Assembly Overview

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.

Illumina

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.