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Prerelease of Medicago truncatula genome sequences
Version: 2.0
Data frozen: 06/15/2007
Release Date: 08/10/2007

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Data release Policy 

The Medicago Genome Sequence Consortium (MGSC) is pleased to release assembly Mt2.0. This assembly may be freely downloaded, used in analyses, and repackaged in databases with appropriate attribution and with the following conditions: 

** Users are free to use the data in scientific papers analyzing specific genes and genome regions, provided that the MGSC is properly acknowledged.

** The MGSC reserves the right to publish the initial large-scale analyses of the dataset, including large-scale characterization of regions of evolutionary interest and large-scale genomic assembly. Large-scale refers to regions 1 Mbp or more.

** Mt2.0 is incomplete and should be regarded as preliminary. Data characteristics and limitations are described in the Readme and Fact Sheet at http://medicago.org/genome/downloads/Mt2/
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Files included in this release

  1) README: This file. A brief description file on the release.
  2) Mt2.0_pgp.txt: Assembly Pseudo Golden Path.
  3) Mt2.0_pseudomolecule.tar.gz: FASTA format sequences of the pseudomolecules.
  4) 20080103_imgag_cdsMAPPED_NO_OVERLAP.fa: Coding sequences of MT2.0, including redundant ones but excluding overlapping.
  5) 20080103_imgag_proteinMAPPED_NO_OVERLAP.fa: Protein sequences of MT2.0, including redundant ones but excluding overlapping.
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Additional files available

	(6) medicago_chrX_20061010_NR.xml: Detailed Psuedomolecules annotation in TIGR XML format
	(7) Mt2.0_FrozenBAC.tar.gz: Frozen BAC sequences in FASTA format

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PGP(Pseudo Golden Path): describes the assembly of a chromosome. The structure:

	chromosome: is the chromosome to which the BAC relates.
	chromosome start coordinate: is the start absolute coordinate for a DNA sequence in the tiling path.
	chromosome stop coordinate: is the end absolute coordinate for a DNA sequence in the tiling path.
	ordinal: counts for the components that make up the chromosome. All components (sequence and gaps) are counted.
	type: the sequence status of a BAC. 'U' for phase1,'A' for phase2, 'F' for phase3, 'N' for gap.
	GenBank accession : is the accession number and sequence version for a BAC in GenBank.
	BAC start coordinate : the beginning of the BAC sequence that contributes to the chromosome.
	BAC stop coordinate : the end of the BAC sequence that contributes to the chromosome.
	orientation: the strand of the BAC. '+' for plus strand and '-' for minus strand.
	length: is the total DNA sequence length for a BAC.
	
	* 100 Ns were inserted between un-ordered sequence segment whithin a BAC. 
	* 5000 Ns were inserted to delimit phase1 BACs.
	* 50000 Ns were inserted for a clone in the tiling path file which has no DNA sequence yet; The type is 'clone' and the evidence of linkage between the adjacent contigs is 'yes'; 
	* 100000 Ns were inserted for a type-3 gap. The type is 'contig' and there is 'no' evidence of linkage. 
	* Two types of gaps could be concatenated, giving a gap size greater than 100,000.

	NOTE: The assembled psuedomolecule sequences contain redudant sequences, as the overlapping sequences between phase 1 BAC and other BACs were not removed. 

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About Medicago Genome sequencing project

	The Medicago truncatula sequencing project was initiated with a generous grant from Samuel Roberts Noble Foundation to the University of Oklahoma. Beginning in 2003 (and renewed in 2006), the National Science Foundation and the European Union's Sixth Framework Programme provided funding to complete sequencing of the remaining euchromatic genespace. Among the eight chromosomes in Medicago, six are being sequenced by NSF project "Sequencing the Gene Space of the Model Legume, Medicago Truncatula," and two are being sequenced by partners in Europe. Nevin Young (University of Minnesota), Bruce Roe (ACGT, University of Oklahoma; chromosomes 1, 4, 6, 8), and Chris Town (TIGR; chromosomes 2, 7) are principal investigators of the U.S. project. In Europe, collaborators include Giles Oldroyd (John Innes Center) coordinating sequencing of chromosome 3 at the Sanger Center, and Frederic Deballe (INRA-CNRS) coordinating sequencing of chromosome 5 at Genoscope. The genome annotation was carried out by the International Medicago Genome Annotation Group (IMGAG), which involves participants from TIGR, INRA-CNRS, MIPS, UMN, Ghent University and NCGR.

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Contact: 

Nevin Dale Young
Distinguished McKnight University Professor
Office: 320 Cargill Building for Microbial and Plant Genomics
Mail: 495 Borlaug Hall
University of Minnesota
St. Paul, Minnesota USA 55108
Voice: 612-625-2225 / Fax: 612-625-9728
Email: neviny@umn.edu
URL:  http://umn.edu/home/neviny