Chlamydomonas reinhardtii is a model organism for fundamental discovery in photosynthesis and ciliary biology. Its genome is one of five flagship genomes at the Joint Genome Institute, indicative of their commitment to finishing and investment in infrastructure for maintaining the database. We will add value to the JGI effort by using transcriptome data, generated via RNA-seq methodology on lllumina's platform, to a) derive better gene models, b) identify differentially expressed genes and alternate transcript forms under various experimental conditions, and c) deduce the pattern of expression of every gene in the genome and the absolute abundance of every transcript. Although >300,000 ESTs have been sequenced, only 59% of the ~16,000 gene models are supported by EST coverage, and only 21% have both 5'and 3'UTR information. Therefore, many gene models, both computationally predicted as well as homology-based are incorrect or at best incomplete. With RNA-seq approaches we obtain much greater coverage of the transcriptome, which can significantly elevate the quality of annotation. In any given condition, there is a range of four orders of magnitude for transcript abundance, but by increasing the number of runs we can sample even low abundance transcripts. Therefore, to increase the coverage of the transcriptome, transcript sequence data will be collected from cells grown under various environmental and physiological conditions, including variation in macro- and micro-nutrients, pH, temperature, light intensity, C02 and 02 partial pressures, and under different developmental situations (gametogenesis, zygote, cell wall and flagella regeneration). Each sample will be handled separately so that we can compare specific RNA abundance within and among each sample, which will elucidate transcription networks associated with specific environmental and developmental conditions. The primary sequence data will be deposited with associated metadata periodically at NCBI SRA and the derived data will be loaded onto a publicly accessible browser maintained at UCLA and periodically uploaded to Chlamybase and the JGI genome browser for long term public access.

Public Health Relevance

Chlamydomonas is an important model organism for the study of ciliary biology, chloroplast function, metabolism and sexual differentiation, and their associated human diseases such as ciliopathies. Using next-generation sequencing technology we plan to comprehensively study the transcriptional landscape of Chlamydomonas in order to define gene models and gene expression levels across disparate samples.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Resource-Related Research Projects (R24)
Project #
5R24GM092473-02
Application #
8331508
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Sledjeski, Darren D
Project Start
2011-09-15
Project End
2015-07-31
Budget Start
2012-08-01
Budget End
2013-07-31
Support Year
2
Fiscal Year
2012
Total Cost
$308,000
Indirect Cost
$108,000
Name
University of California Los Angeles
Department
Genetics
Type
Schools of Medicine
DUNS #
092530369
City
Los Angeles
State
CA
Country
United States
Zip Code
90095
Li, Xiaobo; Zhang, Ru; Patena, Weronika et al. (2016) An Indexed, Mapped Mutant Library Enables Reverse Genetics Studies of Biological Processes in Chlamydomonas reinhardtii. Plant Cell 28:367-87
Blaby-Haas, Crysten E; Castruita, Madeli; Fitz-Gibbon, Sorel T et al. (2016) Ni induces the CRR1-dependent regulon revealing overlap and distinction between hypoxia and Cu deficiency responses in Chlamydomonas reinhardtii. Metallomics 8:679-91
Hamaji, Takashi; Lopez, David; Pellegrini, Matteo et al. (2016) Identification and Characterization of a cis-Regulatory Element for Zygotic Gene Expression in Chlamydomonas reinhardtii. G3 (Bethesda) 6:1541-8
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Lopez, David; Hamaji, Takashi; Kropat, Janette et al. (2015) Dynamic Changes in the Transcriptome and Methylome of Chlamydomonas reinhardtii throughout Its Life Cycle. Plant Physiol 169:2730-43
Zones, James Matt; Blaby, Ian K; Merchant, Sabeeha S et al. (2015) High-Resolution Profiling of a Synchronized Diurnal Transcriptome from Chlamydomonas reinhardtii Reveals Continuous Cell and Metabolic Differentiation. Plant Cell 27:2743-69
Blaby, Ian K; Blaby-Haas, Crysten E; Tourasse, Nicolas et al. (2014) The Chlamydomonas genome project: a decade on. Trends Plant Sci 19:672-80
Hong-Hermesdorf, Anne; Miethke, Marcus; Gallaher, Sean D et al. (2014) Subcellular metal imaging identifies dynamic sites of Cu accumulation in Chlamydomonas. Nat Chem Biol 10:1034-42

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