| Towards experimental verification of protein coding transcripts and comprehensive metabolic network modeling of Chlamydomonas reinhardtii |
| Erik F.Y. Hom1*, Ryan Murray2*, Chenwei Lin2*, Ani Manichaikul3*, Arvind Chavali3*, Lila Ghamsari2, Xinping Yang2, Mario Stanke4, Chun Liang5, Mark O'Connor1, David E. Hill2, Marc Vidal2, Andrew W. Murray1, Jason Papin3, and Kourosh Salehi-Ashtiani2 |
| 1Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA 2Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA 3Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA 4Department of Bioinformatics, Institute of Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany 5Department of Botany, Miami University, Oxford, OH 45056 USA *These authors have contributed equally to this work. |
| We describe our consortium's efforts to define and validate metabolism-related genes of C. reinhardtii and to produce a comprehensive metabolic map for in silico studies based on the recently published C. reinhardtii genome (JGI v3.1 frozen release, 9/13/07). At the time of abstract submission, our RT-PCR-RACE experiments on ~470 transcripts (with a future target of ~2,000 transcripts) show that only ~40% of these could be confirmed, suggesting that many v3.1 transcripts may be incorrectly annotated. To improve baseline annotation quality and jump-start an iterative process of refinement, we have initiated a genome re-annotation effort using a new v4 genome assembly kindly provided by the JGI/Stanford Human Genome Center. We have generated a draft network of central metabolism for C. reinhardtii : a snap-shot of the network to date accounts for 224 genes, 96 reactions, and 140 metabolites in 6 unique compartments; about 82% of these reactions are gene-associated. Based on our experimental and computational efforts, a number of refinements to the current set of genome annotations are proposed. |
| e-mail address of presenting author: erik@mcb.harvard.edu |