Transcriptional profiling and annotation of the Chlamydomonas genome

衣藻基因组的转录谱和注释

• 批准号: 8017674
• 负责人: SABEEHA MERCHANT
• 金额: $ 30.8万
• 依托单位: UNIVERSITY OF CALIFORNIA LOS ANGELES
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-15 至 2015-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8017674
• 关键词: 3' Untranslated Regions; Address; Animal Model; Biology; Cell Wall; Cells; Chlamydomonas; Chlamydomonas reinhardtii; Chloroplasts; Chromosomes, Human, Pair 17; Cilia; Collecting Cell; Communities; Data; Data Analyses; Databases; Deposition; Development; Environment; Exons; Expressed Sequence Tags; Flagella; Gametogenesis; Gene Expression; Gene Expression Profile; Genes; Genetic; Genetic Transcription; Genome; Genomics; Genotype; Growth; Home environment; Human body; Imagery; Institutes; Introns; Investments; Joints; Letters; Maintenance; Messenger RNA; Metabolism; Metadata; Methodology; Modeling; Natural regeneration; Nematoda; Nuclear; Nutrient; Open Reading Frames; Organelles; Organism; Partial Pressure; Pattern; Photosynthesis; Physiological; Principal Investigator; Proteins; RNA; RNA Sequences; Reading; Regulatory Element; Research Infrastructure; Resources; Running; Sampling; Services; Structure; Technology; Temperature; Transcript; Untranslated Regions; Variant; base; ciliopathy; comparative; gene function; genome database; human disease; improved; light intensity; mutant; next generation; novel; research study; transcriptomics; zygote

DESCRIPTION (provided by applicant): 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.

描述（由申请人提供）：Chlamydomonas Reinhardtii是光合作用和睫状生物学中基本发现的模型生物。它的基因组是联合基因组研究所的五个旗舰基因组之一，这表明他们致力于维护数据库的基础设施完成和投资。我们将通过使用转录组数据来增加JGI工作的价值，该数据通过Lllumina平台上的RNA-Seq方法生成，a）得出更好的基因模型，b）识别在各种实验条件下识别差异表达的基因和替代转录物，并且c）推迟。每个基因组中每个基因的表达模式以及每个转录本的绝对丰度。尽管已经测序了> 300,000个EST，但〜16,000个基因模型中只有59％受EST覆盖范围的支持，只有21％的UTR信息具有5'和3'UTR信息。因此，许多基因模型，无论是计算上预测的还是基于同源的基因模型都是不正确的，或者最多是不完整的。通过RNA-Seq方法，我们获得了转录组的更大覆盖率，这可以显着提高注释的质量。在任何给定的条件下，都有四个数量级的转录物丰度范围，但是通过增加运行次数，我们可以采样甚至低丰度转录本。因此，为了增加转录组的覆盖范围，将从各种环境和生理条件下生长的细胞收集转录序列数据，包括宏观和微量营养素的变化，pH，温度，光强度，C02和02部分压力，以及02部分压力，以及02个部分压力，以及在不同的发育情况下（配子生成，合子，细胞壁和鞭毛再生）。每个样本将分别处理，以便我们可以比较每个样品内部和中间的特定RNA丰度，这将阐明与特定环境和发育条件相关的转录网络。主要序列数据将与NCBI SRA定期存放在相关的元数据中，并将派生的数据加载到UCLA维护的公共访问浏览器上，并定期上传到Chlamybase和JGI基因组浏览器以进行长期公共访问。 公共卫生相关性：衣原体是研究睫状生物学，叶绿体功能，代谢和性别分化及其相关人类疾病（例如纤毛病）的重要模型生物体。使用下一代测序技术，我们计划全面研究衣原体的转录格局，以定义不同样本中的基因模型和基因表达水平。