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Open Access Highly Accessed Methodology article

Construction and evaluation of a whole genome microarray of Chlamydomonas reinhardtii

Jörg Toepel1, Stefan P Albaum2, Samuel Arvidsson3, Alexander Goesmann2, Marco la Russa1, Kristin Rogge1 and Olaf Kruse1*

Author affiliations

1 Algae Biotechnology & Bioenergy, Dept. of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany

2 Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany

3 AG Bioinformatics, GoFORSYS, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany

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Citation and License

BMC Genomics 2011, 12:579  doi:10.1186/1471-2164-12-579

Published: 25 November 2011

Abstract

Background

Chlamydomonas reinhardtii is widely accepted as a model organism regarding photosynthesis, circadian rhythm, cell mobility, phototaxis, and biotechnology. The complete annotation of the genome allows transcriptomic studies, however a new microarray platform was needed. Based on the completed annotation of Chlamydomonas reinhardtii a new microarray on an Agilent platform was designed using an extended JGI 3.1 genome data set which included 15000 transcript models.

Results

In total 44000 probes were determined (3 independent probes per transcript model) covering 93% of the transcriptome. Alignment studies with the recently published AUGUSTUS 10.2 annotation confirmed 11000 transcript models resulting in a very good coverage of 70% of the transcriptome (17000). Following the estimation of 10000 predicted genes in Chlamydomonas reinhardtii our new microarray, nevertheless, covers the expected genome by 90-95%.

Conclusions

To demonstrate the capabilities of the new microarray, we analyzed transcript levels for cultures grown under nitrogen as well as sulfate limitation, and compared the results with recently published microarray and RNA-seq data. We could thereby confirm previous results derived from data on nutrient-starvation induced gene expression of a group of genes related to protein transport and adaptation of the metabolism as well as genes related to efficient light harvesting, light energy distribution and photosynthetic electron transport.