Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

Sequencing The Gene Space Of The Model Legume, Medicago truncatula

NEVIN D YOUNG¹ , BRUCE A ROE² , CHRISTOPHER D TOWN³ , STEVEN B CANNON¹ , JOANN MUDGE¹ , SHELLEY WANG¹ , ROXANNE DENNY¹ , ERNIE RETZEL⁴

¹  Dept of Plant Pathology, University of Minnesota, 495 Borlaug Hall, St Paul, MN 55108 USA

²  Advanced Center for Genome Technology (ACGT), Stephenson Research & Technology Center, Norman, OK 73019 USA

³  The Institute for Genomic Research (TIGR), 9712 Medical Center Drive, Rockville, MD 20850 USA

⁴  Center for Computational Biology and Bioinformatics, University of Minnesota, MMC 43, 420 Delaware Street SE, Minneapolis, MN 55455 USA

Among legumes, Medicago truncatula is a model for genomic research because of its compact genome, simple genetics, short generation time, reasonable transformation, and well-characterized symbioses with rhizobia and mycorrhizae. The M. truncatula genome is highly syntenic with other cool season legumes and moderately syntenic with soybean. A 12X physical map, ~155,000 BAC-ends, and ~190,000 ESTs are all available for M. truncatula. With NSF funding, we are collaborating with scientists in the E.U. to sequence the gene space of M. truncatula, with the completion of 200 Mbp projected by December 2006. Cytogenetic evidence and available sequence data demonstrate that the genome is organized into distinct gene-rich euchromatin and separate pericentromeric heterochromatin, so most of the gene space can be sequenced in a highly efficient manner. The eventual result of our BAC-by-BAC sequencing effort will be pseudomolecules representing the 16 euchromatic chromosome arms of M. truncatula. A centralized website (www.medicago.org/genome) acts as a portal for the sequencing project with additional informatic resources found at the websites of the participating sequencing centers. As of September 2004, 102 Mbp of non-redundant sequence was sequenced or in progress, with 73 Mbp anchored to the genetic map and 51 Mbp at Phase 3 (ie, finished). Nearly 7900 gene models are predicted within the finished BAC clones, and the finished BACs match between 17% (stringent) and 21% (lenient) of all M. truncatula TC’s. These results suggest that the entire gene space is between 240 and 300 Mbp in size, with a total of 37,000 - 46,000 genes.