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Transcriptome-wide expression landscape and starch synthesis pathway co-expression network in sorghum
Zhenbin Hu1, Junhao Chen1, Marcus O Olatoye2
1Department of Biology, Saint Louis University, Saint Louis, Missouri, USA.
The Plant Genome
|April 11, 2024
Summary
This study presents the first comprehensive sorghum transcriptome atlas, identifying thousands of housekeeping and tissue-specific genes. This resource aids in understanding gene function and agricultural trait discovery.
Area of Science:
- Genomics
- Plant Biology
- Functional Genomics
Background:
- Understanding gene expression across tissues and developmental stages is crucial for deciphering biological functions and evolutionary patterns.
- Comprehensive transcriptomic analyses are limited in sorghum, hindering the discovery of genetic underpinnings for complex agricultural traits.
- A detailed gene expression landscape is essential for advancing sorghum functional genomics.
Purpose of the Study:
- To create the most comprehensive transcriptomic atlas for sorghum to date.
- To identify and characterize housekeeping genes (HKGs) and tissue-specific expression genes (TEGs).
- To investigate gene features, selective constraints, and co-expression networks within the sorghum transcriptome.
Main Methods:
- Utilized 873 RNA-sequencing (RNA-seq) datasets covering 19 distinct sorghum tissues.
- Performed integrative analysis to construct a genome-wide expression landscape.
- Developed transcriptome-wide co-expression networks (TW-CEN) and pathway-specific networks.
Main Results:
- Established a comprehensive sorghum transcriptomic atlas.
- Identified 595 housekeeping genes (HKGs) and 2080 tissue-specific expression genes (TEGs).
- Revealed that HKGs exhibit stronger selective constraints than TEGs and high-connectivity genes are under intensive selective pressure.
- Discovered roles for photosynthesis and microtubule-based movement in starch synthesis via co-expression networks.
Conclusions:
- The sorghum transcriptome atlas is a valuable resource for functional gene characterization and trait discovery.
- Distinct features and evolutionary pressures exist between HKGs and TEGs.
- Co-expression network analysis provides insights into complex biological pathways like starch synthesis.
