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. 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不同发育阶段果实开展转录组测序（RNA-seq）分析，以探究类胡萝卜素潜在积累机制。
研究方法：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不同发育阶段果实的转录组序列。经质量过滤的序列读段通过HISAT2软件比对至甜瓜基因组（http://cucurbitgenomics.org/organism/18）。差异表达基因的筛选阈值为|log₂(倍数变化)|>0且校正后P值（padj）≤0.05；同时采用SYBR Green法进行定量实时聚合酶链反应（qRT-PCR）验证。
研究结果：通过优化的数据分析流程，本研究将每个样本约4000万条序列读段比对至甜瓜基因组。通过基因本体（Gene Ontology, GO）富集分析与京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）富集分析，对差异表达基因进行功能分类。本研究重点关注类胡萝卜素代谢相关基因，并通过qRT-PCR完成验证。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不同发育阶段果实的转录组序列。本研究报道的优化数据分析流程可为表达谱比较分析提供研究框架。本转录组特征分析有助于解析东方甜瓜的基因功能及代谢过程，同时提供了两个栽培品种东方甜瓜不同发育阶段果实的mRNA表达谱数据。