Medicago truncatula Genome Release Version 4

Medicago truncatula, a close relative of alfalfa, is a preeminent model for the study of process 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 medicago genome through BAC tiling path, culminating in a BAC-based assembly (Mt version 3.5) as well as an in-depth analysis of the genome published in Nature. Here we describe a much improved version of Medicago truncatula genome (Mt version 4) based on de novo whole genome shotgun assembly by ALLPATHS-LG using mostly Illumina and 454 reads. The ALLPATHS scaffolds were anchored onto the pseudomolecules on the basis of alignments to both optical map and genotyping-by-sequencing (GBS) map. High quality contiguous BAC sequences in phase 3 (complete) and some phase 2 (ordered draft) were patched into the new v4 pseudomolecules to close sequencing gaps in the ALLPATHS assembly, where possible. The Mt v4 pseudomolecules now encompass approximately 360 Mb of sequences spanning 390 Mb of which ~ 330 Mb aligns accurately with the optical map. This is a huge improvement over Mt version 3.5 that contained ~ 250 Mb of sequence in pseudomolecules. Most of the sequences and genes that were previously on unanchored portion of v3.5 have now been incorporated into v4 pseudomolecules, with the exception of only ~20Mb of unplaced sequences. A total of 57,069 (91.5%) out of the 62,379 genes annotated in Mt 3.5 can be lifted over onto the new assemblies with no or minimal changes in gene structures. Novel sequences that are newly placed onto the v4 pseudomolecules have been re-annotated in our gene prediction pipeline, integrating a number of evidences from ESTs, RNA-seq and proteomic data. The significantly improved version of the Medicago genome assembly (Mt version 4) and the associated gene annotations will soon released. Our web site (http://www.jcvi.org/medicago) which has been a host of the Medicago genome browser and blastable datasets will be sync’d to the version 4 accordingly. Finally, we have developed a Community Annotation Portal (EuCAP) and will be enrolling experts to annotate various gene families, as a complementary and long-term solution to the continuing Medicago genome curation at JCVI.