Medicago Genome/Hapmap resources

Release policies:

Collaboration Portal

Medicago Hapmap
Medicago Genome

SNPs based on Mt3.5 genome assembly will be released in early 2012. Please contact us if you have any questions about the release schedule.

Deep 30 Medicago Accessions based on InStruct clustering and visualization of ancestral genome contribution. Accessions sorted according to geographic origin.

Click on chromosome image to enter the Medicago SNP Gbrowse and other viewers. Reference genome for variant calls was Mt3.0

Medicago Genome
	1	2	3	4	5	6	7	8	unanchored	total	*current*
BACs in Mt3.0: 3/15/2009	264	290	402	337	396	171	315	309	148	2632	3143
BACs in Mt3.5: 2/10/2010	267	304	391	380	413	170	337	276	146	2538	3143

Downloads

Germplasm
SNPs
Mt3.0
Mt3.5
Others

Request Germplasm Seeds

These files have been released to the web site on 12/09/2011. They contain corrected 'Nearest Gene Distance' values. The description of that column in SNP Data Description file has also been amended. Please note that this data is based on Mt3.0 reference genome. SNPs based on Mt3.5 genome assembly will be released in early 2012. Please contact us if you have any questions about the release schedule.

SNP Data Description

View SNPs on Gbrowse

The Medicago genome assembly version 3 was finalized in March 2009.

Medicago_3.0_all_sequences.fa.tar.gz: 8 pseudochromosome sequences, 148 unanchored BAC sequences PLUS the fpc256 sequence together with the pseudo golden path file.
Medicago_3.0_annotation.tar.gz: IMGAG gene predictions on the 8 pseudochromosome sequences plus the unanchored BACs in FASTA, TIGRXML and MIPS GFF format.
MT3_all_BACs.tar.gz: Sequences for all of the 2633 BACs that were used in the MT3 assemblies.
medicago_3.0_Simap_GOs.tbl: GOs annotaions on genecalls.
GeneMap_Mt30-Mt35_20100830.txt.gz File that maps equivalent genes between assemblies Mt3.0 and Mt3.5

Mt3.0 release Genome assembly tables Genome assembly browser CViT
Blast search Mt3.0 Statistics

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).

Data freeze: 12/31/2009; Assembly release: 02/15/2010; Annotation release: 08/25/2010

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

README
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

Mt3.5 release Genome assembly tables Genome assembly browser CViT
Blast search Mt3.5 Statistics

Download files for markers/BACs/BAC-ends/Fosmid etc ......

Mt_genetic_markers_Oct_2009.txt:A report on all markers: marker location, the associated BACs, primers/full squences.
Mt_BES_mth2.fas.gz: All BAC end sequences from the Hind III library.
Mt_BES_mte1.fas.gz: All BAC end sequences from the French Eco RI library.
Mt_BES_mth4.fas.gz: BAC ends from a small supplemental Hind III library.
Mt_BES_mth4_new.fas.gz: New BAC ends from a small supplemental Hind III library with large inserts (up to more than 200kb).

News

November 2010 Medicago HapMap SNP/indel calls for "Deep 30" available.
November 2010 New Mt3.5 genome assembly annotation available on-line.
July 2010 Medicago Hapmap project was highlighted at the International Legume Genetics and Genomics Congress in Asilomar, CA.
March 2010 First set of Medicago Hapmap SNP/Indel calls go live.
January 2010 Hapmap posters [1] [2] presented at Plant and Animal Genome Conference, January 2010.
September 2009 Mt3.0 genome assembly released.
June 2009 Medicago Hapmap announced at Model Legume Congress in Asilomar, CA.
March 2009 National Science Foundation funding for the Medicago Hapmap project is finalized.

Site hosted by: Nevin Young's Lab at University of Minnesota

Primary Collaborators: INRA - Montpellier ENSAT - Toulouse Noble Foundation Nuzhdin Lab at USC

Co-Principal Investigators: University of Minnesota N. Young, P. Tiffin, M. Sadowsky NCGR J. Mudge, G. May Boyce Thompson Institute M. Harrison Hamline University B. Martinez-Vaz