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

University Of Minnesota-Twin Cities, Minneapolis MN

Investigators

Abstract

Nevin D. Young (P.I.) University of Minnesota Bruce A. Roe (Co-P.I.) University of Oklahoma Chris 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 outcomes To 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.