Genome-wide analysis of the rice and arabidopsis <it>non-specific lipid transfer protein </it>(<it>nsLtp</it>) gene families and identification of wheat <it>nsLtp </it>genes by EST data mining

<p>Abstract</p> <p>Background</p> <p>Plant non-specific lipid transfer proteins (nsLTPs) are encoded by multigene families and possess physiological functions that remain unclear. Our objective was to characterize the complete <it>nsLtp </it>gene family in rice and arabidopsis and to perform wheat EST database mining for <it>nsLtp </it>gene discovery.</p> <p>Results</p> <p>In this study, we carried out a genome-wide analysis of <it>nsLtp </it>gene families in <it>Oryza sativa </it>and <it>Arabidopsis thaliana </it>and identified 52 rice <it>nsLtp </it>genes and 49 arabidopsis <it>nsLtp </it>genes. Here we present a complete overview of the genes and deduced protein features. Tandem duplication repeats, which represent 26 out of the 52 rice <it>nsLtp </it>genes and 18 out of the 49 arabidopsis <it>nsLtp </it>genes identified, support the complexity of the <it>nsLtp </it>gene families in these species. Phylogenetic analysis revealed that rice and arabidopsis nsLTPs are clustered in nine different clades. In addition, we performed comparative analysis of rice <it>nsLtp </it>genes and wheat (<it>Triticum aestivum</it>) EST sequences indexed in the UniGene database. We identified 156 putative wheat <it>nsLtp </it>genes, among which 91 were found in the 'Chinese Spring' cultivar. The 122 wheat non-redundant nsLTPs were organized in eight types and 33 subfamilies. Based on the observation that seven of these clades were present in arabidopsis, rice and wheat, we conclude that the major functional diversification within the nsLTP family predated the monocot/dicot divergence. In contrast, there is no type VII nsLTPs in arabidopsis and type IX nsLTPs were only identified in arabidopsis. The reason for the larger number of <it>nsLtp </it>genes in wheat may simply be due to the hexaploid state of wheat but may also reflect extensive duplication of gene clusters as observed on rice chromosomes 11 and 12 and arabidopsis chromosome 5.</p> <p>Conclusion</p> <p>Our current study provides fundamental information on the organization of the rice, arabidopsis and wheat <it>nsLtp </it>gene families. The multiplicity of nsLTP types provide new insights on arabidopsis, rice and wheat <it>nsLtp </it>gene families and will strongly support further transcript profiling or functional analyses of <it>nsLtp </it>genes. Until such time as specific physiological functions are defined, it seems relevant to categorize plant nsLTPs on the basis of sequence similarity and/or phylogenetic clustering.</p>