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

模式植物拟南芥的基因组已经被注释，显示了近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，并得到了实验证据的支持，即它们与植物、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缘甘蓝属(甘蓝/花椰菜/球芽甘蓝家族)进行比较，发现了许多目前尚未注释为基因的序列保守区域。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到目前为止还没有被注释过程识别的基因。全长cDNA既为通过将其序列与基因组DNA比对而极大地改进基因结构注释提供了基础，也为通过表达和其他类型的分析来分析其功能提供了试剂。本研究的目标是为大约2,000个代表基因组中了解最少的基因的基因生成全长cDNA。我们将使用5和3个RACE来定义每个基因的精确结构，然后在适合研究社区功能研究的重组载体中生成蛋白质编码基因(ORF)的全长cDNA克隆。在项目开始的三个月内，我们将以每月约100个克隆的速度生成克隆和测序，目标是在项目期间产生2000个新的和以前未描述的克隆。克隆的序列将在生成时提交给GenBank，也可以从TIGR ftp站点获得。克隆本身将通过拟南芥生物资源中心(ABRC)免费提供给研究社区。该项目的细节将保持在项目特定的网络sitehttp://www.tigr.org/tdb/e2k1/ath1/2010_cDNAsAt科学水平上，该项目将通过增加拟南芥基因总数~10%来增强拟南芥基因组注释，并将是朝着完成第一个完全测序的植物基因组中所有基因的鉴定和验证迈出的重要一步。这些DNA将作为社区资源提供。在拟议的研究中纳入了一个课程开发部分，它将向高中科学教育工作者提供研究经验，他们将在该项目中工作，并使用项目材料开发新的课程模块，旨在向高中生提供接触植物基因组学基本概念的机会。

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.