Assembly Method

The much improved version of Medicago truncatula genome assembly (Mt4.0) was derived via de novo whole genome shotgun assembly by ALLPATHS-LG using mostly Illumina and 454 reads and annotation (Mt4.0v1). The ALLPATHS scaffolds were anchored onto the 8 linkage groups on the basis of alignments to both the optical map (OM) and genetic map derived from genotyping-by-sequencing (GBS) data. High quality contiguous BAC sequences were patched into the new Mt4.0 pseudomolecules to close gaps and reduce polymorphisms between the assembly versions, where possible.