Estimating genome conservation between crop and model legume species

Hong Kyu Choi, Jeong Hwan Mun, Dong Jin Kim, Hongyan Zhu, Jong Min Baek, Joanne Mudge, Bruce Roe, Noel Ellis, Jeff Doyle, Gyorgy B. Kiss, Nevin D Young, Douglas R. Cook

Research output: Contribution to journalArticle

378 Scopus citations

Abstract

Legumes are simultaneously one of the largest families of crop plants and a cornerstone in the biological nitrogen cycle. We combined molecular and phylogenetic analyses to evaluate genome conservation both within and between the two major clades of crop legumes. Genetic mapping of orthologous genes identifies broad conservation of genome macrostructure, especially within the galegoid legumes, while also highlighting inferred chromosomal rearrangements that may underlie the variation in chromosome number between these species. As a complement to comparative genetic mapping, we compared sequenced regions of the model legume Medicago truncatula with those of the diploid Lotus japonicus and the polyploid Glycine max. High conservation was observed between the genomes of M. truncatula and L. japonicus, whereas lower levels of conservation were evident between M. truncatula and G. max. In all cases, conserved genome microstructure was punctuated by significant structural divergence, including frequent insertion/deletion of individual genes or groups of genes and lineage-specific expansion/contraction of gene families. These results suggest that comparative mapping may have considerable utility for basic and applied research in the legumes, although its predictive value is likely to be tempered by phylogenetic distance and genome duplication.

Original languageEnglish (US)
Pages (from-to)15289-15294
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume101
Issue number43
DOIs
StatePublished - Oct 26 2004

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    Choi, H. K., Mun, J. H., Kim, D. J., Zhu, H., Baek, J. M., Mudge, J., Roe, B., Ellis, N., Doyle, J., Kiss, G. B., Young, N. D., & Cook, D. R. (2004). Estimating genome conservation between crop and model legume species. Proceedings of the National Academy of Sciences of the United States of America, 101(43), 15289-15294. https://doi.org/10.1073/pnas.0402251101