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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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Unrooted phylogenetic tree between rice, arabidopsis and wheat nsLTP gene families. The mature sequences of the 122 non-redundant wheat nsLTPs, the 49 rice nsLTPs, and the 45 arabidopsis nsLTPs were aligned using HMMalign and then manually refined. The phylogenetic tree was built from the protein alignment (Additional file 3) with the maximum-likelihood method using the PHYML program [75]. When possible, subtrees including sequences of the same type are grouped and represented by a grey triangle close to which is indicated, in brackets, the number of sequences of arabidopsis, rice and wheat respectively. Subtrees are detailed in Figure 7. Bootstrap values (% of 100 re-sampled data set) are indicated for each node.
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Figure 6: Unrooted phylogenetic tree between rice, arabidopsis and wheat nsLTP gene families. The mature sequences of the 122 non-redundant wheat nsLTPs, the 49 rice nsLTPs, and the 45 arabidopsis nsLTPs were aligned using HMMalign and then manually refined. The phylogenetic tree was built from the protein alignment (Additional file 3) with the maximum-likelihood method using the PHYML program [75]. When possible, subtrees including sequences of the same type are grouped and represented by a grey triangle close to which is indicated, in brackets, the number of sequences of arabidopsis, rice and wheat respectively. Subtrees are detailed in Figure 7. Bootstrap values (% of 100 re-sampled data set) are indicated for each node.

Mentions: In order to analyze the phylogenetic organization of the nsLTP families, we constructed a phylogenetic tree from the alignment of respectively 45, 49 and 122 sequences of arabidopsis, rice and wheat nsLTPs, using the maximum-likelihood inference. Redundant mature wheat nsLTPs were eliminated but the arabidopsis and rice complete families were included. The solidity of the nodes was assessed by 100 bootstrap resampling repetitions. The seven arabidopsis and rice nsLTPY proteins were first included but due to the fact that their position was not well supported (nodes with weak bootstrap values) and consequently risked muddling the phylogenetic signal, they were excluded from the alignment. In the first attempt, several cysteine-rich protein sequences (metallothioneins, thionins and defensins from arabidopsis and rice) were tested as potential roots, but their position was different and none were supported by significant bootstrap values. Moreover, the phylogenetic relationships between types were not reliable whatever the root chosen. Consequently, we chose to present the complete condensed unrooted tree (Figure 6) where each of the subtrees (detailed in Figure 7) is rooted by all the other sequences.


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)

Unrooted phylogenetic tree between rice, arabidopsis and wheat nsLTP gene families. The mature sequences of the 122 non-redundant wheat nsLTPs, the 49 rice nsLTPs, and the 45 arabidopsis nsLTPs were aligned using HMMalign and then manually refined. The phylogenetic tree was built from the protein alignment (Additional file 3) with the maximum-likelihood method using the PHYML program [75]. When possible, subtrees including sequences of the same type are grouped and represented by a grey triangle close to which is indicated, in brackets, the number of sequences of arabidopsis, rice and wheat respectively. Subtrees are detailed in Figure 7. Bootstrap values (% of 100 re-sampled data set) are indicated for each node.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Unrooted phylogenetic tree between rice, arabidopsis and wheat nsLTP gene families. The mature sequences of the 122 non-redundant wheat nsLTPs, the 49 rice nsLTPs, and the 45 arabidopsis nsLTPs were aligned using HMMalign and then manually refined. The phylogenetic tree was built from the protein alignment (Additional file 3) with the maximum-likelihood method using the PHYML program [75]. When possible, subtrees including sequences of the same type are grouped and represented by a grey triangle close to which is indicated, in brackets, the number of sequences of arabidopsis, rice and wheat respectively. Subtrees are detailed in Figure 7. Bootstrap values (% of 100 re-sampled data set) are indicated for each node.
Mentions: In order to analyze the phylogenetic organization of the nsLTP families, we constructed a phylogenetic tree from the alignment of respectively 45, 49 and 122 sequences of arabidopsis, rice and wheat nsLTPs, using the maximum-likelihood inference. Redundant mature wheat nsLTPs were eliminated but the arabidopsis and rice complete families were included. The solidity of the nodes was assessed by 100 bootstrap resampling repetitions. The seven arabidopsis and rice nsLTPY proteins were first included but due to the fact that their position was not well supported (nodes with weak bootstrap values) and consequently risked muddling the phylogenetic signal, they were excluded from the alignment. In the first attempt, several cysteine-rich protein sequences (metallothioneins, thionins and defensins from arabidopsis and rice) were tested as potential roots, but their position was different and none were supported by significant bootstrap values. Moreover, the phylogenetic relationships between types were not reliable whatever the root chosen. Consequently, we chose to present the complete condensed unrooted tree (Figure 6) where each of the subtrees (detailed in Figure 7) is rooted by all the other sequences.

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