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Genome-wide analysis of the rice and Arabidopsis non-specific lipid transfer protein (nsLtp) gene families and identification of wheat nsLtp genes by EST data mining.

Boutrot F, Chantret N, Gautier MF - BMC Genomics (2008)

Bottom Line: We identified 156 putative wheat nsLtp genes, among which 91 were found in the 'Chinese Spring' cultivar.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: UMR1098 Développement et Amélioration des Plantes, INRA, F-34060 Montpellier, France. freddy.boutrot@sainsbury-laboratory.ac.uk

ABSTRACT

Background: 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 nsLtp gene family in rice and arabidopsis and to perform wheat EST database mining for nsLtp gene discovery.

Results: In this study, we carried out a genome-wide analysis of nsLtp gene families in Oryza sativa and Arabidopsis thaliana and identified 52 rice nsLtp genes and 49 arabidopsis nsLtp 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 nsLtp genes and 18 out of the 49 arabidopsis nsLtp genes identified, support the complexity of the nsLtp 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 nsLtp genes and wheat (Triticum aestivum) EST sequences indexed in the UniGene database. We identified 156 putative wheat nsLtp 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 nsLtp 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.

Conclusion: Our current study provides fundamental information on the organization of the rice, arabidopsis and wheat nsLtp gene families. The multiplicity of nsLTP types provide new insights on arabidopsis, rice and wheat nsLtp gene families and will strongly support further transcript profiling or functional analyses of nsLtp 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.

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Organization of nsLtp genes in rice and arabidopsis genomes. Positions of nsLtp genes are indicated on chromosomes (scale in Mbp).
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Figure 1: Organization of nsLtp genes in rice and arabidopsis genomes. Positions of nsLtp genes are indicated on chromosomes (scale in Mbp).

Mentions: Analysis of the physical chromosomal loci revealed that 26 out of the 52 rice nsLtp genes and 18 out of the 49 arabidopsis nsLtp genes are arranged in tandem duplication repeats (Figure 1). To cover nomenclature in different species, we named rice and arabidopsis nsLtp genes encoding nsLTPs OsLtp and AtLtp, respectively. Genes encoding mature proteins sharing more than 30% identity were grouped in the same type [32]. Genes encoding rice and arabidopsis type I nsLTPs were named OsLtpI and AtLtpI respectively, and consecutive roman numbers were assigned for the other types.


Genome-wide analysis of the rice and Arabidopsis non-specific lipid transfer protein (nsLtp) gene families and identification of wheat nsLtp genes by EST data mining.

Boutrot F, Chantret N, Gautier MF - BMC Genomics (2008)

Organization of nsLtp genes in rice and arabidopsis genomes. Positions of nsLtp genes are indicated on chromosomes (scale in Mbp).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2277411&req=5

Figure 1: Organization of nsLtp genes in rice and arabidopsis genomes. Positions of nsLtp genes are indicated on chromosomes (scale in Mbp).
Mentions: Analysis of the physical chromosomal loci revealed that 26 out of the 52 rice nsLtp genes and 18 out of the 49 arabidopsis nsLtp genes are arranged in tandem duplication repeats (Figure 1). To cover nomenclature in different species, we named rice and arabidopsis nsLtp genes encoding nsLTPs OsLtp and AtLtp, respectively. Genes encoding mature proteins sharing more than 30% identity were grouped in the same type [32]. Genes encoding rice and arabidopsis type I nsLTPs were named OsLtpI and AtLtpI respectively, and consecutive roman numbers were assigned for the other types.

Bottom Line: We identified 156 putative wheat nsLtp genes, among which 91 were found in the 'Chinese Spring' cultivar.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: UMR1098 Développement et Amélioration des Plantes, INRA, F-34060 Montpellier, France. freddy.boutrot@sainsbury-laboratory.ac.uk

ABSTRACT

Background: 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 nsLtp gene family in rice and arabidopsis and to perform wheat EST database mining for nsLtp gene discovery.

Results: In this study, we carried out a genome-wide analysis of nsLtp gene families in Oryza sativa and Arabidopsis thaliana and identified 52 rice nsLtp genes and 49 arabidopsis nsLtp 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 nsLtp genes and 18 out of the 49 arabidopsis nsLtp genes identified, support the complexity of the nsLtp 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 nsLtp genes and wheat (Triticum aestivum) EST sequences indexed in the UniGene database. We identified 156 putative wheat nsLtp 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 nsLtp 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.

Conclusion: Our current study provides fundamental information on the organization of the rice, arabidopsis and wheat nsLtp gene families. The multiplicity of nsLTP types provide new insights on arabidopsis, rice and wheat nsLtp gene families and will strongly support further transcript profiling or functional analyses of nsLtp 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.

Show MeSH