six a17 bac and one fosmid library were used to create mt3.5 ( table s1 ) .
most were processed by sanger paired - end sequencing of 3 - 6 kb shotgun libraries .
sequences were downloaded in february / march 2009 with scaffolding performed by aligning all bac and fosmid ends against contigs and then anchored and ordered primarily by optical mapping .
separately , 25 gb of illumina sequence was generated using short ( 375 nt ) inserts plus 2.1 gb from a 5 kb mate - pair library , then assembled using clcbio ( www.clcbio.com ) and soap ( http://soap.genomics.org.cn/ ) .
five tissues were used for rna - seq analysis with ~10 million illumina 36 bp reads per library ( table s12 ) .
three tissues were used for small rna analysis with ~3 million reads per illumina library ( figures s17-s18 , table s16 , datafile s9 ) .
six a17 bac and one fosmid library were used to create mt3.5 ( table s1 ) .
most were processed by sanger paired - end sequencing of 3 - 6 kb shotgun libraries .
sequences were downloaded in february / march 2009 with scaffolding performed by aligning all bac and fosmid ends against contigs and then anchored and ordered primarily by optical mapping .
separately , 25 gb of illumina sequence was generated using short ( 375 nt ) inserts plus 2.1 gb from a 5 kb mate - pair library , then assembled using clcbio ( www.clcbio.com ) and soap ( http://soap.genomics.org.cn/ ) .
five tissues were used for rna - seq analysis with ~10 million illumina 36 bp reads per library ( table s12 ) .
three tissues were used for small rna analysis with ~3 million reads per illumina library ( figures s17-s18 , table s16 , datafile s9 ) .
 legumes ( fabaceae or leguminosae ) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria , a process that takes place in a specialized structure known as the nodule . 
 legumes belong to one of the two main groups of eurosids , the fabidae , which includes most species capable of endosymbiotic nitrogen fixation 1 . 
 legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago ( mya ) . 
 papilionoids are the largest clade , dating nearly to the origin of legumes and containing most cultivated species 2 . 
 medicago truncatula ( mt ) is a long - established model for the study of legume biology . 
 here we describe the draft sequence of the mt euchromatin based on a recently completed bac - assembly supplemented with illumina - shotgun sequence , together capturing ~94% of all mt genes . a whole - genome duplication ( wgd ) 
 approximately 58 mya played a major role in shaping the mt genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation . 
 subsequent to the wgd , the mt genome experienced higher levels of rearrangement than two other sequenced legumes , glycine max ( gm ) and lotus japonicus ( lj ) . 
 mt is a close relative of alfalfa ( m. sativa ) , a widely cultivated crop with limited genomics tools and complex autotetraploid genetics . as such 
 , the mt genome sequence provides significant opportunities to expand alfalfa s genomic toolbox . 
METHODS SUMMARY
DNA sequencing
RNA sequencing
Supplementary Material