INSIGHTS ABOUT THE Medicago truncatula GENOME BASED ON EXTENSIVE BAC SEQUENCING

¹ The Advanced Center for Genome Technology (ACGT), Dept. of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, OK 73019

² Dept. of Plant Pathology, University of California-Davis, 1 Shields Avenue, Davis, CA 95616

³ Dept of Plant Pathology, University of Minnesota, 495 Borlaug Hall, Saint Paul, MN 55108

Medicago truncatula is widely considered a model legume, with a genome of ~470 Mbp, simple genetics, short generation time, reasonable transformation, and excellent collections of mutants and ecotypes. Recent work resulted in a ~12X BAC physical map and ~180,000 ESTs representing most tissues, stages, and growth conditions. We have begun sequencing the gene-space of M. truncatula. As of October, 2003, BACs representing ~75 Mbp of genome sequence have been completed or in progress at ACGT. Previously, 25,000 whole genome shotgun (WGS) reads were generated, assembling the chloroplast genome, identifying 1,000 with similarity to M. truncatula ESTs, and discovering several M. truncatula-specific repeat families. Five pericentromeric repeat families comprised >10% of the genome, confirming cytogenic data indicating the genome is organized into separate gene-rich euchromatic and pericentromeric repeat-rich regions. Based on the ~75 Mbp to date, there is one gene per 6-7 kbp — slightly less dense than Arabidopsis. Approximately 63% of predicted genes show strong similarity to an EST. The G-C content is 34%, average gene size ~4,000 bp, average exon ~800 bp, and average intron ~250 bp. Blast identifies 1 EST per 10 kbp, consistent with other species where 60–65% of predicated genes have a match. With NSF funding, we are collaborating with partners in Europe to sequence ~200 Mbp of the M. truncatula genome in a BAC-by-BAC approach, targeting the euchromatin. We project ~33,000 genes will be discovered, in line with the number in Arabidopsis. Sequence data will be freely and rapidly available through international databases. Keywords: Medicago truncatula; Legumes; Genome Sequencing; Euchromatin