Sequencing Medicago truncatula Cultivar Jemalong A17 at the University of Oklahoma
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.
A pilot project to test the feasibility of a Whole Genome
Shotgun sequencing project in collaboration with Rick Dixon, Greg May,
Lloyd Sumner and Bob Gonzales at the Noble Foundation,
Ardmore, Oklahoma began in the Spring of 2001.
The initial goal of the Medicago truncatula genome
project is to generate approximately 1-fold whole genome shotgun sequence data
from a double-stranded pUC-based genomic library and obtain target
shotgun clones for additional primer walking-based sequencing after
analysis vs the ~100,000 Medicago truncatula ESTs and the genome
of Arabidopsis thaliana.
We now have been funded by the NSF to sequence Medicago truncatula
chromosomes 1, 4, 6 and 8 in a collaboration with
Nevin Young's group at
the University of Minnesota and
Chris Town's group at TIGR,
who are
sequencing chromosomes 2 and 7. Chromosome 3 is being sequenced at
Sanger/JIC and chromosome 5 is being sequenced at Genoscope/INRA as part
of the European Consortium.
In accord with the Bermuda Agreement and NHGRI policy, we
are releasing all our assembled genomic sequence data on our
ftp site
now that this sequencing project can be assembled
by Phrap
into contigs greater than 2 kb.
View the Phrap whole genome shotgun assembly statistics
The Medicago
truncatula Genome:a progress report as presented on January 11, 2004
at the Plant and Animal Genome Meeting in San Deigo, California.
Medicago truncatula Genome Informatics Workshop Conference Notes.
Medicago truncatula Genome Informatics Workshop
ASILOMAR, California
June 9 and 10, 2005
asilomar_workshop2005.pdf (93508 bytes)
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.
-
The National Academy of Sciences has published a report entitled:
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.
Obtaining the sequence data via ftp
All of our shotgun sequence data is available via ftp (see below) but at the present time, the various contigs are in "random" order and do not correspond to any specific relationship one to another.
Please be aware that the order and contig number will change with each new
release of data.
Caution: the data has been neither proof read nor edited and thus should be
considered preliminary raw sequence data.
Also, because the sequence assembly program, Phrap,
has the tendency to include inaccurate sequence reads on the ends of contigs, be
cautious when using sequences within 1-200 bases of the ends of individual contigs.
Please take this into account when using this data
If you have determined which contig is of interest to you using the
above Blast search capability on the OU Server, this contig(s) are in the
'medicago-2k.fa' file or the 'contigs-2k' directory on our ftp site.
If however, you determined which contig was of interest using the
'KeyWord Search' option, then the contig(s) of interest will be found
in the 'medicago_weekly-2k.fa' file or the 'contigs_weekly-2k' directory
- Obtaining the Medicago truncatula Whole Genome Shotgun Sequencing 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
Should you find this data useful and wish to reference it, please acknowledge
the Medicago truncatula Genome Sequencing Project at the Advanced
Center for Genome Technology of the University of Oklahoma, Norman, Oklahoma
and the Noble Foundation, Ardmore, Oklahoma.
Thanks,
Bruce A. Roe, Shaoping Lin, HongGui Jia and HongMin Wu at OU,
Nevin Young and Steven Cannon at the Universiy of Minnesota,
Chris Town at TIGG and
Rick Dixon, Greg May, Lloyd Sumner and Bob Gonzales at the Noble Foundation.
Bruce Roe, broe@ou.edu
Shaoping Lin,
shaoping@aardvark.ucs.ou.edu
Nevin Young, neviny@umn.edu
Steven Cannon, cann0010@umn.edu
Chris Town, cdtown@tigr.org
Rick Dixon, radixon@noble.org
Greg May, gdmay@noble.org
Lloyd Sumner, lwsumner@noble.org
Bob Gonzales,
ragonzales@noble.org
Bruce Roe, broe@ou.edu
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.
