Consortium for Maize Genomics

玉米既是植物研究的经典遗传模型，又是一种重要的经济作物。获得玉米的基因序列将对玉米遗传和作物改良产生根本性的影响。然而，玉米基因组是庞大而复杂的，由包含基因岛的高度重复的DNA组成的海洋。目前的估计表明，基因岛只占基因组的15%-20%。因此，仅对基因岛进行选择性测序将是对整个基因组进行测序的一种快速且具有成本效益的替代方案。该项目的总体目标是开发和评估高通量和健壮的策略来分离和测序玉米基因。将测试两种前景看好的方法。第一种被称为“甲基化过滤”，是基于这样的发现：高度重复的DNA被修饰(甲基化)，而基因基本上没有这种修饰。第二种被称为“高Cot选择”，它利用基因序列相对较低的丰度，这些基因序列在基因组中只有少量的拷贝。每种方法都会产生基因高度浓缩的基因组的一小部分。这些DNA片段的文库将被测序，这些序列将被组装和注释，以给出玉米基因的序列和组织的第一张图片。所有序列信息将立即发布到GenBank中，项目数据分析将通过基于网络的资源提供。该项目的成果将为研究界提供强大的玉米遗传学、生物学和育种资源。他们还将帮助确定尝试大规模玉米基因测序的最佳战略。交付内容：玉米图书馆有关图书馆的信息，请联系丹福斯中心的Karel Schubert(www.danforcenter.org)。联系AGI(www.genome.arizona.edu)的Rod Wing博士，获取来自玉米甲基化过滤和高cot文库的克隆。玉米测序结果：序列读数将提交给GenBank的HTGS部门，跟踪文件将每周提交给NCBI跟踪数据库。在向NCBI提交序列数据和跟踪文件的同时，可以从Donald Danforth植物科学中心玉米网站访问，供更广泛的玉米研究社区使用。生物信息学：至少每三个月发布一次序列组装，目标是每月更新一次。组装后的序列将从TIGR网站上获得。

Maize is both a classical genetic model for plant research and an economically important crop. Having a sequence of the genes of maize will have a fundamental impact on maize genetics and crop improvement. However, the maize genome is large and complex, comprising a sea of highly repetitive DNA containing islands of genes. Current estimates indicate that the gene islands only make up 15-20% of the genome. Selective sequencing of just the gene islands would thus be a rapid and cost-effective alternative to sequencing the whole genome. The overall goal of this project is to develop and evaluate high-throughput and robust strategies to isolate and sequence maize genes. Two promising approaches will be tested. The first, termed "methylation-filtering", is based on the finding that the highly repetitive DNA is modified (methylated) while the genes are largely free of such modification. The second, termed "high Cot selection", exploits the relatively low abundance of the gene sequences, which are present in a small number of copies in the genome. Each method yields a fraction of the genome highly enriched for the genes. Libraries of these DNA fragments will be sequenced and the sequences assembled and annotated to give a first picture of the sequence and organization of maize genes. All sequence information will be released immediately into GenBank and project data analyses will be available through web-based resources. The outcomes of this project will provide the research community with a powerful resource for maize genetics, biology, and breeding. They will also facilitate determination of the best strategy for attempting large-scale sequencing of maize genes.Deliverables:Maize LibrariesContact Karel Schubert at the Danforth Center (www.danforthcenter.org) for information on the libraries. Contact Dr. Rod Wing at AGI (www.genome.arizona.edu) for access to the clones from the methylation filtered and high CoT libraries of maize.Maize Sequencing Results:Sequence reads will be submitted to the HTGS division of GenBank and the trace files submitted to the NCBI trace database on a weekly basis. Concomitant with submission to NCBI both the sequence data and trace files will accessible from the Donald Danforth Plant Science Center maize website for use by the broader Maize research community.Bioinformatics:At a minimum, assemblies of the sequence will be released every three months, with the goal of providing monthly updates. Assembled sequences will be available from the TIGR website.