morphological and molecular characteristics. Phycologia 45: 190-198.
20. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C[T]) method. Methods 25: 402-408.
21. Lovdal T, Lillo C (2009) Reference gene selection for quantitative real-time PCR normalization in tomato subjected to nitrogen, cold, and light stress. Anal Biochem 387: 238-242.
22. Martin R, Hollenbeck V, Dombrowski J (2008) Evaluation of reference genes for quantitative RT-PCR in Lolium perenne. Crop Sci 48: 1881-1887.
23. Mock T, Thomas DN (2005) Recent advances in sea-ice microbiology. Environ Microbiol 7: 605-619.
24. Morgan-Kiss RM, Priscu JC, Pocock T, Gudynaite-Savitch L, Huner NPA (2006) Adaptation and acclimation of photosynthetic microorganisms to permanently cold environments. Microbiol Mol Biol Rev 70: 222-252.
25. Nicot N, Hausman J, Hoffmann L, Evers D (2005) Housekeeping gene selection for real-time RT-PCR normalization in potato during biotic and abiotic stress. J Exp Bot 56: 2907-2914.
26. Provasoli L (1968) Media and prospects for the cultivation of marine algae. In: Watanabe A, Hattori R (eds) Culture and collections of algae. Proc. U. S.-Japan Conference, Hakone.
27. Reid KE, Olsson N, Schlosser J, Peng F, Lund ST (2006) An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development. BMC Plant Biol 6: 27.
28. Rosic N, Pernice M, Rodriguez-Lanetty M, Hoegh-Guldberg O (2010) Validation of housekeeping genes for gene expression studies in Symbiodinium exposed to thermal and light stress. Mar Biotech 29: 1-11.
29. Udvardi MK, Czechowski T, Scheible WR (2008) Eleven golden rules of quantitative RT-PCR. Plant Cell 20: 1736-1737.
30. Upchurch RG (2008) Fatty acid unsaturation, mobilization, and regulation in the response of plants to stress. Biotech Lett 30: 967-977.
31. Vandesompele J, De Preter K, Pattyn F, Poppe B, van Roy N, De Paepe A, Speleman F (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3: RESEARCH0034.
32. Vicentini R, Sassaki FT, Gimenes MA, Maia IG, Menossi M (2005) In silico evaluation of the Eucalyptus transcriptome. Gene Mol Biol 28: 487-495.
33. Wu G, Liu C, Liu S, Cong B, Huang X (2010) High-quality RNA preparation for cDNA library construction of the Antarctic sea-ice alga Chlamydomonas sp. ICE-L. J Appl Phycol 22(6): 779-783.
34. Zhang Z, Hu J (2007) Development and validation of endogenous reference genes for expression profiling of Medaka (Oryzias latipes) exposed to endocrine disrupting chemicals by quantitative real-time RT-PCR. Toxicol Sci 95: 356-368.
35. Zhang P, Liu S, Cong B, Wu G, Liu C, Lin X, Shen J, Huang X (2010) A novel omega-3 fatty acid desaturase involved in acclimation processes of polar condition from Antarctic ice Algae Chlamydomonas sp. ICE-L. Mar Biotechnol 13: 393-401.