# Integrated Transcriptome and Metabolome Analysis of Fruit Quality Variation in ‘Sweet100’ Tomato Across Different Growth Stages

## TL;DR

This study explores how tomato fruit quality changes across growth stages by analyzing gene and metabolite patterns, revealing stable and variable factors affecting flavor and quality.

## Contribution

The study identifies stable and variable metabolic and transcriptional modules across growth stages, offering new insights into tomato quality formation.

## Key findings

- 192 metabolites and 5546 genes were grouped into modules showing distinct or stable trends across growth stages.
- Soluble sugar levels remained stable, while total phenols and flavonoids varied significantly.
- Key flavor metabolites like aspartic acid and glucose showed no significant changes in content.

## Abstract

Previously, research has primarily focused on how the environment affects fruit quality, but there is a lack of studies investigating the impact of different growth stages on fruit quality. In this study, a total of 192 differentially abundant metabolites and 5546 differentially expressed genes were categorized into eight modules exhibiting distinct trends, along with an additional module that remained unchanged throughout all growth stages. These modules elucidate the primary metabolic alterations and transcriptional regulatory networks underlying quality variations in tomato fruits at the mature stage across different growth stages (Spike1–Spike3). Furthermore, an investigation was conducted on the module that remained constant throughout the growth stages. It was observed that the soluble sugar content remained stable across the different growth stages, whereas the levels of total phenols and flavonoids exhibited significant variation. Additionally, the principal metabolites influencing tomato flavor—namely aspartic acid, glutamic acid, glucose, fructose, citric acid, α-linolenic acid, and linoleic acid—did not demonstrate significant changes in content. The findings of this study provide novel insights into the formation of tomato quality and establish a theoretical foundation for the cultivation of long-season tomatoes with stable fruit quality.