Medicago Truncatula Genome Release Version 4

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 Medicago sequencing project began in 2003 with the initial goal to decipher the sequences from the euchromatic portion of the genome through BAC tiling path, culminating in a BAC-based assembly (Mt3.5) as well as an in-depth analysis of the genome, published in Nature. Here, we describe a much improved version of the Medicago truncatula genome assembly (Mt4.0), based on de novo whole genome shotgun assembly by ALLPATHS-LG using mostly Illumina and 454 reads and its subsequent annotation. 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. This new version of the genome was annotated using our 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 (Mt4.0v1). A total of 50,894 gene loci (encompassing 62,319 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 observed levels of EST/RNA-seq/protein support and synteny to related plant genomes. Our web site (http://www.jcvi.org/medicago), which has been a host to resources such as identifier/keyword-based search, genome browsers, blastable datasets and bulk downloads, has been updated to serve data from this release.  Finally, we have developed a Community Annotation Portal (EuCAP, http://medicago.jcvi.org/eucap) and will be enrolling experts to help curate gene loci, families and mutants as a complementary and long-term solution to the continuing Medicago genome curation.