Medicago truncatula Genome Database
Medicago truncatula, a close relative of alfalfa, is a preeminent model for the study of the processes of nitrogen fixation, symbiosis, and legume genomics. The genome was initially sequenced in a collaboration between the University of Oklahoma, TIGR (now JCVI), the Sanger Institute in the UK and Genoscope in France with funding from Samuel Roberts Noble Foundation, the National Science Foundation and the European Union's Sixth Framework Programme INRA (France) , and the BBSRC (UK).in the United Kingdom with funding from the EU and BBSRC.
The initial published sequence Mt3.5 assembly was based upon a BAC-by-BAC approach. Later, we generated 454 mate pair sequence and extensive Illumina paired end (PE) and mate pair (MP) sequence that was used together with the previously generated BAC- and fosmid-end sequences to produce an AllPaths assembly. The ALLPATHS scaffolds were anchored onto the 8 linkage groups on the basis of alignments to both the optical map (OM) and genetic map derived from genotyping-by-sequencing (GBS) data. High quality contiguous BAC sequences were patched into the new Mt4.0 pseudomolecules to close gaps and reduce polymorphisms between the assembly versions, where possible.
The new version of the genome (Mt4.0) was re-annotated using JCVI in-house structural and functional annotation pipelines, integrating a number of tiers of evidence: ab initio gene predictors, legacy Mt3.5v5 annotation, EST/RNA-seq assemblies and proteomic data, culminating in an annotation release, Mt4.0v2. A total of 50,376 gene loci (encompassing 57,585 gene models) were annotated by this pipeline, which were then binned into high (HC) and low (LC) confidence classes (~32k HC and ~19k LC loci), based on different levels of EST/RNA-seq/protein support and synteny to related plant genomes.
The Medicago Genome DataBase and Legume Data Federation
JCVI hosts the M. truncatula genome sequence and annotation in three forms: a Tripal database, JBrowse and an instance of InterMine named MedicMine. These databases also form part of a larger consortium of legume databases known as the Legume Federation (legumefederation.org). The Legume Federation is a joint project with USDA-ARS-Iowa State and the National Center for Genome Resources. Together, these three centers house genomic, genetic and phenotypic (QTL) data for around 10 legume crop species including soybean, common bean, peanut, chickpea, clover, lupin and others. The goal of the project is to provide cross-species links between these plants at the genomic, genetic and phenotypic levels to further legume research and breeding.
Funding provided through the National Science Foundation (NSF).