Bioinformatics prediction of mitochondrial and chloroplast transcripts possibly involved in maize abiotic stress signaling

Abstract

In plants, the expression of mitochondrial and chloroplast genomes is continuously changing to enable adequate functional adjustments related to overall metabolic changes needed for plant adaptation to fluctuating environmental conditions. In order to identify mitochondrial and chloroplast transcripts expressed prior to stresses, we have analyzed mitochondrial and chloroplast transcriptomes of 46 maize inbred lines chosen from three main heterotic groups (BSSS, Lancaster, Iowa dent) regularly used in elite maize breeding programs. Organelles’ data were extracted from transcriptome data obtained by next generation sequencing of total leaf transcriptomes of 46 maize inbred lines grown under the optimal conditions in the greenhouse. All data manipulation and differential gene expression analysis were performed by using Galaxy software (https://usegalaxy.eu/). Detected organellar complex transcripts milieus were expected to contain candidates that modulate responses of their genomes by activating certain signaling pathways upon exposure to abiotic stresses. With the aim to identify such candidates we focused on selecting transcripts that were differentially expressed between 46 maize inbred lines grown under the optimal breeding conditions and also annotated as important for abiotic stresses response in different plant species. Selected transcripts/genes were then subjected to freely available tools for gene networking analysis with the aim to depict possible anterograde and retrograde signaling between nucleus and mitochondria/chloroplasts under the abiotic stresses. Obtained results are promising in terms of planning biological experiments for testing the roles of genes that were bioinformatically predicted as novel members of abiotic stress signaling network between nucleus and organelles in maize.