Transcriptome-wide expression landscape and starch synthesis pathway co-expression network in sorghum

The gene expression landscape across different tissues and developmental stages reflects their biological functions and evolutionary patterns. Integrative and comprehensive analyses of all transcriptomic data in an organism are instrumental to obtaining a comprehensive picture of gene expression landscape. Such studies are still very limited in sorghum, which limits the discovery of the genetic basis underlying complex agricultural traits in sorghum. We characterized the genome-wide expression landscape for sorghum using 873 RNA-sequencing (RNA-seq) datasets representing 19 tissues. Our integrative analysis of these RNA-seq data provides the most comprehensive transcriptomic atlas for sorghum, which will be valuable for the sorghum research community for functional characterizations of sorghum genes. Based on the transcriptome atlas, we identified 595 housekeeping genes (HKGs) and 2080 tissue-specific expression genes (TEGs) for the 19 tissues. We identified different gene features between HKGs and TEGs, and we found that HKGs have experienced stronger selective constraints than TEGs. Furthermore, we built a transcriptome-wide co-expression network (TW-CEN) comprising 35 modules with each module enriched in specific Gene Ontology terms. High-connectivity genes in TW-CEN tend to express at high levels while undergoing intensive selective pressure. We also built global and seed-preferential co-expression networks of starch synthesis pathways, which indicated that photosynthesis and microtubule-based movement play important roles in starch synthesis. The global transcriptome atlas of sorghum generated by this study provides an important functional genomics resource for trait discovery and insight into starch synthesis regulation in sorghum. Large-scale transcriptome data were analyzed to characterize the sorghum gene and long noncoding RNA expression landscape. Housekeeping and tissue-specific genes were identified. The co-expression network was constructed to identify the regulatory network of the starch synthesis pathway. To characterize the genome-wide gene expression landscape and provide functional genomics resources for future gene mining for complex traits, we comprehensively analyzed large-scale RNA-seq data from different tissues. We built an atlas of sorghum gene/lncRNA expression and identified housekeeping and tissue-specific expression genes. We observed that gene expression patterns were closely related to gene features and selection pressure. The co-expression network showed that photosynthesis and microtubule-based movement play important roles in starch synthesis. The global transcriptome atlas provides an important functional genomics resource for trait discovery and insight into starch synthesis regulation in sorghum.