Genome-wide analysis of the Solanum tuberosum (potato) trehalose-6-phosphate synthase (TPS) gene family: evolution and differential expression during development and stress

Qijiang Jin,Yingchun Xu,Yanjie Wang,Liu Yang,Neil Mattson

doi:10.1186/s12864-017-4298-x

Abstract

BackgroundTrehalose-6-phosphate synthase (TPS) serves important functions in plant desiccation tolerance and response to environmental stimuli. At present, a comprehensive analysis, i.e. functional classification, molecular evolution, and expression patterns of this gene family are still lacking in Solanum tuberosum (potato).ResultsIn this study, a comprehensive analysis of the TPS gene family was conducted in potato. A total of eight putative potato TPS genes (StTPSs) were identified by searching the latest potato genome sequence. The amino acid identity among eight StTPSs varied from 59.91 to 89.54%. Analysis of dN/dS ratios suggested that regions in the TPP (trehalose-6-phosphate phosphatase) domains evolved faster than the TPS domains. Although the sequence of the eight StTPSs showed high similarity (2571-2796 bp), their gene length is highly differentiated (3189-8406 bp). Many of the regulatory elements possibly related to phytohormones, abiotic stress and development were identified in different TPS genes. Based on the phylogenetic tree constructed using TPS genes of potato, and four other Solanaceae plants, TPS genes could be categorized into 6 distinct groups. Analysis revealed that purifying selection most likely played a major role during the evolution of this family. Amino acid changes detected in specific branches of the phylogenetic tree suggests relaxed constraints might have contributed to functional divergence among groups. Moreover, StTPSs were found to exhibit tissue and treatment specific expression patterns upon analysis of transcriptome data, and performing qRT-PCR.ConclusionsThis study provides a reference for genome-wide identification of the potato TPS gene family and sets a framework for further functional studies of this important gene family in development and stress response.

Highlights

Trehalose-6-phosphate synthase (TPS) serves important functions in plant desiccation tolerance and response to environmental stimuli
TPSs might function as regulatory molecules in linking trehalose metabolism to glucose transport and glycolysis [3]
QRT-PCR results of genes under various treatment were similar in magnitude to those obtained by deep sequencing. qRT-PCR results suggested that two genes including StTPS1 and StTPS7 were frequently regulated by various treatments, which indicating they might be the Conclusions In summary, we identified eight StTPS genes from potato and characterized their conserved protein motif, gene structure, chromosomal distribution, cis-acting elements in promoter regions and molecular evolution

Summary

Introduction

Trehalose-6-phosphate synthase (TPS) serves important functions in plant desiccation tolerance and response to environmental stimuli. T6-P is catalyzed by T-6-P phosphatase (TPP) and releases trehalose Both plants and yeast (Saccharomyces cerevisiae) share a similar biosynthesis pathway [7, 8]. TPS proteins have been purified from several organisms, including S. lepidophylla [9, 10], yeast [11], Mycobacterium smegmatis [12], and Mycobacterium tuberculosis [13]. Among these organisms, the biosynthesis of trehalose in Escherichia coli and Saccharomyces cerevisiae has been well studied. Further studies indicated that T-6-P could restrict glucose influx by its interaction with sugar kinase activities and glucose transport [15]

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