LEGUME GENOME EVOLUTION VIEWED THROUGH THE MEDICAGO TRUNCATULA AND LOTUS JAPONICUS GENOMES

Authors: Cannon, Steven; STERCK, LIEVEN - GHENT UNIV; ROMBAUTS, STEPHANE - GHENT UNIV; SATO, SHUSEI - KAZUSA DNA RES INST; CHEUNG, FOO - INST FOR GENOMIC RES; GOUZY, JEROME - INRA-CNRS; WANG, XIAOHONG - UNIV OF MINNESOTA; MUDGE, JOANN - UNIV OF MINNESOTA; VASDEWANI, JAYPRAKASH - UNIV OF MINNESOTA; HUMPHRAY, SEAN - WELLCOME TRUST SANGER; NICHOLSON, CHRISTINE - WELLCOME TRUST SANGER; SPANNAGL, MANUEL - MIPS/IBI INST; SCHIEX, THOMAS - INFORMATIQUE APPLIQUEES; MAYER, KLAUS - MIPS/IBI INST; SCHOOF, HEIKO - MAX PLANCK INST; ROGERS, JANE - WELLCOME TRUST SANGER; QUETIER, FRANCIS - CENTRE NATIONALE DE SEQUE; OLDROYD, GILES - JOHN INNES CENTRE; DEBELLE, FREDERIC - INRA-CNRS; COOK, DOUGLAS - UNIV OF CA; ROE, BRUCE - UNIV OF OKLAHOMA; TOWN, CHRISTOPER - INST GENOMIC RESEARCH; TABATA, SATOSHI - KAZUSA DNA RES INST; VAN DE PEER, YVES - GHENT UNIV; YOUNG, NEVIN - UNIV MINNESOTA

Submitted to: Proceedings of the National Academy of Sciences (PNAS)
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/2/2006
Publication Date: 10/3/2006
Citation: Cannon, S.B., Sterck, L., Rombauts, S., Sato, S., Cheung, F., Gouzy, J., Wang, X., Mudge, J., Vasdewani, J., Humphray, S.J., Nicholson, C., Spannagl, M., Schiex, T., Mayer, K., Schoof, H., Rogers, J., Quetier, F., Oldroyd, G., Debelle, F., Cook, D.R., Roe, B., Town, C.D., Tabata, S., Van De Peer, Y., Young, N.D. 2006. Legume genome evolution viewed through the medicago truncatula and lotus japonicus genomes. Proceedings of the National Academy of Sciences. 103(40):14959-14964.

Interpretive Summary: The genetic material in all organisms changes slowly enough that the orders of genes on chromosomes is often retained for tens of millions of years. This is important in the study of agronomic characteristics because it means genetic information from one crop may apply to another. All the hereditary material (DNA) of two model legume species are being sequenced. Legumes include soybeans, peas, alfalfa, clover, and most nitrogen-fixing plants on the planet. The models, Medicago truncatula (a relative of alfalafa) and Lotus japonicus (another forage legume), had a common ancestor about 40 million years ago. In the hereditary code of each, about half of the approximately 250 million bases (or "letters") of the code have now been determined. The authors compared the DNA code of these two species and report that despite the long evolutionary time separating these plants, the order of the genes have been retained across whole chromosome arms, and in some cases whole chromosomes. The authors also confirm initial reports that an early common ancestor in the legumes underwent a duplication of the entire genetic material. Such a duplication may provide for the rapid evolution of new traits, possibly including the development of novel chemistries in the family and the ability (with the assistance of symbiotic bacteria) to fix atmospheric nitrogen. These findings are good news for scientists and breeders working with this plant family because it means that information from these model plants can be used directly to understand agronomically important species in the family.

Technical Abstract: Genome sequencing of two model legumes, Medicago truncatula and Lotus japonicus, provides one of the first opportunities for genome-scale and sequence-based comparisons of multiple genomes in the same family. Sequence comparisons show no evidence for recent large-scale genome duplications in either Medicago or Lotus, but there is evidence for one or more ancient large-scale duplications in a common ancestor of both. The youngest genome duplication shared by both species substantially predates the separation of Medicago and Lotus at approximately 40 Mya. Phylogenetic comparisons place this duplication within the Rosid-I clade, early in the evolution of legumes and after the split between legumes and the Salicaceae. The Lotus and Medicago genomes have retained substantial gene collinearity, with synteny frequently extending to the scale of whole chromosome arms. Generally, the majority of each Medicago and Lotus chromosome corresponds with one or two chromosomes in the other genome. Medicago-Lotus comparisons also show similar and relatively homogeneous gene densities, unlike the apparent gene-dense and gene-poor regions of euchromatin (“gene islands”) observed in some plant genomes such as maize. These features – relatively high gene densities, an absence of recent whole genome duplications, and relatively few genome rearrangements – make these two genomes particularly valuable references for crop legumes and for dicot genomes generally. The features are also favorable for the development of an integrated genomic model for legumes consisting of a composite derived from Medicago and Lotus sequences.