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Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes

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Abstract
Genome sequencing of the model legumes, Medicago truncatula and Lotus japonicus, provides an opportunity for large-scale sequence-based comparison of two genomes in the same plant family. Here we report synteny comparisons between these species, including details about chromosome relationships, large-scale synteny blocks, microsynteny within blocks, and genome regions lacking clear correspondence. The Lotus and Medicago genomes share a minimum of 10 large-scale synteny blocks, each with substantial collinearity and frequently extending the length of whole chromosome arms. The proportion of genes syntenic and collinear within each synteny block is relatively homogeneous. Medicago-Lotus comparisons also indicate similar and largely homogeneous gene densities, although gene-containing regions in Mt occupy 20-30% more space than Lj counterparts, primarily because of larger numbers of Mt retrotransposons. Because the interpretation of genome comparisons is complicated by large-scale genome duplications, we describe synteny, synonymous substitutions and phylogenetic analyses to identify and date a probable whole-genome duplication event. There is no direct evidence for any recent large-scale genome duplication in either Medicago or Lotus but instead a duplication predating speciation. Phylogenetic comparisons place this duplication within the Rosid I clade, clearly after the split between legumes and Salicaceae (poplar).
Keywords
synteny, polyploidy, genome duplication, ARABIDOPSIS-THALIANA, PHYLOGENETIC ANALYSIS, DUPLICATE GENES, LINKAGE MAP, MODEL, SEQUENCE, MICROSYNTENY, ALIGNMENT, DATABASE, CROP

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MLA
Cannon, Steven B, Lieven Sterck, Stephane Rombauts, et al. “Legume Genome Evolution Viewed Through the Medicago Truncatula and Lotus Japonicus Genomes.” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 103.40 (2006): 14959–14964. Print.
APA
Cannon, S. B., Sterck, L., Rombauts, S., Sato, S., Cheung, F., Gouzy, J., Wang, X., et al. (2006). Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103(40), 14959–14964.
Chicago author-date
Cannon, Steven B, Lieven Sterck, Stephane Rombauts, Shusei Sato, Foo Cheung, Jérôme Gouzy, Xiaohong Wang, et al. 2006. “Legume Genome Evolution Viewed Through the Medicago Truncatula and Lotus Japonicus Genomes.” Proceedings of the National Academy of Sciences of the United States of America 103 (40): 14959–14964.
Chicago author-date (all authors)
Cannon, Steven B, Lieven Sterck, Stephane Rombauts, Shusei Sato, Foo Cheung, Jérôme Gouzy, Xiaohong Wang, Joann Mudge, Jayprakash Vasdewani, Thomas Schiex, Manuel Spannagl, Erin Monaghan,, Christine Nicholson, Sean J Humphray, Heiko Schoof, Klaus FX Mayer, Jane Rogers, Francis Quétier, Giles E Oldroyd, Frédéric Debellé, Douglas R Cook, Ernest F Retzel, Bruce A Roe, Christopher D Town, Satoshi Tabata, Yves Van de Peer, and Nevin D Young. 2006. “Legume Genome Evolution Viewed Through the Medicago Truncatula and Lotus Japonicus Genomes.” Proceedings of the National Academy of Sciences of the United States of America 103 (40): 14959–14964.
Vancouver
1.
Cannon SB, Sterck L, Rombauts S, Sato S, Cheung F, Gouzy J, et al. Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2006;103(40):14959–64.
IEEE
[1]
S. B. Cannon et al., “Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes,” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 103, no. 40, pp. 14959–14964, 2006.
@article{371619,
  abstract     = {Genome sequencing of the model legumes, Medicago truncatula and Lotus japonicus, provides an opportunity for large-scale sequence-based comparison of two genomes in the same plant family. Here we report synteny comparisons between these species, including details about chromosome relationships, large-scale synteny blocks, microsynteny within blocks, and genome regions lacking clear correspondence. The Lotus and Medicago genomes share a minimum of 10 large-scale synteny blocks, each with substantial collinearity and frequently extending the length of whole chromosome arms. The proportion of genes syntenic and collinear within each synteny block is relatively homogeneous. Medicago-Lotus comparisons also indicate similar and largely homogeneous gene densities, although gene-containing regions in Mt occupy 20-30% more space than Lj counterparts, primarily because of larger numbers of Mt retrotransposons. Because the interpretation of genome comparisons is complicated by large-scale genome duplications, we describe synteny, synonymous substitutions and phylogenetic analyses to identify and date a probable whole-genome duplication event. There is no direct evidence for any recent large-scale genome duplication in either Medicago or Lotus but instead a duplication predating speciation. Phylogenetic comparisons place this duplication within the Rosid I clade, clearly after the split between legumes and Salicaceae (poplar).},
  author       = {Cannon, Steven B and Sterck, Lieven and Rombauts, Stephane and Sato, Shusei and Cheung, Foo and Gouzy, Jérôme and Wang, Xiaohong and Mudge, Joann and Vasdewani, Jayprakash and Schiex, Thomas and Spannagl, Manuel and Monaghan,, Erin and Nicholson, Christine and Humphray, Sean J and Schoof, Heiko and Mayer, Klaus FX and Rogers, Jane and Quétier, Francis and Oldroyd, Giles E and Debellé, Frédéric and Cook, Douglas R and Retzel, Ernest F and Roe, Bruce A and Town, Christopher D and Tabata, Satoshi and Van de Peer, Yves and Young, Nevin D},
  issn         = {0027-8424},
  journal      = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA},
  keywords     = {synteny,polyploidy,genome duplication,ARABIDOPSIS-THALIANA,PHYLOGENETIC ANALYSIS,DUPLICATE GENES,LINKAGE MAP,MODEL,SEQUENCE,MICROSYNTENY,ALIGNMENT,DATABASE,CROP},
  language     = {eng},
  number       = {40},
  pages        = {14959--14964},
  title        = {Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes},
  url          = {http://dx.doi.org/10.1073/pnas.0603228103},
  volume       = {103},
  year         = {2006},
}

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