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An Efficient Method for the Isolation of Highly Purified RNA from Seeds for Use in Quantitative Transcriptome Analysis
Published on: January 11, 2017
Transcript assembly and quantification by RNA-Seq reveals differentially expressed genes between soft-endocarp and
Hongyan Dai1, Guofen Han, Yujiao Yan
1College of Horticulture, Shenyang Agricultural University, Shenyang, China.
Plos One
|September 17, 2013
Summary
Researchers identified key genes involved in hawthorn (Crataegus spp.) fruit development. This study reveals that down-regulated lignin biosynthesis and up-regulated flavonoid biosynthesis contribute to soft endocarp formation in hawthorn.
Area of Science:
- Plant Biology
- Genomics
- Biochemistry
Background:
- Hawthorn (Crataegus spp.) is a significant pome fruit with historical uses in food, horticulture, and traditional medicine.
- A unique hawthorn variety with a soft, thin endocarp was discovered in China, contrasting with the typical hard, stony endocarp.
Purpose of the Study:
- To investigate the molecular mechanisms responsible for the soft endocarp trait in hawthorn.
- To compare gene expression profiles between soft- and hard-endocarp hawthorn varieties.
Main Methods:
- Performed de novo assembly of the fruit transcriptome from Crataegus pinnatifida.
- Compared gene expression profiles between soft- and hard-endocarp hawthorn.
- Utilized quantitative RT-PCR to validate gene expression levels.
Main Results:
- Assembled 52,673 putative unigenes, with 35,979 matching existing gene models.
- Identified 1,218 differentially expressed genes between the two hawthorn types.
- Observed down-regulation of lignin biosynthesis genes and strong up-regulation of flavonoid biosynthesis genes in soft-endocarp hawthorn.
Conclusions:
- The study provides the first transcriptome analysis for the Crataegus genus.
- Altered expression of lignin and flavonoid biosynthesis pathways, potentially regulated by MYB and NAC transcription factors, underlies soft endocarp formation.
- Generated high-quality expressed sequence tags (ESTs) to facilitate future hawthorn gene cloning and research.
