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Published on: May 21, 2020
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Full-length transcriptome analysis of pecan (Carya illinoinensis) kernels
Chengcai Zhang1, Huadong Ren1, Xiaohua Yao1
1Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China.
G3 (Bethesda, Md.)
|December 1, 2021
Summary
This study used long-read sequencing to reveal full-length pecan kernel transcripts, identifying novel isoforms and regulatory elements. This enhances understanding of fatty acid and flavonoid biosynthesis in pecans.
Area of Science:
- Plant Molecular Biology
- Nutritional Genomics
- Bioinformatics
Background:
- Pecan nuts are globally important and rich in bioactive compounds like fatty acids (FAs) and flavonoids.
- Understanding the molecular basis of phytochemical biosynthesis in pecans is crucial for improving nut quality.
- Previous genomic and transcriptomic studies lacked full-length mRNA transcript data and comprehensive regulatory insights.
Purpose of the Study:
- To generate a comprehensive full-length transcriptome dataset for pecan kernels.
- To investigate the regulatory mechanisms governing phytochemical biosynthesis, particularly fatty acids and flavonoids.
- To identify novel transcripts, alternative splicing events, and regulatory factors in pecan.
Main Methods:
- Employed single-molecule long-read sequencing technology to capture full-length mRNA transcripts from pecan kernels.
- Mapped obtained transcripts to the reference genome, quantifying known, new, and novel isoforms.
- Utilized bioinformatics tools for functional annotation, alternative splicing (AS) and alternative polyadenylation (APA) event detection, and prediction of long noncoding RNAs (lncRNAs) and transcription factors (TFs).
Main Results:
- Generated 37,504 isoforms from 16,702 genes, with over 80% functionally annotated.
- Identified 15,465 AS events, with retained introns being the most frequent type (36.55%).
- Detected 65,761 APA events and predicted 1894 lncRNAs and 1643 TFs. Notably, FA synthesis genes showed high AS accuracy (70.31%).
Conclusions:
- This study provides the first full-length transcriptome dataset for pecan kernels.
- The findings offer significant insights into the regulation of phytochemical biosynthesis, especially fatty acids and flavonoids.
- The data will serve as a valuable resource for future research on pecan quality improvement and genetic studies.
