番茄含糖量不同的两个材料果实转录组初步分析

doi:10.16420/j.issn.0513-353x.2023-0761

摘要/Abstract

摘要：

以高含糖量（8%）和普通含糖量（4.5%）番茄为研究材料，选取绿熟期、转色期、粉红期和红熟期的果实样品，通过转录组测序比较两种材料间的基因表达差异。分析表明，普通番茄与高糖番茄4个时期共有的差异基因有288个，其中下调的有174个，上调的有114个，转色期特有的差异表达基因数量最多。GO分析表明，差异表达基因显著富集在转色期，且富集的GO功能类也最多。KEGG分析表明，转色期富集的差异表达基因及相关通路最多，主要集中在糖、酸代谢等通路。对糖、酸代谢过程关键酶的相关基因进行聚类分析，发现有30个关键差异表达基因。

关键词: 番茄, 含糖量, 成熟期, 转录组分析

Abstract:

High sugar（8%）and common sugar（4.5%）tomatoes were used as the research materials. Fruit samples were collected at the mature green stage，the breaker stage，the pink stage，and the red ripe stage. Transcriptome sequencing was conducted to analyze the differences in gene expression between these two materials. The analysis revealed there 288 differentially expressed genes（DEGs）between common and high sugar tomatoes across these four stages，with 174 down-regulated DEGs and 114 up-regulated DEGs. Notably，the breaker stage showed the highest number of DEGs between these two materials. GO analysis demonstrated significant enrichment of DEGs and GO terms at the breaker stage with the greatest number of GO terms identified at this stage. Furthermore，KEGG analysis showed that the DEGs and related pathways，particularly sugar and acid metabolism pathways，were concentrated at the breaker stage. Clustering analysis of key enzyme genes involved in sugar and acid metabolism identified 30 DEGs.

Key words: tomato, sugar content, maturity stage, transcriptome analysis

张文昊, 张辉, 刘雨婷, 王艳, 张迎迎, 王馨曼, 王全华, 朱为民, 杨学东. 番茄含糖量不同的两个材料果实转录组初步分析[J]. 园艺学报, 2024, 51(2): 281-294.

ZHANG Wenhao, ZHANG Hui, LIU Yuting, WANG Yan, ZHANG Yingying, WANG Xinman, WANG Quanhua, ZHU Weimin, YANG Xuedong. Preliminary Transcriptome Analysis in Two Tomato Fruits Materials with Different Sugar Content[J]. Acta Horticulturae Sinica, 2024, 51(2): 281-294.

图/表 11

图1 普通番茄与高糖番茄主要糖酸含量的变化同一材料中不同小写字母表示不同时期差异显著（P < 0.05）。

Fig. 1 The changes in main sugars and acids between common and high sugar tomatoes Different lowercase letters in the same material indicate significant differences among different stage at 0.05 level.

图2 普通番茄与高糖番茄基因表达量（FPKM）分布盒形图

Fig. 2 The box diagram of gene expression distribution between common and high sugar tomatoes

图3 普通番茄与高糖番茄差异表达基因数

Fig. 3 Number of DEGs between common and high sugar tomatoes

表1 普通番茄与高糖番茄的差异表达基因GO富集数量

Table 1 The enrichment quantity of DEGs in GO between common and high sugar tomatoes

时期 Developmental stage	GO数量 All GOs	总差异基因 All DEGs	下调差异基因 Down-regulated DEGs	上调差异基因 Up-regulated DEGs
绿熟期Mature green	673	5 163	2 524	2 639
转色期Breaker	768	8 544	3 351	5 193
粉红期Pink	651	3 293	1 832	1 461
红熟期Red ripe	657	4 552	2 495	2 057

图4 普通番茄与高糖番茄差异显著的前30个GO功能组

Fig. 4 The top 30 GO terms with significant difference between common and high sugar tomatoes

表2 普通番茄与高糖番茄的差异表达基因通路富集分析

Table 2 The enrichment analysis of DEGs in pathways between common and high sugar tomatoes

发育时期 Developmental stage	通路数量 Pathways	总差异基因 All DEGs	下调差异基因 Down-regulated DEGs	上调差异基因 Up-regulated DEGs
绿熟期Mature green	105	802	443	359
转色期Breaker	116	1 406	668	738
粉红期Pink	100	521	252	269
红熟期Red ripe	106	725	392	333

图5 普通番茄与高糖番茄关键KEGG通路比较

Fig. 5 The comparison of key KEGG pathways between common and high sugar tomatoes

图6 高糖番茄与普通番茄KEGG富集到的糖、酸代谢途径

Fig. 6 The pathways of sugar and acid metabolism enriched by KEGG between high sugar and common tomatoes

图7 KEGG富集到的高糖番茄与普通番茄在糖酸代谢途径中差异表达的基因热图 A：SS：蔗糖合成酶、SPS：磷酸蔗糖合成酶；B：HXK：己糖激酶、FK：果糖激酶；C：AI：酸性转化酶、NI：中性转化酶；D：PEPC：磷酸烯醇式丙酮酸羧化酶、MDH：苹果酸脱氢酶、CS：柠檬酸合酶；E：Starch synthase：淀粉合成酶、α-amylase：α淀粉酶、β-amylase：β淀粉酶；F：TPS：海藻糖合成酶、TPP：海藻糖酸化酶。H：高糖番茄；L：普通番茄；G：绿熟期；B：转色期；P：粉红期；R：红熟期。

Fig. 7 The heat map of DEGs in sugar and acid metabolism pathways between high sugar and common tomatoes enriched by KEGG A：Sucrose synthase SS，sucrose phosphate synthase SPS；B：Hexokinase HXK，fructose kinase FK；C：Acid and neutral invertase；D：Phosphoenolpyruvate carboxylase PEPC，malate dehydrogenase MDH，citrate synthase CS；E：Starch synthase，α-amylase，β-amylase；F：Trehalose synthase TPS，trehalose acidification enzyme TPP. H：High sugar tomato；L：Common tomato；G：Mature green stage；B：Breaker stage；P：Pink stage；R：Red ripe stage.

图8 高糖番茄与普通番茄在糖、酸代谢途径中差异表达基因的聚类分析 H：高糖番茄；L：普通番茄。G：绿熟期；B：转色期；P：粉红期；R：红熟期。

Fig. 8 The clustering analysis of DEGs in sugar and acid metabolism pathways between high sugar and common tomatoes H：High sugar tomato；L：Common tomato；G：Mature green stage；B：Breaker stage；P：Pink stage；R：Red ripe stage.

图9 高糖番茄（H）与普通番茄（L）差异表达基因转录组测序（FPKM）与qRT-PCR相对表达量（relative）检测验证

Fig. 9 Validation of DEGs transcriptome sequencing（FPKM）and qRT-PCR relative expression（relative）assays between high sugar and common tomatoes

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