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Roll out the barrel medic!

January 11, 2012

In the last Nature of 2011, Nevin Young and colleagues (many, many colleagues!**) described the genome of the barrel medic, Medicago truncatula [1].  This little legume is one of the model host species for investigation of the rhizobium-legume symbiosis, and in recent years many plant genes involved in the establishment of the interaction have been identified and characterised in this species.

This is not the first legume genome to be published: that of the other main model species, Lotus japonicus, was published in 2008 [2], and the genome of soybean, Glycine max, which is not a ‘model’ but a major crop plant, of course, appeared in 2010 [3].

All three legumes are in the subfamily Papilionoideae and their genomes share a significant feature.  About 58 million years ago, their common ancestor underwent a whole genome duplication, creating two versions (called paralogs* or homeologs) of every gene.  Over time, many of these copies became lost, but others diversified to acquire distinctive functions.  Young et al. argue that this was critical for the evolution of the nodule symbiosis.  Their evidence is that several genes that are known to have special roles in symbiosis have paralogs, dating back to this genome duplication, that serve a more general function in the plant, and many other pairs of paralogs have one partner that is much more highly expressed in the nodule than the other, suggesting that they have evolved a specialised symbiotic function.  The authors suggest that an early form of nodule symbiosis probably existed before the whole genome duplication, but that the sudden acquisition of many ‘redundant’ genes allowed the symbiosis to be greatly refined in papilionoid legumes through the adaptation of some of these genes to symbiosis-specific roles.

In their paper, Young et al. make extensive comparisons with previously published plant genomes, particularly those of the two legumes.  I was sorry to see that, although they cited the publication describing the soybean genome [3], they failed to mention the corresponding publication for L. japonicus [2] despite using the data described in it.  I hope that this egregious breach of good publishing manners was merely an oversight.  There has, of course, been a certain amount of rivalry over the years between the champions of M. truncatula and the supporters of L. japonicus as they have vied to demonstrate that their chosen legume is the perfect model.  In terms of important discoveries about the symbiosis, the honours are rather evenly divided, but the Japanese Team Lotus has been consistently out in front in the genomics races.  Not only did they get their legume genome out several years ahead (with similar coverage, though arguably a less polished assembly) but, more than a decade ago, the same team neatly slipped out the Mesorhizobium loti MAFF303099 genome [4] just months ahead of the massive multinational effort on Sinorhizobium meliloti 1021 [5].

In my view, the fact that rhizobium-legume symbiosis research has never coalesced around a single model system has been one of the great strengths of the field, as it has allowed us to identify the features that are truly general, but also to understand some of the differences that underlie the remarkable degree of specificity that is characteristic of this symbiosis.

Peter

[1]  Young, N.D., Debellé, F., Oldroyd, G.E.D., Geurts, R., Cannon, S.B., Udvardi, M.K. et al. (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480: 520-524. DOI:  10.1038/nature10625

[2]  Sato, S., Nakamura, Y., Kaneko, T., Asamizu, E., Kato, T., Nakao, M. et al. (2008) Genome structure of the legume, Lotus japonicus. DNA Research 15: 227-239. DOI:  10.1093/dnares/dsn008

[3]  Schmutz, J., Cannon, S.B., Schlueter, J., Ma, J., Mitros, T., Nelson, W. et al. (2010) Genome sequence of the palaeopolyploid soybean. Nature 463: 178-183. DOI:  10.1038/nature08670

[4]  Kaneko, T., Nakamura, Y., Sato, S., Asamizu, E., Kato, T., Sasamoto, S. et al. (2000) Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Research 7: 331-338. DOI:  10.1093/dnares/7.6.331

 [5]  Galibert, F., Finan, T.M., Long, S.R., Pühler, A., Abola, P., Ampe, F. et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293: 668-672. DOI:  10.1126/science.106096

* According to the dictionary, we are supposed to write ‘paralogue’ in British English, while Americans write ‘paralog’.  Personally, I dislike the pointless French frippery at the end, and always write it without the ‘ue’.

** If you really want to know, the authors were:

Nevin D. Young,

Frédéric Debellé,

Giles E. D. Oldroyd,

Rene Geurts,

Steven B. Cannon,

Michael K. Udvardi,

Vagner A. Benedito,

Klaus F. X. Mayer,

Jérôme Gouzy,

Heiko Schoof,

Yves Van de Peer,

Sebastian Proost,

Douglas R. Cook,

Blake C. Meyers,

Manuel Spannagl,

Foo Cheung,

Stéphane De Mita,

Vivek Krishnakumar,

Heidrun Gundlach,

Shiguo Zhou,

Joann Mudge,

Arvind K. Bharti,

Jeremy D. Murray,

Marina A. Naoumkina,

Benjamin Rosen,

Kevin A. T. Silverstein,

Haibao Tang,

Stephane Rombauts,

Patrick X. Zhao,

Peng Zhou,

Valérie Barbe,

Philippe Bardou,

Michael Bechner,

Arnaud Bellec,

Anne Berger,

Hélène Bergès,

Shelby Bidwell,

Ton Bisseling,

Nathalie Choisne,

Arnaud Couloux,

Roxanne Denny,

Shweta Deshpande,

Xinbin Dai,

Jeff J. Doyle,

Anne-Marie Dudez,

Andrew D. Farmer,

Stéphanie Fouteau,

Carolien Franken,

Chrystel Gibelin,

John Gish,

Steven Goldstein,

Alvaro J. González,

Pamela J. Green,

Asis Hallab,

Marijke Hartog,

Axin Hua,

Sean J. Humphray,

Dong-Hoon Jeong,

Yi Jing,

Anika Jöcker,

Steve M. Kenton,

Dong-Jin Kim,

Kathrin Klee,

Hongshing Lai,

Chunting Lang,

Shaoping Lin,

Simone L. Macmil,

Ghislaine Magdelenat,

Lucy Matthews,

Jamison McCorrison,

Erin L. Monaghan,

Jeong-Hwan Mun,

Fares Z. Najar,

Christine Nicholson,

Céline Noirot,

Majesta O’Bleness,

Charles R. Paule,

Julie Poulain,

Florent Prion,

Baifang Qin,

Chunmei Qu,

Ernest F. Retzel,

Claire Riddle,

Erika Sallet,

Sylvie Samain,

Nicolas Samson,

Iryna Sanders,

Olivier Saurat,

Claude Scarpelli,

Thomas Schiex,

Béatrice Segurens,

Andrew J. Severin,

D. Janine Sherrier,

Ruihua Shi,

Sarah Sims,

Susan R. Singer,

Senjuti Sinharoy,

Lieven Sterck,

Agnès Viollet,

Bing-Bing Wang,

Keqin Wang,

Mingyi Wang,

Xiaohong Wang,

Jens Warfsmann,

Jean Weissenbach,

Doug D. White,

Jim D. White,

Graham B. Wiley,

Patrick Wincker,

Yanbo Xing,

Limei Yang,

Ziyun Yao,

Fu Ying,

Jixian Zhai,

Liping Zhou,

Antoine Zuber,

Jean Dénarié,

Richard A. Dixon,

Gregory D. May,

David C. Schwartz,

Jane Rogers,

Francis Quétier,

Christopher D. Town

& Bruce A. Roe.

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