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Background  Trehalose-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).    Results  In 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 d N /d S  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.    Conclusions  This 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.    Electronic supplementary material  The online version of this article (10.1186/s12864-017-4298-x) contains supplementary material, which is available to authorized users.

bmc genomics

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