Completing the Sequence of Medicago truncatula's Gene-Rich Euchromatin

内文·D Young（P.I.）明尼苏达大学Bruce A. Roe（Co-P.I.）俄克拉荷马大学Chris D.镇（Co-P.I.）基因组研究所（TIGR）的蒺藜苜蓿是豆科植物基因组学的典范，目前是国际基因组测序计划的目标。Medicago的常染色质序列已经完成了一半以上，为发现植物-微生物共生和其他重要植物过程所必需的基因提供了资源。毫不奇怪，苜蓿序列在其他植物基因组序列的组装中也被证明是至关重要的，包括白杨。很快，苜蓿将在大豆基因组和其他豆类作物基因组的组装中发挥同样重要的作用。在测序开始之前，有说服力的细胞遗传学证据表明苜蓿基因组被组织成不同的富含基因的常染色质和单独的富含重复序列的近着丝粒异染色质。这意味着苜蓿“基因空间”可以以高效的方式进行测序，这一预测得到了目前测序工作的证实，其中175 Mbp（约占总基因组的35%）已经发现了超过65%的苜蓿基因。由于测序使用了基因组DNA的大插入亚克隆，因此保留了有关基因组背景的有价值信息，从而能够进行强大的比较基因组分析。 到2006年9月，将完成大约2亿个碱基对（Mbp）的苜蓿基因组序列。但此时只有75%的常染色质完成 另外还需要80 Mbp来竞争基因空间;其中60 Mbp将由本项目进行。豆类研究界，从育种家到基因组学家，都将受益于获得完整的Medicahgo基因空间序列。Medicago为翻译基因组学和候选基因的发现，与拟南芥、莲花和杨树的进化比较，以及其他植物基因组序列的组装提供了极好的参考。该项目将通过一个面向两所四年制大学本科生和教师的创新项目，将基因组学知识扩展到更广泛的教育界。位于俄克拉荷马州的主要由非洲裔美国人组成的兰斯顿学院和位于明尼苏达州的四年制文科院校麦卡莱斯特大学的教师们已经同意参加M。truncatula测序工作。来自这些机构的六到八名学生，加上他们的两名教授，将在夏季在参与测序项目的实验室工作，最终在TIGR进行为期多日的实地考察。获得项目成果为了能够有效地获得基因组序列和序列组装，所有序列数据将立即发布到GenBank（http：//www.ncbi.nlm.nih.gov/Genbank/）。已经由一个国际工作组协调的自动基因组注释将得到扩大。有关测序项目的信息将通过一个综合门户网站（www.medicago.org/genome）轻松访问，包括与负责基础数据的中心和豆类信息系统（LIS）的直观链接。该门户网站将收集、组织和储存序列数据，并提供对所有基本数据集的有效公共访问，允许灵活的基于网络的查询和可视化工具用于映射、组装和序列。

Nevin D. Young (P.I.) University of MinnesotaBruce A. Roe (Co-P.I.) University of OklahomaChris D. Town (Co-P.I.) The Institute for Genomic Research (TIGR)Medicago truncatula, a model for legume genomics, is currently the target of an international genome sequencing initiative. More than half of Medicago's euchromatin sequence has already been completed, providing a resource for the discovery of genes essential for plant-microbe symbiosis and other important plant processes. Not surprisingly, the Medicago sequence is also proving crucial in the assembly of other plant genome sequences, including poplar. Soon, Medicago will play an equally important role in the assembly of the soybean genome and those of other crop legumes. Prior to the start of sequencing, persuasive cytogenetic evidence demonstrated that the Medicago genome is organized into distinct gene-rich euchromatin and separate repeat-rich pericentromeric heterochromatin. This implied that the Medicago "gene-space" could be sequenced in a highly efficient manner, a prediction confirmed by the current sequencing effort where 175 Mbp (approximately 35% of the total genome) has uncovered more than 65% of Medicago's genes. Because sequencing has used large-insert subclones of genomic DNA, valuable information about genomic context is retained, enabling powerful comparative genomic analyses. About 200 million base pairs (Mbp) of the Medicago genome sequence will be completed by September 2006. but only 75% of the euchromatin will be complete at this point. An additional 80 Mbp will be needed to compete the gene space; 60 Mbp of this total will be carried out by this project.The legume research community, all the way from breeders to genomicists, will benefit from access to a complete Medicahgo gene space sequence. Medicago provides an excellent reference for translational genomics and candidate gene discovery, evolutionary comparisons with Arabidopsis, Lotus, and Populus, and assembly of other plant genome sequences.The project will extend genomics knowledge to the broader educational community through an innovative program for undergraduates and faculty from two 4-year colleges. Faculty at Langston College, a primarily African-American college in Oklahoma, and Macalester University, a 4-year liberal arts institution in Minnesota, have agreed to participate in the M. truncatula sequencing effort. Six to eight students from these institutions, plus two of their professors, will work in participating laboratories during the summer on the sequencing project, culminating in a multi-day field trip to TIGR.Access to project outcomesTo enable effective access to the genome sequence and sequence assemblies, all sequence data will be released immediately to GenBank (http://www.ncbi.nlm.nih.gov/Genbank/). Automated genome annotation, already coordinated by an international working group, will be expanded. Information about the sequencing project will be easily accessible through an integrated portal (www.medicago.org/genome), including intuitive links to the centers responsible for underlying data and with the Legume Information System (LIS). The portal will collect, organize, and warehouse sequence data and provide efficient public access to all basic data sets, allowing flexible web-based querying and visualization tools for map, assembly, and sequence.