Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer reviewed journal
Publication Acceptance Date: 12/4/2008
Publication Date: 1/23/2009
Citation: Bertioli, D., Moretzsohn, M., Madsen, L.H., Sandal, N., Leal-Bertioli, S., Guimaraes, P., Hougaard, B.K., Fredslund, J., Schauser, L., Nielsen, A.M., Sato, S., Tabata, S., Cannon, S.B. 2009. An analysis of synteny of Arachis with Lotus and Medicago sheds new light on the structure, stability and evolution of legume genomes. BMC Genomics. 10:45. Interpretive Summary: This paper examines the stability of chromosomes in the legume plant family. This information will help plant breeders and researchers make use of knowledge gained in any species in the family to any other species. To provide some background, the legume plant family is one of the most diverse in the plant world. The family includes more than 20,000 species, including beans, peas, clovers, and many tropical shrubs and trees. Plants in this family are also some of the most important in agricultural and natural ecosystems because they are uniquely able, through an association with a beneficial soil bacterium, to convert atmospheric nitrogen to a useable form of nitrogen fertilizer. This paper compares the peanut genetic map with the nearly-completed genome sequences (the DNA sequences from chromosomes) of two other legumes that are used as biological "models": Medicago truncatula (a close relative of alfalfa) and Lotus japonicus (a pasture plant similar to clovers). This comparison is important because it uses information from these two models to understand a valuable, but relatively poorly funded, crop species. It is also of basic interest because the plant lineage containing peanut separated from most other legumes very early in the evolution of the legumes, at around 55 million years ago (while the legumes themselves separated from other plant families around 60 million years ago). A key finding is that the legume genomes have remained relatively stable over 55 million years in these three comparison plants. A full-genome duplication, known to have affected many legume species, is present in all three species, so must have predated their separation 55 million years ago. This information will be valuable to plant breeders and researchers because it means knowledge gained in the model species can be transferred more easily to other crop species.
Technical Abstract: Most agriculturally important legumes fall within the phaseoloids (containing beans) and galegoids (containing peas and clovers). A notable exception is peanut (Arachis hypogaea) which comes from a basally diverged tropical lineage. To improve our understanding of the Arachis genome, single-copy genic “anchor” markers were placed on the Arachis genetic map allowing its integration with the substantially sequenced genomes of the model legumes Lotus japonicus and Medicago truncatula. The placement of Arachis basally in the Papilionoid phylogeny, with divergence approximately 55 million years ago, allows new inferences about early legume genome evolution. First, chromosome comparisons indicate that the last whole genome duplication predates the divergence of Arachis from the galegoids and phaseoloids. Second, distinct genome regions show relatively high levels of conservation across multiple taxa. In contrast, other more variable regions only show poor synteny – again, across multiple taxa. We show that in Medicago and Lotus, retrotransposons tend to be more frequent in the variable regions. While these variable regions generally have lower densities of single copy genes than synteny blocks, some harbor high densities of the fast evolving disease resistance genes. We suggest that the Papilionoid legumes illustrate a principle of useful “genomic inertia”: euchromatic regions tend either to remain conserved (or disrupted) across independent lineages. In variable regions, rich with retrotransposons, frequent restructuring may fuel the evolution of some multigene families. This information will be valuable to plant researchers because it means knowledge gained in model species (particularly Medicago, Lotus, and soybean) can be transferred more easily to other crop legume species such as peanut.