The Archives data are based on Mtv3.5 release.

BAC based

Fluorescence in situ hybridization (FISH) of the pachytene chromosomes demonstrated that the Mt genome is organized into predominantly euchromatic chromosome arms with the centromeric and pericentromeric regions constituted by heterochromatin. BAC-by-BAC sequencing of the euchromatin was conducted by extending out from gene-rich seed clones using a combination of BAC-end sequence overlaps (187,000 BES reads) and a high density fingerprint map (42,000 BAC clones). The resulting assembly was impoved greatly based on a high quality optical map, used to order and orient the sequence contigs.


As part of the HapMap project, whole genome shotgun sequence of M. truncatula (cultivar A17) was generated using Illumina technology (Illumina, San Diego). Approximately 2.5Gb of 2 x 54bp and 22.4Gb of 2 x 76bp paired end (375bp insert) including 2.1Gb of 36bp reads from a 5kb mate-pair library generated. This sequence set was assembled using CLCbio and resulting contigs >=500bp were retained.

IMGAG Annotation Pipeline

The International Medicago Genome Annotation Group (IMGAG) was established to coordinate the generation of a reference genome annotation for the model legume Medicago truncatula. Under the supervision of the project Steering Committee, the aim of IMGAG is to provide high quality automated gene prediction and annotation for all finished sequences generated by the Medicago genome sequencing project.

Illumina Pipeline

As part of the Annotation project, the assembled Illumina contigs were annotated in-house, by the JCVI Plant Genomics group. As more sequence data becomes available, the contig assembly will be improved and anchored onto the pseudomolecules, subsequently transferring the annotation as well.