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Background  The ubiquitous LysM motif recognizes peptidoglycan, chitooligosaccharides (chitin) and, presumably, other structurally-related oligosaccharides. LysM-containing proteins were first shown to be involved in bacterial cell wall degradation and, more recently, were implicated in perceiving chitin (one of the established pathogen-associated molecular patterns) and lipo-chitin (nodulation factors) in flowering plants. However, the majority of  LysM  genes in plants remain functionally uncharacterized and the evolutionary history of complex  LysM  genes remains elusive.    Results  We show that LysM-containing proteins display a wide range of complex domain architectures. However, only a simple core architecture is conserved across kingdoms. Each individual kingdom appears to have evolved a distinct array of domain architectures. We show that early plant lineages acquired four characteristic architectures and progressively lost several primitive architectures. We report plant  LysM  phylogenies and associated gene, protein and genomic features, and infer the relative timing of duplications of  LYK  genes.    Conclusion  We report a domain architecture catalogue of LysM proteins across all kingdoms. The unique pattern of LysM protein domain architectures indicates the presence of distinctive evolutionary paths in individual kingdoms. We describe a comparative and evolutionary genomics study of  LysM  genes in plant kingdom. One of the two groups of tandemly arrayed plant  LYK  genes likely resulted from an ancient genome duplication followed by local genomic rearrangement, while the origin of the other groups of tandemly arrayed  LYK  genes remains obscure. Given the fact that no animal  LysM  motif-containing genes have been functionally characterized, this study provides clues to functional characterization of plant  LysM  genes and is also informative with regard to evolutionary and functional studies of animal  LysM  genes.

Evolutionary genomics of LysM genes in land plants