Construction and characterization of a normalized cDNA library of Nannochloropsis oculata (Eustigmatophyceae)

Jianzhong Yu; Xiaolei Ma; Kehou Pan; Guanpin Yang; Wengong Yu

doi:10.1007/s00343-010-9924-2

Your Location：

Home >

Browse articles >

Construction and characterization of a normalized cDNA library of Nannochloropsis oculata (Eustigmatophyceae)

OriginalPaper | Updated：2023-05-16

- Construction and characterization of a normalized cDNA library of Nannochloropsis oculata (Eustigmatophyceae)
- Construction and characterization of a normalized cDNA library of Nannochloropsis oculata (Eustigmatophyceae)
- 海洋湖沼学报（英文） 2010年28卷第4期页码：802-807
- Affiliations：
  
  1. Ministry of Education Key Laboratory of Marine Culture Ocean University of China
  2. Ministry of Education Key Laboratory of Marine Drugs Ocean University of China
  3. College of Marine Life Sciences Ocean University of China
- Author bio：
- Funds：
  
  Supported by National Key Technology R&D Program in the 11;th;-Five-Year Plan of China (No. 2006BAD09A03-2) and National High Technology Research and Development of China (863 Program) (No. 2007AA09Z427)
- DOI：10.1007/s00343-010-9924-2
  中图分类号：
- 网络首发：2010-06-29，
  
  纸质出版：2010
- Accepted：
Scan QR Code
Construction and characterization of a normalized cDNA library of Nannochloropsis oculata (Eustigmatophyceae)[J]. 海洋湖沼学报（英文）, 2010,28(4):802-807.

Yu, J., Ma, X., Pan, K. et al. Construction and characterization of a normalized cDNA library of Nannochloropsis oculata (Eustigmatophyceae)., Chin. J. Ocean. Limnol. 28, 802–807 (2010). https://doi.org/10.1007/s00343-010-9924-2
Construction and characterization of a normalized cDNA library of Nannochloropsis oculata (Eustigmatophyceae)[J]. 海洋湖沼学报（英文）, 2010,28(4):802-807. DOI： 10.1007/s00343-010-9924-2.

Yu, J., Ma, X., Pan, K. et al. Construction and characterization of a normalized cDNA library of Nannochloropsis oculata (Eustigmatophyceae)., Chin. J. Ocean. Limnol. 28, 802–807 (2010). https://doi.org/10.1007/s00343-010-9924-2 DOI：

摘要

Abstract

We constructed and characterized a normalized cDNA library of Nannochloropsis oculata CS-179

and obtained 905 nonredundant sequences (NRSs) ranging from 431–1 756 bp in length. Among them

496 were very similar to nonredundant ones in the GenBank (E ≤1.0e-05)

and 349 ESTs had significant hits with the clusters of eukaryotic orthologous groups (KOG). Bases G and/or C at the third position of codons of 14 amino acid residues suggested a strong bias in the conserved domain of 362 NRSs (>60%). We also identified the unigenes encoding phosphorus and nitrogen transporters

suggesting that N. oculata could efficiently transport and metabolize phosphorus and nitrogen

and recognized the unigenes that involved in biosynthesis and storage of both fatty acids and polyunsaturated fatty acids (PUFAs)

which will facilitate the demonstration of eicosapentaenoic acid (EPA) biosynthesis pathway of N. oculata. In comparison with the original cDNA library

the normalized library significantly increased the efficiencies of random sequencing and rarely expressed genes discovering

and decreased the frequency of abundant gene sequences.

关键词

Keywords

references

Adl S M, Simpson A G, Farmer M A, Andersen R A, Anderson O R, Barta J R, Bowser S S, Brugerolle G, Fensome R A, Fredericq S, James T Y, Karpov S, Kugrens P, Krug J, Lane C. 2005. The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J. Eukaryot. Microbiol., 52: 399–451.

Becker B, Feja N, Melkonian M. 2001. Analysis of expressed sequence tags (ESTs) from the scaly green flagellate Scherffelia dubia Pascher emend. Melkonian et Preisig. Protist., 152: 139–147.

Carninci P, Shibata Y, Hayatsu N, Sugahara Y, Shibata K, Itoh M, Konno H, Okazaki Y, Muramatsu M, Hayashizaki Y. 2000. Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes. Genome. Res., 10: 1 617–1 630.

Chen H L, Li S S, Huang R, Tsai H J. 2008. Conditional Production of a Functional Fish Growth Hormone in the Transgenic Line of Nannochloropsis oculata (Eustigmatophyceae). J. Phycol., 44(3): 768–776.

Chini Zittelli G, Rodolfi L, Tredici M R. 2004. Industrial Production of Microalgal Cell-Mass and Secondary Products-Species of High Potential. In: Richmond A ed. Handbook of Microalgal Culture: Biotechnology and Applied Phycology. Blackwell Science Ltd., Oxford. p. 298–303.

Chini Zittelli G, Lavista F, Bastianini A, Rodolfi L, Vincenzini M, Tredici M R. 1999. Production of eicosapentaenoic acid by Nannochloropsis sp. cultures in outdoor tubular photobioreactors. J. Biotechnol., 70: 299–312.

Chisti Y. 2007. Biodiesel from microalgae. Biotechnol. Adv., 25: 294–306.

Chomczynski P, Sacchi N, 1987. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal. Biochem., 162: 156–159.

Ewing B, Green P. 1998a. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res., 8: 186–194.

Ewing B, Hillier L, Wendl M C, Green P. 1998b. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome. Res., 8: 175–185.

Fawleya K P, Fawleya M W. 2007. Observations on the diversity and ecology of freshwater Nannochloropsis (Eustigmatophyceae), with descriptions of new taxa. Protist., 158: 325–336.

Fogg G E. 1995. Some comments on picoplankton and its importance in the pelagic ecosystem. Aquat. Microb. Ecol., 9: 33–39.

Grossman A R. 2005. Paths toward algal genomics. Plant Physiol., 137: 410–27.

Guillard R R L, Ryther J H. 1962. Studies of marine planktonic diatoms. I. Cyclotella nana Hustedt and Detonula conferraceae Cleve. Can. J. Microbiol., 8: 229–239.

Hackett J D, Scheetz T E, Yoon H S, Soares M B, Bonaldo M F, Casavant T L, Bhattacharya D. 2005. Insights into a dinoflagellate genome through expressed sequence tag analysis. BMC Genomics, 6: 80.

Hawkins R L, Nakamura M. 1999. Expression of human growth hormone by the eukaryotic alga, Chlorella. Curr. Microbiol., 38: 335–341.

Hibberd D J. 1981. Notes on the taxonomy and nomenclature of the algal classes Eustigmatophyceae and Tribophyceae (synonym Xantophyceae). Bot. J. Linnean Soc., 82: 93–99.

Hu H H, Gao K S. 2006. Response of growth and fatty acid compositions of Nannochloropsis sp. to environmental factors under elevated CO2 concentration. Biotechnol. Lett., 28: 987–992.

Karlson B, Potter D, Kuylenstierna M, Andersen R A. 1996. Ultrastructure, pigment composition, and 18S rRNA gene sequence for Nannochloropsis granulata sp. nov. (Monodopsidaceae, Eustigmatophyceae), a marine ultraplankter isolated from the Skagerrak, northeast Atlantic Ocean. Phycologia, 35: 253–260.

La Claire II J W. 2006. Analysis of expressed sequence tags from the harmful alga, Prymnesium parvum (Prymnesiophyceae, Haptophyta). Mar. Biotech., 8: 534–546.

Lanier W, Moustafa A, Bhattacharya D, Comeron J M. 2008. EST analysis of Ostreococcus lucimarinus, the most compact eukaryotic genome, shows an excess of introns in highly expressed genes. PLoS ONE., 3(5): e2171.

Lavens P, Sorgeloos P. 1996. Manual on the production and use of life food for aquaculture. FAO Fish. Tech. Pap., 361: 7–42.

Leggat W, Hoegh-Guldberg O, Dove S, Yellowlees D. 2007. Analysis of an EST library from the dinoflagellate (Symbiodinium sp.) symbiont of reef-building corals. J. Phycol., 43(5): 1 010–1 021.

Lidie K B, Ryan J C, Barbier M, Van Dolah F M. 2005. Gene expression in Florida red tide dinoflagellate Karenia brevis: analysis of an expressed sequence tag library and development of a DNA microarray. Mar. Biotechnol., 7: 481–493.

Marchler-Bauer A, Panchenko A R, Shoemaker B A, Thiessen P A, Geer L Y, Bryant S H. 2002. CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucl. Acids Res., 30: 281–283.

Sharp P M, Tuohy T M F, Mosurski K R. 1986. Codon usage in yeast: Cluster analysis clearly differentiates highly and lowly expressed genes. Nucl. Acids Res., 14: 5 125–5 143.

Shi J, Pan K H, Yu J Z, Zhu B H, Yang G P, Yu W G, Zhang X Y. 2008. Analysis of expressed sequence tags from the marine microalga Nannochloropsis oculata (Eustigmatophyceae). J. Phycol., 44: 99–102.

Stephen F A, Madden T L, Schaffer A A, Zhang J, Zhang Z, Miller W, Lipman J D. 1997. Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucl. Acids Res., 25: 3 389–3 402.

Sukenik A. 1999. Production of EPA by marine eustigmatophyte Nannochloropsis. In: Cohen, E. ed. Chemicals from Microalgae. Taylor and Francis, London. p. 41–56.

Tonon T, Harvey D, Larson T R, Graham I A. 2002. Long chain polyunsaturated fatty acid production and partitioning to triacylglycerols in four microalgae. Phytochem., 61: 15–24.

Volkman J K, Brown M R, Dunston G A, Jeffre S W. 1993. The biochemical composition of marine microalgae from the class Eustigmatophyceae. J. Phycol., 29: 69–78.

Wahlund T M, Hadaegh A R, Clark R, Nguyen B, Fanelli M, Read B A. 2004. Analysis of expressed sequence tags from calcifying cells of marine coccolithophorid (Emiliania huxleyi). Mar. Biotechnol., 6: 278–290.

Whittle S, Casselton P. 1975. The chloroplast pigments of the algal class Eustigmatophyceae and Xanthophyceae. I. Eustigmatophyceae. Br. Phycol. J., 10: 179–191.

Zhang Z X, Zhang F D, Tang W H, Pi Y J, Zheng Y L. 2005. Construction and characterization of normalized cDNA Library of maize inbred M017 from multiple tissues and developmental stages. Mol. Biol., 39: 198–206.

Zhulidov P A, Bogdanova E A, Shcheglov A S, Vagner L L, Khaspekov G L, Kozhemyako V B, Matz M V, Meleshke-Vitch E, Moroz L L, Lukyanov S A. 2004. Simple cDNA normalization using kamchatka crab duplex-specific nuclease. Nucl. Acids Res., 32: e37.

浏览量

Downloads

CSCD

文章被引用时，请邮件提醒。

Submit

工具集

关联资源

Characterization of genic microsatellite markers derived from expressed sequence tags in Pacific abalone (Haliotis discus hannai)

Cloning and characterization of a delta-6 desaturase encoding gene from Nannochloropsis oculata

Temperature effects on lipid properties of microalgae Tetraselmis subcordiformis and Nannochloropsis oculata as biofuel resources

双转子轴间滑油颗粒运动轨迹参数化模型

基于半经验模型的霍尔推力器壁面腐蚀形貌预测方法研究