Medicago truncatula Genome Sequencing Project Release version : Mt3.5.1 DATA FREEZE : 12/31/2009 RELEASE DATE : 02/15/2010 -------------------------------------------------------------------------------------------------------------------------- RELEASE POLICY This release is intended for use by the members of IMGAG and MGSC for the purposes of annotation and analysis -------------------------------------------------------------------------------------------------------------------------- INFORMATION REGARDING THIS RELEASE (1) Mt3.5 was put together by including all BACs newly sequenced and improved/updated, since Mt3.0. The pseudomolecules were reassembled on the basis of a reference Medicago truncatula A17 Optical Map (version 1). (2) Further minor updates were made to Mt3.5 to conform to the Optical Map, resulting in version Mt3.5.1. File names of modified assemblies and their corresponding AGP files have been renamed to incorporate the new version. (3) The assembly of Chromosome 3 has not changed since Mt3.5 -------------------------------------------------------------------------------------------------------------------------- FILES INCLUDED IN THIS RELEASE (1) Mt3.5.1_pseudomolecules.tar.gz : FASTA formatted sequences of the pseudomolecules and 146 unanchored BACs (2) Mt3.5.1_gb_files.tar.gz : Preliminary GenBank Accessioned Golden Path (AGP) files describing the assembly of each chromosome (3) Mt3.5.1_all_BACs.fa.tar.gz : FASTA format sequences for all of the 2533 BACs used in the assemblies (contains 8 BACs from Chromosome 5 which are not in GenBank yet) (4) Mt_all_BAC_ends.fa.tar.gz : FASTA format sequences of Medicago BAC ends (5) README : This file -------------------------------------------------------------------------------------------------------------------------- Structure of the AGP (Accessioned Golden Path) Official Specifications ------------------------ http://www.ncbi.nlm.nih.gov/projects/genome/assembly/agp/AGP_Specification.shtml ========================================================================================================================== Column Content Description ========================================================================================================================== 1 object chromosome to which the BAC relates -------------------------------------------------------------------------------------------------------------------------- 2 object_beg chromosomal start coordinate for a DNA sequence in the tiling path -------------------------------------------------------------------------------------------------------------------------- 3 object_end chromosomal end coordinate for a DNA sequence in the tiling path -------------------------------------------------------------------------------------------------------------------------- 4 part_number counts for the components that make up the chromosome. All components (sequence and gaps) are counted -------------------------------------------------------------------------------------------------------------------------- 5 component_type sequence status of a BAC 'D' for draft HTG (phase1 or phase2) 'F' for finished HTG (phase3) 'N' for gap -------------------------------------------------------------------------------------------------------------------------- 6a component_id GenBank accession number and sequence version for a BAC if component_type is equal to 'D' or 'F' 6b gap_length gap size if component_type is equal to 'N' -------------------------------------------------------------------------------------------------------------------------- 7a component_beg start coordinate of the BAC sequence that contributes to the chromosome 7b gap_type type of the gap. 'clone' for gap inserted between non-overlapping clones 'contig' for gap between contigs -------------------------------------------------------------------------------------------------------------------------- 8a component_end end coordinate of the BAC sequence that contributes to the chromosome 8b linkage evidence of linkage between adjacent lines. Values: 'yes' or 'no' -------------------------------------------------------------------------------------------------------------------------- 9a orientation the strand of the BAC '+' for plus strand '-' for minus strand 9b filler if column 5 is equal to 'N', this column should be empty ========================================================================================================================== Gap Sizing Rules: * 100 Ns were inserted between un-ordered sequence segments within a BAC * 5000 Ns were inserted to delimit BACs with high-quality overlaps which aren't towards the ends * 50000 Ns were inserted for a clone in the tiling path which has no DNA sequence yet; The component_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 can be concatenated thus resulting in gap sizes greater than 100,000 NOTE: The assembled psuedomolecule sequences contain redudant sequences, as the overlapping sequences between phase 1 BACs and other BACs were not removed. -------------------------------------------------------------------------------------------------------------------------- ABOUT THE 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 (JCVI/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 JCVI/TIGR, INRA-CNRS, MIPS, UMN, Ghent University and NCGR. -------------------------------------------------------------------------------------------------------------------------- If you have any questions, please contact: Plant Genomics Group J. Craig Venter Institute 9704 Medical Center Drive Rockville, MD 20850 USA email: mtruncatula at jcvi dot org web : http://www.jcvi.org/medicago