About Medicago Truncatula
Motivated initially by the needs to understand the molecular basis of symbiotic nitrogen fixation, researchers selected the legume Medicago truncatula as a model system for legume biology.
(i) M. truncatula is part of the Galegoid phylum and is therefore phylogenetically related to the most importantlegume crops, pea, faba bean, chickpea, lentils, alfalfa and clover; this genetic proximity provides the potential to easily transfer information on the genome structure of the model legume to the legume crops.
(ii) M.truncatula has a simple diploid genome(2*8 chromosomes) and its feature like self-fertile and relatively small size genome, greatly facilitating genetic analysis.

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About our database MtED
MtED is a database which contains expression data of model legume Medicago truncatula through The Affymetrix GeneChip® Medicago Genome Array,built by PHP and MySQL under a Linux Apache Server. Medicago Genome Array was designed specifically to monitor gene expression in Medicago truncatula, Medicago sativa, and additionally the symbiotic organism Sinorhizobium meliloti. Sequence information for this array was selected from diverse data sources including the TIGR M. truncatula gene index (MtGI Release 8.0), gene predictions from IMGAG, gene predictions for the S. meliloti genome and M. sativa EST information released by TIGR. The array contains over 32,167 M. truncatula EST/mRNA-based and chloroplast gene-based probe sets, as well as 18,733 M. truncatula IMGAG and phase 2/3 BAC prediction-based probe sets, which are believed to cover the transcribed part of Medicago truncatula genome.
Our Experiment
We use Medicago truncatula genotype Jemalong line A17 in this work. We place the dried seeds (provided by Medicago truncatula Biological Resource Center in France) of M.truncatula A17 in concentrated sulfate acid for about 15min for scarified purpose and help easy to germination. The scarified seeds were rinsed with distilled water for 6 times and then transferred into Petri dishes (diameter 15cm) on filter paper soaked with 5ml sterile deionized water in a dark fridge for 2 days and then transfer to room temperature dark environment for germination for another 2 days. The young seedlings were then transferred to Petri dishes (diameter 15cm) on filter paper soaked with 5ml 180mM of sodium chloride for stress treatment. Each dish has 100 seedlings. The young seedlings were grown in darkness until their roots were collected at indicated time points and frozen in liquid nitrogen immediately for further analysis.
We collect roots at 0 hour,6 hour,24 hour,48 hour after salt stress for further microarray experiment,each time point with 3 biological replicates.
Microarray data analysis procedure
We use affylmGUI package in R and BioConductor environment for microarray data analysis. There is some step by step tutorials (with screenshots) in affylmGUI's site about how to analysis microarray data.
Cite MtED
Li D, Su Z, Dong J, Wang T. An expression database for roots of the model legume Medicago truncatula under salt stress. BMC Genomics. 2009 Nov 11;10(1):517. [PubMed]
Citation of MtED will be greatly appreciated.
User Guide
An user guide of our database is now available as a PDF file.
External transcriptome resources
Medicago truncatula Gene Expression Atlas Version 2 (MtGEA V2) is a comprehensive platform contains expression profile of all major organs and under many treantments of Medicago truncatula.
Currently used data sources
  1. Consensus sequences of Medicago truncatula probe sets -- Affymetrix
  2. Tentative Consensus sequences (TCs) of Medicago truncatula (Release 9.0) -- DFCI - Medicago Gene Index
  3. Protein sequences of Medicago truncatula (Mt3.0 release) -- Medicago Genome Sequence Consortium (MGSC)
  4. Genome sequences of Medicago truncatula (Mt3.0 release) -- Medicago Genome Sequence Consortium (MGSC)
  5. Protein sequences of Arabidopsis thaliana (TAIR9_genome_release) -- TAIR (The Arabidopsis Information Resource)
Other tools and data sources
  1. Short Time-series Expression Miner (STEM) -- for clustering, comparing, and visualizing short time series gene expression data from microarray experiments.
  2. BLAST like alignment tool (BLAT) -- for mapping probe sets to genome.
  3. GeneBins -- a database for classifying gene expression data Application to plant genome arrays.
  4. Open Flash Chart -- an open source software can generate very nice graph for many use.
  5. Medicago truncatula 3.0 assembly release -- 3rd release of Medicago truncatula Genome by Medicago Genome Sequence Consortium (MGSC).
  6. Medicago truncatula transcription factors -- a database collecting 1022 predicted transcription factors (TFs) from barrel medic transcripts at PlantTFDB.
  7. Pathway information of Medicago truncatula (barrel medic) (EST) at KEGG -- KEGG FTP Repository.
News
  1. Apr/17/2010, New util added: Fetch sequence according to the chromosome coordinates.(New)
  2. Oct/10/2009, All relevant updates to Medicago truncatula assembly Mt3.0 (just released today) have been finished.
  3. Aug/29/2009, Add two flash represented dynamic view of functional categories of significant regulated probe sets to Browse page.
  4. Aug/25/2009, Improvement of GO annotation batch search page. Some other pages were modified for friendly usage.
  5. Jul/18/2009, Change expression profile outer link to Medicago truncatula Gene Expression Atlas Version 2.
  6. Jul/4/2009, BLAST search against protein sequences of Arabidpsis thaliana of TAIR Version 9 updated.
  7. Jul/3/2009, Update of KEGG pathway information is completed, according to the newest data (release at Jul/2/2009) from KEGG.
  8. Jun/25/2009, Update of KEGG pathway information is completed, according to the newest data from KEGG.
Tao Wang Lab and Zhen Su Lab ©2009 Some comments? Feel free to contact Last Update: Apr 17 2010