Arabidopsis 2010: Large Scale Analysis of Novel Arabidopsis Genes Predicted by Comparative Genomics

拟南芥 2010：通过比较基因组学预测的新拟南芥基因的大规模分析

• 批准号: 0312656
• 负责人: Christopher Town
• 金额: --
• 依托单位: Institute for Genomic Research
• 依托单位国家: 美国
• 项目类别: Continuing grant
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-09-01 至 2006-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0312656&HistoricalAwards=false
• 关键词: Arabidopsis; 2010; Large; Scale; Analysis

The genome of the model plant Arabidopsis thaliana has been annotated to show the presence ofclose to 30,000 genes. Many of these genes are both predicted by computer programs andsupported by experimental evidence ' their similarity to characterized genes from plants, animalsand microbes. However, 15-20 % of the gene annotations are based only on computer evidence.In addition, comparison of the Arabidopsis genome sequence with its close relative Brassicaoleracea (the cabbage/cauliflower/Brussels sprouts family) reveals many regions of sequenceconservation that are not at present annotated as genes. Preliminary experimental analysis ofsome of these regions indicates that a significant fraction do encode genes that have so far beenunrecognized by the annotation process. Full-length cDNAs provide both the basis for greatlyimproved gene structure annotation by alignment of their sequences with genomic DNA, andalso the reagents with which to analyze their function by expression and other kinds of analysis.The objective of this research is to generate full-length cDNAs for approximately 2,000 of thesegenes that represent the least well-understood genes in the genome. We will use 5 and 3 RACEto define the precise structure of each gene and then generate full-length cDNA clones forprotein-coding genes (ORFs) in a recombination vector suitable for functional studies by theresearch community.We will generate clones and sequence at a rate of approximately 100 clones per month withinthree months of the start of the project with a goal of producing 2,000 novel and previouslyuncharacterized clones over the period of the project.Sequences of the clones will be submitted to GenBank as they are generated and will also beavailable from the TIGR ftp site. The clones themselves will be made freely available to theresearch community through the Arabidopsis Biological Resource Center (ABRC). Details of theproject will be maintained at a project-specific web sitehttp://www.tigr.org/tdb/e2k1/ath1/2010_cDNAsAt the scientific level, this project will enhance the Arabidopsis genome annotation by increasingthe total gene count in Arabidopsis by ~10% and will be a major step towards completing theidentification and validation of all the genes in the first fully sequenced plant genomeArabidopsis thaliana. The cDNAs will be available as community resources. Integrated into theproposed research is a curriculum development component that will provide research experienceto high school science educators in which they will work on the project and use project materialsfor the development of new curricular modules designed to provide exposure to fundamentalconcepts in plant genomics to high school students.

模式植物拟南芥的基因组已经被注释，显示出接近30,000个基因的存在。这些基因中的许多都是由计算机程序预测的，并得到实验证据的支持，它们与植物、动物和微生物的特征基因相似。然而，15- 20%的基因注释仅基于计算机证据。此外，将拟南芥基因组序列与其近亲甘蓝（卷心菜/花椰菜/布鲁塞尔芽甘蓝家族）进行比较，揭示了许多目前未被注释为基因的序列同源区域。对其中一些区域的初步实验分析表明，有相当一部分确实编码了迄今为止未被注释过程识别的基因。全长cDNA为基因结构注释提供了基础，通过将它们的序列与基因组DNA进行比对，也为通过表达和其他分析来分析它们的功能提供了试剂。本研究的目标是产生大约2,000个基因的全长cDNA，这些基因代表了基因组中最不清楚的基因。我们将使用5和3 RACE来确定每个基因的精确结构，然后在适合研究界进行功能研究的重组载体中产生蛋白编码基因（ORF）的全长cDNA克隆。我们将在项目开始后的三个月内以每月约100个克隆的速度产生克隆和测序，目标是产生2，这些克隆的序列将被提交到GenBank，同时也可以从TIGR的ftp站点上获得。克隆本身将通过拟南芥生物资源中心（ABRC）免费提供给研究团体。该项目的详细信息将在一个项目专用网站http：//www.example.com上进行维护www.tigr.org/tdb/e2k1/ath1/2010_cDNAsAt科学水平上讲，该项目将通过增加拟南芥中的总基因数来增强拟南芥基因组注释，并将是完成第一个完全测序的植物基因组拟南芥中所有基因的鉴定和验证的重要一步。cDNA将作为社区资源提供。整合到拟议的研究是一个课程开发的组成部分，将提供研究经验，高中科学教育工作者，他们将在该项目上工作，并使用项目材料，为新的课程模块的发展，旨在提供接触到植物基因组学的基本概念，以高中学生。