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Obtaining High-Quality Transcriptome Data from Cereal Seeds by a Modified Method for Gene Expression Profiling

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Transcriptome analysis of Ginkgo biloba kernels.

Bing He¹, Yincong Gu¹, Meng Xu¹

¹Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University Nanjing, China.

Frontiers in Plant Science

|October 27, 2015

Summary

This study presents the first transcriptome sequencing of Ginkgo kernels, identifying key genes involved in terpenoid biosynthesis. Findings suggest bilobalide synthesis may impact ginkgolide production in Ginkgo biloba.

Keywords:

Ginkgo biloba differentially expressed genes (DEGs)kernel terpenoid backbone biosynthesis transcriptome

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Area of Science:

Plant genomics
Molecular biology
Biochemistry

Background:

Ginkgo biloba, a medicinally important species, has limited genomic resources.
Understanding its genetic makeup is crucial for research and applications.

Purpose of the Study:

To perform the first transcriptome sequencing of Ginkgo kernels.
To identify genes involved in metabolic pathways, particularly terpenoid biosynthesis.
To investigate gene expression patterns during kernel development.

Main Methods:

Illumina paired-end sequencing of Ginkgo kernels across five time points.
De novo assembly of transcriptome data to generate unigenes.
Differential gene expression analysis and metabolic pathway analysis.

Main Results:

Generated 68,547 unigenes from 25.08-Gb clean reads.
Annotated 43.74% of unigenes in public databases.
Identified 3,869 differentially expressed genes.
Revealed 66 unigenes in terpenoid backbone biosynthesis, with 12 up-regulated for ginkgolide and bilobalide synthesis.
Indicated potential interference between bilobalide and ginkgolide synthesis.

Conclusions:

This study significantly expands transcriptome resources for Ginkgo.
Provides a valuable platform for studying developmental and metabolic mechanisms in Ginkgo.
Uncovers insights into the complex biosynthesis of ginkgolides and bilobalides.