Genome-wide Identification and Expression Pattern Profiling of the Trehalose-6-phosphate Synthase（TPS）Gene Family in Tea Plant（Camellia sinensis）

doi:10.13560/j.cnki.biotech.bull.1985.2024-0252

Abstract

Abstract:

【Objective】Trehalose-6-phosphate synthase（TPS）is a key enzyme in the trehalose biosynthetic pathway in plants. The TPS gene family of the tea plant[Camellia sinensis（L.）O. Kuntze]was identified, analyzed, and its expression pattern under adverse stress was studied. This study aims to provide a foundation for the functional validation of TPS genes.【Method】Utilizing biological information methods, we identified members of CsTPS gene family and analyzed the physical and chemical properties of their encoded protein, conserved motifs and domains, chromosomal location, phylogenetic relationships, promoter cis-acting elements, and other biological information. Subsequently, we employed transcriptome data in conjunction with RT-qPCR technology to investigate the expression patterns of CsTPS family members under drought, salt, and cold stress.【Result】The 16 TPS gene family members were identified in C. sinensis genome, which were classified into two subfamilies: Class I and Class II based on phylogenetic study. Members of the same subfamily presented similar motif composition and gene structure. The covariance and evolutionary studies revealed that CsTPS genes were duplicated within the tea plant genome and experienced purifying selection during the evolutionary process. RT-qPCR results revealed that the six candidate genes, CsTPS3, CsTPS5, CsTPS6, CsTPS9, CsTPS11, and CsTPS14, were all induced by PEG, NaCl, and low-temperature stress, and their expression patterns were similar with transcriptome information.【Conclusion】Sixteen TPS family members were identified systematically across the tea plant's genome. The CsTPS3, CsTPS5, CsTPS6, CsTPS9, CsTPS11, and CsTPS14 genes all are sensitive to drought, salt, and low-temperature stresses, though their sensitivity levels differed.

Key words: tea plant, trehalose-6-phosphate synthase gene, phylogeny, expression pattern, abiotic stress

LIU Dan-dan, WANG Lei-gang, SUN Ming-hui, JIAO Xiao-yu, WU Qiong, WANG Wen-jie. Genome-wide Identification and Expression Pattern Profiling of the Trehalose-6-phosphate Synthase（TPS）Gene Family in Tea Plant（Camellia sinensis）[J]. Biotechnology Bulletin, 2024, 40(8): 152-163.

Figures/Tables 8

Table 1 Primer sequences for real-time PCR

基因名称Gene name	正向引物序列Forward primer sequence（5'-3'）	反向引物序列Reverse primer sequence（5'-3'）
β-actin	GCCATCTTTGATTGGAATGG	GGTGCCACAACCTTGATCTT
CsTPS3	TTCTCACAGAGAGTGATTGAGGTG	GGACTATGGAGAAAGAACCCCATT
CsTPS5	TTCTCACAGAGAGTGATTGAGGTG	GGACTATGGAGAAAGAACCCCATT
CsTPS6	TGTCTTTATTGTTAGTGGGAGGGG	CACAATTTCCTTCCACTCAAGGTC
CsTPS9	GCAAGATATGGAGAGAACTTGTGC	TGGGGCATTACAGTACCATCATAG
CsTPS11	GGTTACCTGTCTCTGCAGTTAGAA	CAAAGCTTTAGTAAGTGCCCTCTG
CsTPS14	GCCCTGATGATGATTTTGTATGGG	TTCAACTCTGACAGGTAGTGTACG

Fig. 1 Phylogenetic relationship of TPS genes in A. thali-ana, C. sinensis ‘SCZ’, C. sinensis ‘DASZ’ and C. chekiangoleosa

Fig. 2 Phylogenetic relationships（A）, motif compositions（B）and gene structure（C）of TPS genes in C. sinensis

Fig. 3 Distribution of TPS genes on the chromosome in C. sinensis

Fig. 4 Predicted cis-elements of promotors in TPS gene family of C. sinensis

Fig. 5 Analysis of syntenic and Ka/Ks of TPS genes in Camellia plants A: Syntenic analysis of TPS genes in C. sinensis. The inner gray lines indicate all the collinearity relationships in the whole genome, and the inner orange and green lines indicate the collinearity relationships of Class I and Class II subfamilies, respectively. B: Syntenic analysis of TPS genes between C. sinensis ‘SCZ’ and C. chekiangoleosa. C: Syntenic analysis of TPS genes between C. sinensis ‘SCZ’ and C. sinensis ‘DASZ’. D: Analysis of Ka/Ks. E: Density distribution of Ks for paralogous gene pairs of the three species of Camellia plants

Fig. 6 Transcriptome expression profiling of TPS genes in C. sinensis A, C and D graphs indicate the expression patterns of CsTPS genes in different tissues, 25% PEG stress and 200 mmol/L NaCl stress, respectively. B: Expression pattern of CsTPS gene under low temperature domestication（CK: 1 month of growth at 25℃ during the day, 20℃ at night, 12 h photoperiod and 70% humidity; CA1-6h: 6 h treatment at 10℃; CA1-7d: 10℃ during the day, 4℃ at night treatment for 7 d; CA2-7d: 4℃ during the day and 0℃ at night for 7 d; DA-7d: 25℃ during the day and 20℃ at night for 7 d）. The log2（FPKM+1）value reflects in the heatmap

Fig. 7 Relative expressions of CsTPS genes under various stress A: Gene expression profiles of CsTPSs under 20% PEG. B: Gene expression profiles of CsTPSs under 200 mmol/L NaCl. C: Gene expression profiles of CsTPSs under 4℃ treatment. D: Circadian expression profiling of the CsTPS genes at 24℃. Error bars indicate the standard deviation of three independent biological replicates, different lowercase letters in indicate significant differences at different time of the same treatment（P<0.05）

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