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

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Transcriptomic Complexity in Strawberry Fruit Development and Maturation Revealed by Nanopore Sequencing.

Qing Chen¹, Ximeng Lin¹, Wenlu Tang¹

¹College of Horticulture, Sichuan Agricultural University, Chengdu, China.

Frontiers in Plant Science

|August 1, 2022

Summary

This summary is machine-generated.

Strawberry fruit development involves complex transcript isoforms generated by alternative transcription start sites (aTSS), alternative transcription termination sites (aTTS), and alternative splicing (AS). These processes impact gene function and fruit maturation.

Keywords:

B-box protein 22 alternative splicing isoform switch nanopore sequencing strawberry fruit

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Area of Science:

Plant molecular biology
Transcriptomics
Fruit development

Background:

Alternative transcription start sites (aTSS), alternative transcription termination sites (aTTS), and alternative splicing (AS) generate transcript isoforms crucial for plant development.
Understanding the role of these isoforms in strawberry fruit development and gene function is limited.

Purpose of the Study:

To systematically investigate transcriptome complexity during strawberry fruit development.
To compare the contributions of aTSS, aTTS, and AS to transcript diversity.
To explore the functional relevance of isoform changes during fruit maturation.

Main Methods:

Long-read Oxford Nanopore Technologies for full-length cDNA sequencing.
Analysis of transcript isoforms across four successive developmental stages.
Comparative analysis of aTSS, aTTS, and AS abundance.
Identification of differentially expressed transcripts and isoform switches.
Yeast two-hybrid analysis for functional validation.

Main Results:

Thousands of previously unexplored transcript isoforms from aTSS, aTTS, and AS were identified.
aTSS and aTTS were more abundant than AS in strawberry fruit transcripts.
The white fruit stage emerged as a key transitional phase.
Isoform switches in 757 genes were linked to changes in protein-coding potential and domain alterations.
Genes with switched isoforms are involved in late-stage maturation processes.

Conclusions:

Strawberry fruit development exhibits a dynamic transcriptomic landscape driven by aTSS, aTTS, and AS.
Alternative transcription start/termination sites play a more significant role than alternative splicing in transcript complexity.
Isoform switching significantly impacts gene function during fruit maturation, with implications for B-box protein 22.
This study provides a comprehensive overview of transcriptomic complexity during strawberry fruit development.