Genome-wide identification and expression analysis of the trehalose-6-phosphate synthase ( TPS ) gene family in cucumber ( Cucumis sativus L.)

• Published in: PeerJ (San Francisco, CA) CA), 2021-04, Vol.9, p.e11398-e11398, Article e11398
• Main Authors: Dan, Yuanyuan, Niu, Yuan, Wang, Chunlei, Yan, Mei, Liao, Weibiao
• Format: Article
• Language: English
• Subjects: Abiotic stress; Agricultural production; Arabidopsis; Bioinformatics; Chromosomes; Conserved motifs; Cucumber TPS; Domains; Evolutionary relationships; Expression patterns; Gene structures; Genes; Genomes; Genomics; Glucose; Hydrolase; Introns; Maximum likelihood method; Molecular Biology; Phase transitions; Phylogenetics; Phylogeny; Physicochemical properties; Plant Science; Proteins; Rice; Seeds; Sucrose; Trehalose; Trehalose-6-phosphate; Trehalose-6-phosphate synthase; Web sites
• ISSN: 2167-8359; 2167-8359
• DOI: 10.7717/peerj.11398

Trehalose-6-phosphate synthase (TPS) is significant in the growth, development and stress resistance of plants. We identified the cucumber family and its physicochemical properties, domains, gene structures, evolutionary relationships, gene locations, -acting elements, conserved motifs, and expression patterns using bioinformatics. Our results uncovered seven genes in the cucumber genome and named according to their locations in the chromosomes. Seven genes were randomly distributed in six cucumber chromosomes. Domain analysis showed that the TPS and TPP domains exist in all CsTPSs, and an additional hydrolase-3 domain exist in CsTPS3, CsTPS5 and CsTPS6. Phylogenetic analysis showed that TPS proteins from , rice, soybean, and cucumber were divided into two subfamilies (Class I and Class II) and they were further divided into seven subgroups. TPS proteins from and cucumber were grouped together, suggesting a close evolutionary relationship. Gene structure analysis indicated that most Class I genes contained 16-17 introns, while Class II genes (except ) had two introns. Motif analysis showed that Class II genes had 10 complete conserved motifs, while Class I genes lacked motif 8 and motif 9. Furthermore, genes possessed numerous -acting elements related to stress, hormone, and light response in the promoter regions. GO analysis indicated multiple functions for the CsTPS proteins. Expression analysis of genes in different tissues found that they were expressed in roots, stems and leaves, with the highest expression levels in roots. The expression analysis of under different treatments showed that genes may participate in the response to abiotic stress, plant hormones and sugar treatments.