Eukaryote common transcriptome sequencing

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mRNA-Seq: Gene structure, expression, function studies
Sequencing and analysis of mRNAs. Can be used for:
Structural analysis: such as constructing transcripts from scratch, optimizing existing gene structure, discovering new genes, discovering new transcripts, discovering fusion genes, identifying RNA edits, detecting variants;
Expression analysis: such as the expression quantification of genes in various samples, the identification of differentially expressed genes between samples, and the expression analysis based on time series;
Functional mining: Functional mining is carried out for structural analysis and expression analysis results, including PCA analysis, expression pattern clustering, co-expression network construction, enrichment analysis, etc.

Successful Case
Transcriptome profiling of Arabidopsis thaliana roots in response to allelopathic effects of Conyza canadensis
Abstract
The molecular mechanisms underlying allelopathy and their role in the interactions between invasive weeds and native species remain unclear. In this study, we aimed to explore the physiological and molecular response of plant roots of a native species to allelopathy from an invasive weed. We examined the growth and development of roots of native Arabidopsis thaliana for a 2-week period after being treated with aqueous extracts at different concentrations from invasive Conyza canadensis. Extracts with higher concentration in the Murashige and Skoog (MS) media (i.e., 4 mg of extract/mL of MS) significantly affected the root growth of A. thaliana. Roots of A. thaliana displayed weakened root tip activity and an accumulation of reactive oxygen species (ROS) in response to extracts from C. canadensis. The transcriptome analysis of A. thaliana roots exposed to phytotoxicity revealed differentially expressed genes (DEGs) involved in cell wall formation, abiotic stress, transporter genes and signal transduction. We found that genes associated with nutrient transport, such as major facilitator superfamily (MFS) and amino acid permease (AAP3) transporters as well as genes involved in stress response, including leucine-rich repeat receptor-like protein kinases (LRR-RLKs) were down-regulated. In addition, we found that many transcription factors associated with plant stress (such as APETALA2/ethylene response factors) were up-regulated while others (e.g., zinc-finger proteins) were down-regulated. Allelochemicals from C. canadensis also induced the up-regulation of detoxification (DTX) genes, ROS related genes, calcineurin B-like interacting protein kinases (CIPKs) and calmodulin. Overall, our findings provided insights into allelopathy in C. canadensis at the molecular level, and contributes to our understanding of invasion mechanisms of alien plant species.

Fig1 Molecular model of allelopathic effect of Conyza canadensis showing cellular
processes and response/ regulatory pathways leading to stress response in roots of
Arabidopsis thaliana
References
Haiyan Zhang, et al. Transcriptome profiling of Arabidopsis thaliana roots in response to
allelopathic effects of Conyza canadensit. BioRxiv,2020