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Phylogeny, structural evolution and functional diversification of the plant PHOSPHATE1 gene family: a focus on Glycine max.

ABSTRACT: BACKGROUND: PHOSPHATE1 (PHO1) gene family members have diverse roles in plant growth and development, and they have been studied in Arabidopsis, rice, and Physcomitrella. However, it has yet to be described in other plants. Therefore, we surveyed the evolutionary patterns of genomes within the plant PHO1 gene family, focusing on soybean (Glycine max) due to its economic importance. RESULTS: Our data show that PHO1 genes could be classified into two major groups (Class I and Class II). Class I genes were only present and expanded in dicotyledonous plants and Selaginella moellendorffii; Class II genes were found in all land plants. Class I sequence losses in other lineages may be attributed to gene loss after duplication events in land plant evolution. Introns varied from 7 to 14, and ancestral state reconstruction analyses revealed that genes with 13 introns were ancestral, thus suggesting that the intron loss was a chief constituent of PHO1 gene evolution. In the soybean genome, only 12 PHO1-like genes (GmaPHO1) were detected at the mRNA level. These genes display tissue-specific or tissue-preferential expression patterns during soybean plant and fruit development. Class I genes were more broadly expressed than Class II. GmaPHO1 genes had altered expression in response to salt, osmotic, and inorganic phosphate stresses. CONCLUSIONS: Our study revealed that PHO1 genes originated from a eukaryotic ancestor and that two major classes formed in land plants. Class I genes are only present in dicots and lycophytes. GmaPHO1genes had diverse expression patterns in soybean, indicating their dramatic functional diversification.

SUBMITTER: He L

PROVIDER: S-EPMC3680083 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Phylogeny, structural evolution and functional diversification of the plant PHOSPHATE1 gene family: a focus on Glycine max.

He Lingli L Zhao Man M Wang Yan Y Gai Junyi J He Chaoying C

BMC evolutionary biology 20130524

<h4>Background</h4>PHOSPHATE1 (PHO1) gene family members have diverse roles in plant growth and development, and they have been studied in Arabidopsis, rice, and Physcomitrella. However, it has yet to be described in other plants. Therefore, we surveyed the evolutionary patterns of genomes within the plant PHO1 gene family, focusing on soybean (Glycine max) due to its economic importance.<h4>Results</h4>Our data show that PHO1 genes could be classified into two major groups (Class I and Class II ...[more]

PMID: 23705930

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Project description:Background and aimsThe Nictaba family groups all proteins that show homology to Nictaba, the tobacco lectin. So far, Nictaba and an Arabidopsis thaliana homologue have been shown to be implicated in the plant stress response. The availability of more than 50 sequenced plant genomes provided the opportunity for a genome-wide identification of Nictaba -like genes in 15 species, representing members of the Fabaceae, Poaceae, Solanaceae, Musaceae, Arecaceae, Malvaceae and Rubiaceae. Additionally, phylogenetic relationships between the different species were explored. Furthermore, this study included domain organization analysis, searching for orthologous genes in the legume family and transcript profiling of the Nictaba -like lectin genes in soybean.MethodsUsing a combination of BLASTp, InterPro analysis and hidden Markov models, the genomes of Medicago truncatula , Cicer arietinum , Lotus japonicus , Glycine max , Cajanus cajan , Phaseolus vulgaris , Theobroma cacao , Solanum lycopersicum , Solanum tuberosum , Coffea canephora , Oryza sativa , Zea mays, Sorghum bicolor , Musa acuminata and Elaeis guineensis were searched for Nictaba -like genes. Phylogenetic analysis was performed using RAxML and additional protein domains in the Nictaba-like sequences were identified using InterPro. Expression analysis of the soybean Nictaba -like genes was investigated using microarray data.Key resultsNictaba -like genes were identified in all studied species and analysis of the duplication events demonstrated that both tandem and segmental duplication contributed to the expansion of the Nictaba gene family in angiosperms. The single-domain Nictaba protein and the multi-domain F-box Nictaba architectures are ubiquitous among all analysed species and microarray analysis revealed differential expression patterns for all soybean Nictaba-like genes.ConclusionsTaken together, the comparative genomics data contributes to our understanding of the Nictaba -like gene family in species for which the occurrence of Nictaba domains had not yet been investigated. Given the ubiquitous nature of these genes, they have probably acquired new functions over time and are expected to take on various roles in plant development and defence.

Dataset Information

Phylogeny, structural evolution and functional diversification of the plant PHOSPHATE1 gene family: a focus on Glycine max.

Publications

Phylogeny, structural evolution and functional diversification of the plant PHOSPHATE1 gene family: a focus on Glycine max.

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