Sequencing of Medicago truncatula genome and studies of metabolic gene organization and expression profile

Medicago truncatula, a model legume, has been sequenced using the combination of the Sanger dideoxynucleotide method with fluorescent terminators and 454 based pyrosequencing method including a BAC pooling approach. The Medicago genome characteristics closely resemble Lotus and have a lot in common with rice. It was discovered that Medicago gene-rich euchromatin is located on chromosome arms and heterochromatin is concentrated in the centromeric, pericentromeric and telomeric regions with an acception of chromosome six where heterochromatin is spread along both chromosome arms. The gene-rich regions of all chromosomes have relatively high percentage of genes and low percentage of repeated sequences with an exception of chromosome five that has elevated content of genes and chromosome six that has reduced amount of genes and elevated level of repeated sequences and transposons. Also, chromosome five has a high content of rRNA and other small RNAs. The centromeric and pericentromeric regions of Medicago may contain some functional genes.;All Medicago chromosomes have the same distribution of major protein functional groups but, at least in case of metabolic genes, have differences in distribution of particular proteins. In addition, 80% of all genes represent primary metabolism and 20% are secondary metabolic genes.;Primary metabolic gene organization is significantly different from that of secondary metabolic genes with low gene copy for the former and a high gene copy for the latter. Duplicated genes are found for both primary and secondary metabolic genes but multiple copies are relatively rare for primary metabolic genes and are predominant for secondary metabolic genes forming tandem duplications and clusters where each member may or may not have sequence homology and/or expression profile. Both primary and secondary metabolic genes undergo purifying selection allowing them to retain the original function.;Only those primary metabolic genes that lead to products directly involved in establishing the symbiosis with Rhizobium are strongly expressed in Medicago genome to provide favorable conditions for bacteria. And only those secondary metabolic genes are upregulated that are involved in reproduction related functions to allow establishment of the symbiosis. There is no tight connection between the aromatic amino acid expression and secondary metabolic gene expression because these aromatic amino acids also are utilized for other product synthesis, direct effect of TCA cycle gene expression on secondary metabolic genes expression does not seem to occur.