A Microarray for Measuring Medicago Expression

Medicago truncatula is an ideal model organism for legumes.  A simple diploid genome, rapid growth, and prolific seed production continue to make M truncatula the choice for basic and complex legume studies. Recently, the Medicago truncatula Sequencing Consortium, an international collaboration of Medicago researchers, released Mt4, the latest version of the Medicago truncatula genome. Mt4 represents the most comprehensive assembly of Medicago to date built de novo from a whole genome shotgun assembly. In addition to an updated genome assembly, transcript resolution  improved with increased transcript placement on the genome. The updated M truncatula genome provided an opportunity to develop a microarray to capture updates made by the consortium. In addition to designing the array against the reference cultivar A17, probes for an alternative cultivar, R108, were also included. Moreover, a closely related legume, Medicago sativa (alfalfa), is represented on the high density array also. The presence of polyploid alfalfa as part of the array design is integral to facilitate research of this extremely important forage crop.   This updated microarray will have probes for all 3 organisms which, in addition to surveying the latest transcriptome content, will facilitate cross-species transcriptome analysis as well as assist in de novo transcript detection for lesser annotated genomes. Each organism has roughly 60k gene models represented in this microarray in addition to a variety of unmapped and novel sequences that have yet to be mapped to the genome. Consequently the array is an optimum tool to further characterize Medicago truncatula and sativa transcriptomes.