Chlamydomonas Transcriptome

from Sabeeha Merchant

We are pleased to report the availability of 2 Gigabases of 454 reads from the JGI that describe the Chlamydomonas transcriptome under various conditions. The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.

RNAs were prepared from cells sampled under various nutrient deficiencies (S, P, Cu, Fe, Zn, Mn, O2, dark), various nutrient sources (CO2, acetate, nitrate), various stages of the cell cycle, after de-flagellation, during the mating pathway. RNAs were provided by Madeli Castruita, Ursula Goodenough, Arthur Grossman, Anja Hemschemeier, Janette Kropat, Karl Lechtreck, Jae-Hyeok Lee, Sabeeha Merchant, Aimee Terauchi, James Umen, Eugen Urzica, George Witman and Matt Zones.

The data have been submitted to the Short Read Archive under accession SRA020135 and may be viewed as alignments to the JGI version 4 genome (C. reinhardtii, October 2007 assembly) at http://genomes.mcdb.ucla.edu/Cre454/

0.5 Gb of Roche Titanium 454 reads from Genoscope are also aligned to the browser. The mRNA was isolated from strains S1D2 (mt-) and cw15 petC-D1 (a 137c mt+ derivative with mutations affecting cell wall synthesis and photosynthesis, abbreviated cw below). Cells were grown under various nutrient regimes (acetate, CO2, dark, low or high light, N-limitation) or stress (heat, chloramphenicol treatment). The Genoscope data are made available for the purpose of structural annotation of the Chlamydomonas genome, including delination of transcripts, analysis of splicing and polyadenylation. As two of the four libraries are made with cDNAs from the S1D2 strain, this data can also be used to mine for polymorphisms, but Genoscope at this stage reserves the right to publish first on this topic.

Please refer also to http://genomes.mcdb.ucla.edu/CreSulfur/ (click on browser) to view alignments from the sulfur-deficiency transcriptome.

Sabeeha Merchant and Matteo Pellegrini, UCLA