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

Chenlin Liu1, Guangting Wu1, Xiaohang Huang1, Shenghao Liu1, Bin Cong1
1The First Institute of Oceanography, Marine Ecological Center, State Oceanic Administration, Qingdao, China

Tóm tắt

Từ khóa


Tài liệu tham khảo

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

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

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

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

De Jonge HJ, Fehrmann RS, de Bont ES, Hofstra RM, Gerbens F (2007) Evidence based selection of housekeeping genes. PLoS ONE 2:e898

Dombrowski JE, Martin RC (2009) Evaluation of reference genes for quantitative RT-PCR in Lolium temulentum under abiotic stress. Plant Sci 176:390–396

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

Gradinger RR (2001) Adaptation of Arctic and Antarctic ice metazoa to their habitat. Zoology 104:339–345

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

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

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

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

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

Huggett J, Dheda K, Bustin S, Zumla A (2005) Real-time RT-PCR normalisation; strategies and considerations. Genes Immun 6:279–284

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

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

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

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

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

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

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

Martin R, Hollenbeck V, Dombrowski J (2008) Evaluation of reference genes for quantitative RT-PCR in Lolium perenne. Crop Sci 48:1881–1887

Mock T, Thomas DN (2005) Recent advances in sea-ice microbiology. Environ Microbiol 7:605–619

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

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

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

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

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

Udvardi MK, Czechowski T, Scheible WR (2008) Eleven golden rules of quantitative RT-PCR. Plant Cell 20:1736–1737

Upchurch RG (2008) Fatty acid unsaturation, mobilization, and regulation in the response of plants to stress. Biotech Lett 30:967–977

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

Vicentini R, Sassaki FT, Gimenes MA, Maia IG, Menossi M (2005) In silico evaluation of the Eucalyptus transcriptome. Gene Mol Biol 28:487–495

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

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

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