Transcriptional profiling and annotation of the Chlamydomonas genome

衣藻基因组的转录谱和注释

基本信息

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
项目类别：
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&apos 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

项目摘要

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）：莱茵衣藻是用于光合作用和纤毛生物学基础发现的模式生物。它的基因组是联合基因组研究所的五个旗舰基因组之一，表明他们致力于完成和投资维护数据库的基础设施。我们将通过使用 lllumina 平台上的 RNA-seq 方法生成的转录组数据为 JGI 工作增加价值，a) 导出更好的基因模型，b) 识别不同实验条件下差异表达的基因和替代转录形式，c) 推断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。尽管超过 300,000 个 EST 已被测序，但约 16,000 个基因模型中只有 59% 得到 EST 覆盖率的支持，并且只有 21% 同时具有 5' 和 3' UTR 信息。因此，许多基因模型，无论是计算预测的还是基于同源性的，都是不正确的或充其量是不完整的。通过 RNA-seq 方法，我们获得了更大的转录组覆盖范围，这可以显着提高注释的质量。在任何给定条件下，转录本丰度存在四个数量级的范围，但通过增加运行次数，我们甚至可以对低丰度转录本进行采样。因此，为了增加转录组的覆盖范围，将从在各种环境和生理条件下生长的细胞收集转录序列数据，包括常量和微量营养素、pH、温度、光强度、CO 2 和O 2 分压的变化，以及在不同的发育情况下（配子发生、合子、细胞壁和鞭毛再生）。每个样本将被单独处理，以便我们可以比较每个样本内部和样本之间的特定 RNA 丰度，这将阐明与特定环境和发育条件相关的转录网络。初级序列数据将与相关元数据定期存放在 NCBI SRA，衍生数据将加载到 UCLA 维护的可公开访问的浏览器上，并定期上传到 Chlamybase 和 JGI 基因组浏览器以供长期公众访问。公共卫生相关性：衣藻是研究纤毛生物学、叶绿体功能、新陈代谢和性分化及其相关人类疾病（如纤毛病）的重要模式生物。我们计划使用下一代测序技术全面研究衣藻的转录景观，以便定义不同样本的基因模型和基因表达水平。