Overview
Full NameMedicago truncatula
GenusMedicago
Speciestruncatula
Common NameBarrel Medic
AbbreviationM.truncatula
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 euchromatic genespace. Among the eight chromosomes in Medicago, six were sequenced in the US by the NSF-funded projects, one (chromosome 5) was sequenced in France by Genoscope with funding from the EU and INRA, and one (chromosome 3) was sequenced in the United Kingdom with funding from the EU and BBSRC.
Pseudomolecule assembly was greatly aided by the construction of an Optical Map by David Schwartz and collueages at Laboratory for Molecular and Computational Genomics at UW-Madison.
Genome annotation was carried out by the International Medicago Genome Annotation Group (IMGAG), which involved participants from INRA-CNRS, JCVI/TIGR, NCGR, MIPS, MPIZ, UMN and VIB-Gent. With the publication of the Genome Paper in Nature, November 2011 the genome project was essentially completed.
At JCVI, we have continued to curate and improve the M. truncatula genome sequence and annotation. We have combined NexGen sequences with the previous BAC-based assemblies to produce the current Mt 4.0 release. Pseudomolecules were constructed from ALLPATHS-LG scaffolds on the basis of alignments to both the Optical and Genetic (Genotyping-by-Sequencing) maps. Where possible, high quality contiguous BAC sequences were patched into the new pseudomolecules to close sequencing gaps in the ALLPATHS assembly. Whereas the Mt3.5 release consisted of ~250 Mb in pseudomolecules and ~100 Mb of unanchored sequence, the Mt4.0 pseudomolecules now encompass approximately 360 Mb of sequences spanning 390 Mb of which ~330 Mb aligns accurately with the Optical Map. Most of the sequences and genes that were previously in the unanchored portion of Mt3.5 have now been incorporated into Mt4.0 pseudomolecules, with the exception of only ~20Mb of unplaced sequence.
The new pseudomolecules were annotated by an in-house pipeline that combined Mt3.5 gene models, predictions from Augustus and FGENESH with expression data and protein matches primarily using Evidence Modeler (EVM). Medtr identifers have been preserved between Mt3.5 and Mt4.0. Many new identifiers have been instantiated to replace the gene identifiers previously found on the unanchored contigs. Lookup tables are provided to allow easy navigation between the two data sets.
GO Analysis Reports
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Feature Browser
The following browser provides a quick view for new visitors. Use the searching mechanism to find specific features.
Feature NameUnique NameType
Medtr8g468680Medtr8g468680gene
Medtr8g468680.1Medtr8g468680.1mRNA
Medtr8g468700Medtr8g468700gene
Medtr8g468700.1Medtr8g468700.1mRNA
Medtr8g468710Medtr8g468710gene
Medtr8g468710.1Medtr8g468710.1mRNA
Medtr8g468720Medtr8g468720gene
Medtr8g468720.1Medtr8g468720.1mRNA
Medtr8g468730Medtr8g468730gene
Medtr8g468730.1Medtr8g468730.1mRNA
Medtr8g468760Medtr8g468760gene
Medtr8g468760.1Medtr8g468760.1mRNA
Medtr8g468780Medtr8g468780gene
Medtr8g468780.1Medtr8g468780.1mRNA
Medtr8g468790Medtr8g468790gene
Medtr8g468790.1Medtr8g468790.1mRNA
Medtr8g468810Medtr8g468810gene
Medtr8g468810.1Medtr8g468810.1mRNA
Medtr8g468810.2Medtr8g468810.2mRNA
Medtr8g468810.3Medtr8g468810.3mRNA
Medtr8g468810.4Medtr8g468810.4mRNA
Medtr8g468810.5Medtr8g468810.5mRNA
Medtr8g468820Medtr8g468820gene
Medtr8g468820.1Medtr8g468820.1mRNA
Medtr8g468830Medtr8g468830gene

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Feature Summary
The following features are currently present for this organism
Feature TypeCount
Chromosomes8
Scaffolds47,899
Genes57,585
mRNA259,548
exon250,130