Journal Article

Construction of drought stress regulation networks in potato based on SMRT and RNA sequencing data

Shang, Lina, Jian, Hongju, Lyu, Dianqiu, Wang, Jichun, Sun, Haonan, Khassanov, Vadim, Liu, Rongrong, Zhang, Wenzhe

2022

Overview

Background Potato ( Solanum tuberosum ) is the fourth most important food crop in the world and plays an important role in food security. Drought stress has a significantly negative impact on potato growth and production. There are several publications involved drought stress in potato, this research contributes to enrich the knowledge. Results In this study, next-generation sequencing (NGS) and single-molecule real-time (SMRT) sequencing technology were used to study the transcription profiles in potato in response to 20%PEG6000 simulates drought stress. The leaves of the variety “Désirée” from in vitro plantlets after drought stress at six time points from 0 to 48 hours were used to perform NGS and SMRT sequencing. According to the sequencing data, a total of 12,798 differentially expressed genes (DEGs) were identified in six time points. The real-time (RT)-PCR results are significantly correlated with the sequencing data, confirming the accuracy of the sequencing data. Gene ontology and KEGG analysis show that these DEGs participate in response to drought stress through galactose metabolism, fatty acid metabolism, plant-pathogen interaction, glutathione metabolism and other pathways. Through the analysis of alternative splicing of 66,888 transcripts, the functional pathways of these transcripts were enriched, and 51,098 transcripts were newly discovered from alternative splicing events and 47,994 transcripts were functionally annotated. Moreover, 3445 lncRNAs were predicted and enrichment analysis of corresponding target genes was also performed. Additionally, Alternative polyadenylation was analyzed by TADIS, and 26,153 poly (A) sites from 13,010 genes were detected in the Iso-Seq data. Conclusion Our research greatly enhanced potato drought-induced gene annotations and provides transcriptome-wide insights into the molecular basis of potato drought resistance.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Abscisic acid / Accuracy / Agricultural production / Agriculture / Alternative polyadenylation / Alternative splicing / Analysis / Annotations / Biomarkers / Biomedical and Life Sciences / Cloning / Cultivars / DNA sequencing / Drought / Drought resistance / Drought stress / drought tolerance / Enrichment / fatty acid metabolism / Fatty acids / food crops / Food security / Galactose / gene expression regulation / gene ontology / Genes / Genetic aspects / Genomes / Glutathione / Growth / Hardiness / host-pathogen relationships / Kinases / Life Sciences / LncRNAs / Morphology / Next-generation sequencing / Physiological aspects / Physiology / Plant cellular control mechanisms / Plant Sciences / Plantlets / Plants / Polyadenylation / Polyethylene glycol / Potatoes / Proteins / Real time / RNA / RNA sequencing / SMRT / Solanum tuberosum / Splicing / Transcriptomes / Tree Biology / Vegetables / Water shortages / water stress