Transcriptome sequence of oriental melon fruit at diferent stages in two cultivars

Purpose: the goals of this study are to compare fruit of two clitivars oriental melon transcriptome profiling (RNA-seq) at different stages to explore carotenoid potentail carotenoid accumulation mechanism Methods:The transcriptome sequence of two cultivars oriental melon fruits at different stages were generated by deep sequencing with three repeats using Illumina. The sequence reads that passed filters were mapped to melon genome (http://cucurbitgenomics.org/organism/18) using HISAT2 software. The differently expressed genes were identify by |log2(FoldChange)| > 0 & padj <= 0.05, and qRT–PCR validation was performed using SYBR Green assays Result:Using an optimized data analysis workflow, we mapped about 40 million sequence reads per sample to the melon genome. The differentially expressed genes were functionally classified by GO and KEGG enrichment. We focused on carotenoid metabolism related gene and validated using qRT-PCR. The results showed RNA-seq and qRT-PCR were highly correlated. Conclusion: Our study provided transcriptome sequence of oriental melon fruits at different stages in two cultivars. The optimized data analysis workflows reported here should provide comparative framework of expression profiles. Our transcriptome characterization contribute to analyze gene functions and metabolic process of oriental melon. Overall design: Oriental melon fruits mRNA profiles of different stages in two cultivars.

研究目的：本研究旨在对两个栽培品种的东方甜瓜果实不同发育阶段的转录组测序（RNA-seq）数据进行比较分析，以探究类胡萝卜素潜在的积累机制。实验方法：采用Illumina平台进行深度测序，设置3次生物学重复，获取两个栽培品种东方甜瓜果实不同发育阶段的转录组序列。将通过质量过滤的测序读段比对至甜瓜参考基因组（http://cucurbitgenomics.org/organism/18），比对工具为HISAT2软件。以|log₂(倍数变化)|>0且校正后P值（padj）≤0.05作为筛选标准，鉴定差异表达基因，并采用SYBR Green染料法进行实时定量聚合酶链反应（qRT-PCR）验证。实验结果：通过优化后的数据分析流程，本研究将每个样本约4000万条测序读段比对至甜瓜参考基因组。通过基因本体（GO）富集分析和京都基因与基因组百科全书（KEGG）富集分析，对差异表达基因进行功能注释分类。本研究重点关注类胡萝卜素代谢相关基因，并通过qRT-PCR进行了验证。结果显示，RNA-seq与qRT-PCR的检测结果具有高度相关性。研究结论：本研究获取了两个栽培品种东方甜瓜果实不同发育阶段的转录组序列。本研究报道的优化数据分析流程，可为基因表达谱的比较分析提供标准化框架。本研究的转录组特征分析有助于解析东方甜瓜的基因功能与代谢过程。实验整体设计：涵盖两个栽培品种东方甜瓜果实不同发育阶段的信使RNA（mRNA）表达谱。