The Sucrose Synthase Gene Family in Chinese Pear (Pyrus bretschneideri Rehd.): Structure, Expression, and Evolution

Abstract

Sucrose synthase (SS) is a key enzyme involved in sucrose metabolism that is critical in plant growth and development, and particularly quality of the fruit. Sucrose synthase gene families have been identified and characterized in plants various plants such as tobacco, grape, rice, and Arabidopsis. However, there is still lack of detailed information about sucrose synthase gene in pear. In the present study, we performed a systematic analysis of the pear (Pyrus bretschneideri Rehd.) genome and reported 30 sucrose synthase genes. Subsequently, gene structure, phylogenetic relationship, chromosomal localization, gene duplications, promoter regions, collinearity, RNA-Seq data and qRT-PCR were conducted on these sucrose synthase genes. The transcript analysis revealed that 10 PbSSs genes (30%) were especially expressed in pear fruit development. Additionally, qRT-PCR analysis verified the RNA-seq data and shown that PbSS30, PbSS24, and PbSS15 have a potential role in the pear fruit development stages. This study provides important insights into the evolution of sucrose synthase gene family in pear and will provide assistance for further investigation of sucrose synthase genes functions in the process of fruit development, fruit quality and resistance to environmental stresses.

Keywords: RNA-seq data analysis; characteristics; expression pattern; phylogenetic analysis; sucrose synthase.

Figure 1

Gene structure and distribution of conserved motif of PbSSs genes in Chinese pear. (A) Phylogenetic relationship and gene structure of pear PbSSs genes. (B) Conserved motifs located on each gene with the relative combined p-value.

Figure 2

Phylogenetic relationships and domain structures of the sucrose synthase genes. (a) Phylogenetic analysis of pear sucrose synthase genes with other ten species (Supplementary Table S2) (b) Domain structures of the sucrose synthase proteins. Sucrose_synth indicated sucrose synthase domains. (c) The phylogenetic tree was generated by using NCBI database (https://www.ncbi.nlm.nih.gov/Taxonomy/CommonTree/wwwcmt.cgi) and presented the history of whole genome duplication of fifteen species. Green and dark orange specify whole genome duplication and triplication, respectively.

Figure 3

Chromosomal location and microsynteny regions of PbSSs genes. (a) Chromosomal location of all PbSSs genes and blue line represent segmental duplication and red highlighted PbSSs genes IDs represent tandem duplication. (b) Synteny analyses of PbSSs genes between Pyrus bretschneideri and Prunus mume. (c) Synteny analyses of PbSSs genes between Pyrus bretschneideri and Fragaria vesca. (d) Synteny analyses of PbSSs genes between Pyrus bretschneideri and Prunus persica.

Figure 4

Sliding window plots of all duplicated PbSSs genes in pear. The window size is 150 bp, and the step size is 9 bp. The X-axis indicated the synonymous distance within each gene.

Figure 5

Investigation of cis-acting element numbers in all sucrose synthase genes of pear. (a) The different colors and numbers of the grid indicated the numbers of different promoter elements in these sucrose synthase genes. (b) The different colored histogram represented the sum of the cis-acting elements in each category. (c) Pie charts of different sizes indicated the ratio of each promoter element in each category, respectively.

Figure 6

Expression pattern of PbSSs genes. (a) Organ-specific expression pattern of PbSSs genes in seven fruit development stages: 15, 30, 55, 85, 115 (DAF), mature stage and senescence stage. Blue and red indicated lower and higher transcript abundance, respectively. (b) Highly expressed PbSSs genes in pear fruit. According to the previous studies [24], blue, green, violet red, red indicated low (1–6.8 FPKM), mid-low (6.8–17.5 FPKM), mid-high (17.5–44.7 FPKM), and high (44.7–17,092 FPKM) expression, respectively. (c) Venn diagram of PbSSs genes in different fruit development stages.

Figure 7

Expression patterns of PbSSs genes during different development stages, including 15, 39, 63, 22, 87, 101, 125 and 149 (DAF) as determined by qRT-PCR experiment. Mean values and standard deviations (SDs) indicated by error bars. ** significant difference (p < 0.01), * significant difference at p < 0.05.