Medicago truncatula Genome Project

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RELEASE NOTES

This version is the most recent stable release of the medicago genome.

DOWNLOADS

Genome Assembly: Files containing all the Mt3.5v4 sequences alongwith all the pseudo-golden paths used to create the assemblies.

MedtrA17_3.5.assemblies.fasta FASTA formatted sequences of the 8 chromosomes, 146 unanchored BACs plus Illumina contigs that are not placed on the chromosomes
MedtrA17_3.5.assemblies.agp 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 Chr5 which were not in GenBank yet)
MT_all_BAC_ends.fa.tar.gz FASTA format sequences of Medicago BAC ends

Genome Annotation: Gene predictions in FASTA and MIPS GFF formats

Mt3.5v4_GenesProteinSeq_20110616.fa Mt3.5v3 Annotation Protein Fasta files
Mt3.5v4_GenesCDSSeq_20110616.fa Mt3.5v3 Annotation CDS Fasta files
Mt3.5v4_GenesTranscriptSeq_20110616.fa Mt3.5v3 Annotation Spliced and Unspliced Transcript Sequences Fasta files
Mt3.5v4_genes_20110616_MIPSGFF.gff MIPS GFF formatted file for GENES on Chr01 - Chr08 plus all extra BACs
Mt3.5v4_TEs_20110616_MIPSGFF.gff MIPS GFF formated file for TRANSPOSABLE ELEMENTS on Chr01 - Chr08 plus all extra BACs
Mt3.5_tRNA_20100723_MIPSGFF.gff MIPS GFF formated file for tRNA on Chr01 - Chr08 plus all extra BACs
Mt3.5v4IlluminaGenes_20110621.MIPSGFF.gff MIPS GFF formatted file for GENES on Illumina Contigs

>>> CLICK HERE TO VISIT THE FTP DOWNLOAD PAGE <<<

RELEASE NOTES

This version contains the dataset described in the medicago genome paper published in the journal Nature.

DOWNLOADS

Genome Assembly: Files containing all the Mt3.5v3 sequences alongwith all the pseudo-golden paths used to create the assemblies.

Mt3.5.1_pseudomolecules.tar.gz FASTA formatted sequences of the pseudomolecules and 146 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 Chr5 which were not in GenBank yet)
Mt_all_BAC_ends.fa.tar.gz FASTA format sequences of Medicago BAC ends

Genome Annotation: IMGAG gene predictions in FASTA, MIPS GFF and TIGRXML formats

Mt3.5_TIGRXMLs_20100825.tgz TIGRXML files of Chr01 - Chr08 plus all extra BACS
Mt3.5v3_annotation_files.tar.gz Mt3.5v3 Annotation Fasta files (Protein, CDS, Spliced and Unspliced transcript sequences
Mt3.5_genes_20100825_MIPSGFF.gff MIPS GFF formatted 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
Mt3.5_tRNA_20100723_MIPSGFF.gff MIPS GFF formated file for tRNA on Chr01 - Chr08 plus all extra BACs

>>> CLICK HERE TO VISIT THE FTP DOWNLOAD PAGE <<<

Version 3.0 was generated before the pseudomolecules were rebuilt, and should only be used for tracking purposes. This data has been deprecated. Use with caution.

RELEASE POLICY

The Medicago Genome Sequence Consortium (MGSC) is pleased to release assembly Mt3.0. 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 of size 1Mbp or more.
Mt3.0 is incomplete and should be regarded as preliminary. Data characteristics and limitations are described in the README and Medicago Fact Sheet

DOWNLOADS

Genome Assembly: Files containing all the Mt3.0 sequences (8 pseudomolecules and 148 unanchored BACs) alongwith all the pseudo-golden paths used to create the assemblies.

Mt3.0_pseudomolecules.tar.gz FASTA formatted sequences of the pseudomolecules and 148 unanchored BACs
Mt3.0_pgp_files.tar.gz Pseudo-golden path files describing the assembly of each chromosome

Genome Annotation: IMGAG gene predictions in FASTA, MIPS GFF and TIGRXML formats

Mt3.0_cds_20090702_NAMED.fa.tar.gz FASTA formatted coding sequences for IMGAG annotated genes
Mt3.0_proteins_20090702_NAMED.fa.tar.gz FASTA formatted protein sequences for IMGAG annotated genes
Mt3.0_20090702_MIPSGFF.gff Annotation in MIPS GFF format
MT3_TIGRXMLs_20091012.tgz Annotation in TIGRXML format

RELEASE VERSIONING

Please take note of the versioning system; it is VERY IMPORTANT

GENOME SEQUENCE

org M.m[.b]

Mt 3.0

Mt 3.5

Mt 3.5.1

org -> Organism code
  M -> Major IMGAG version
  m -> Minor IMGAG version
  b -> Build number

GENOME ANNOTATION

org M.m[vN]

Mt 3.5

Mt 3.5v2

Mt 3.5v3

org -> Organism code
  M -> Major IMGAG version
  m -> Minor IMGAG version
  b -> Annotation version number


NOTE: Any changes to genome sequence (addition, deletion, translocation) in version 3.5.1 will
      get a new build number (2, 3, 4 and so on). Please remember that all chromosomes
      (except Chr3) are at build number 1. Chromosome 3 is still the base build.

NOTE: Any subsequent changes to annotation (changes to gene boundaries, deflines and/or
      Gene<->TE classification, etc.) in Mt3.5v2 will get a  new annotation version
      (v3, v4 and so on).

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