Sequencing Medicago truncatula Cultivar Jemalong A17 at the University of Oklahoma

The sequence of the Medicago truncatula genome has been published.
  • click here to go to a copy of the The Medicago truncatula Genome paper published in Nature December 22, 2011
  • click here to go to a copy of the supplementary data from the Medicago truncatula Genome paper.

Medicago truncatula is an annual relative of alfalfa (annual medic) but with a genome size of ~454 to 526 Mbp, is only half that of alfalfa. It has a diploid genome with 2n = 16 chromosomes and it's genome is ~4-times larger than that of Arabidopsis thaliana.
Clone Availability
  • BAC clones are being distributed for a nominal fee by the Clemson University Genomics Institute (CUGI)
    • The mth1 BACs are from the UCDavis partial HindIII library and the Clemson University Genomics Institute names them BAC Library MT_ABa rather than mth1 (followed by the 384-well, plate-row-column format, e.g. mth1-17n5). Therefore at the CUGI mth1-17n5 would be just 17n5 with the order entered from the MT_ABa page.
    • The mth2 BACs are from the UCDavis partial HindIII library and the Clemson University Genomics Institute names them BAC Library MT_ABb rather than mth2 (followed by the 384-well, plate-row-column format, e.g. mth2-14m14). Therefore at the CIGI, mth2-14m14 would be just 14m14 when entered from the MT_ABb page.


  • In December 2001 we begun receiving well characterized Medicago truncatula BACs from Douglas Cook and Dongjin Kim at the University of California - Davis. Our present plan is to sequence each of these BACs to working draft coverage, i.e. 4 to 5-fold BAC-based shotgun sequencing, this year. All of the data will be released into GenBank following the Bermuda Rules and links to this data are provided at http://www.genome.ou.edu/medicago_totals.html

  • http://www.genome.ou.edu/medicago_totals.html also contains a link (click on the Gbrowse hyperlink on the line containing the BAC of interest on that page) to view our Genome Browser database with preliminary annotation for the contigs greater than 2 kbp for each of the Medicago truncatula BACs.

Selected Medicago truncatula links.


Search the Medicago truncatula Genome sequence data

  • Search the results of blastn vs the GenBank dbest database with the weekly updated Medicago truncatula genome data using Key Words on the OU Server.
  • Enter your keyword here:

    Select your keyword here:


Obtaining the sequence data via ftp


Printrepeats output showing various new and interesting repeated sequences in the Medicago truncatula genome.


The Medicago Chloroplast

  • Our whole genome shotgun approach is allowing us to obtain the sequence of the Medicago truncatula chloroplast genome, since the total genomic DNA preparation not only contains the nuclear genome, but also a significant level of the chloroplast genome.
  • The DNA sequence of the Medicago truncatula chloroplast genome now has been closed to one contigous 124,039 bp circle. We have artificially cut the sequence at the histidine tRNA prior to the psbA gene. Linearizing at this position allows the Medicago chloroplast genomic sequence to be co-linear with the arabadopsis, tobacco and most other chloroplast genomes. The remaining gap is ~150 bp and in the rRNA gene region, and the slight size difference between the data reported in GenBank and this circular representation is due to padding characters added by the Phrap assembly program while aligning.

  • View the computer generated restriction enzyme digest map of the circularized Medicago chloroplast genome


    Web-Artemis Viewer:

  • We now have completed the semi-automated annotation of the Medicago truncatula chloroplast genome using Web-Artemis. You can view these results using the link below.
  • Please note: The Web-Artemis viewer may not work with the Netsccape browser, so please use the latest version of Internet Explorer.
  • Once the Web-Artemis window open, it may take a minute or two depending on your internet connection, click on the box containing: "medicago-chloroplast-04sep2001.fa.all-in-1" and enjoy.
  • Depending on how this is displayed in your window you may have to play with it to fit on your screen.
  • There are lots of features to view. For example, highlight a gene and then use the pull down menu under:
    View:Search Results: Selected Features blastp results
    to open a new window showing the BlastP search vs the nr protein database homology alignments.
  • Some features do not work as we've not yet implemented them. For example, to exit the Web-Artemis, you may have to exit Internet Explorer.

  • View the features in the Medicago chloroplast genome via Web-Artemis


Medicago truncatula Related Links:


Acknowledgments


Home Page


Bruce Roe, broe@ou.edu