About the release:
Data freeze: 12/31/2009 Assembly release date: 02/10/2010 Annotation release date: 05/27/2010
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).
JCVI release site : http://medicago.jcvi.org/cgi-bin/medicago/download.cgi
Data Release Policy:
- Mt3.5.1_pseudomolecules.tar.gz FASTA formatted sequences of the pseudomolecules and 145 unanchored BACs
- Mt3.5.1_gb_files.tar.gz Preliminary GenBank Accessioned Golden Path (AGP) files describing the assembly of each chromosome
- 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 Chromosome5 which are not in GenBank yet)
- Mt_all_BAC_ends.fa.tar.gz FASTA format sequences of Medicago BAC ends
Information regarding all the files from this release
- Mt3.5v3_annotation_files.tar.gz Protein, CDS, Unspliced transcript, Spliced transcript sequences for all gene calls.
- Mt3.5_TIGRXMLs_20100825.tgz TIGRXML files of Chr01 - Chr08 plus all extra BACS
- Mt3.5_genes_20100825_MIPSGFF.gff MIPS GFF formated file for GENES on Chr01 - Chr08 plus all extra BACs
- Mt3.5_transposons_20100825_MIPSGFF.gff MIPS GFF formated file for TRANSPOSABLE ELEMENTS on Chr01 - Chr08 plus all extra BACs
- GeneMap_Mt30-Mt35_20100830.txt.gz File that maps equivalent genes between assemblies Mt3.0 and Mt3.5
- Mt3.5_name_mapping_Genes_20100825.txt MT3.5 gene names mapping file (mapping old/EUGENE identifiers to new/IMGAG identifiers)
- Mt3.5_name_mapping_TEs_20100825.txt MT3.5 transposable element names mapping file (mapping old/EUGENE identifiers to new/IMGAG identifiers)
- README_Mt3.5v3_RELEASE Guidelines for use of unique gene id's for Medicago MT3.5 release
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 (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.