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

Abstract

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.

Construction of heat stress regulation networks based on Illumina and SMRT sequencing data in potato

“…RI was the most frequent type of AS detected, accounted 55.73%, followed by A3, SE, A5, and MX (Figure 7A). Further subdivided at each time point, there was similar number of AS events among heat stressed potato leaves (Figure 7B), which was consistent with previous studies in potato involved in response to drought stress (Jian et al, 2022).…”

RNA-seq provides insights into potato deubiquitinase responses to drought stress in seedling stage

“…DUBs also increase the diversity of gene expression products through alternative splicing, which is an effective mechanism to increase the complexity and flexibility of the transcriptome and is a way for plants to adapt to the environment. Alternative splicing plays a key role in potato growth and abiotic stress responses ( Laloum et al., 2018 ; Punzo et al., 2020 ; Jian et al., 2022 ). We screened 82 different differential alternative splicing in potato DUBs, including SE, A3SS, RI, and A5SS.…”

Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family

“…The study identified 5,508 DEGs and highlighted the significant enrichment of categories related to nucleic acid binding, transporter activity, ion/molecule transport, ion binding, kinase activity, and oxidative phosphorylation. More recently, Jian et al. (2022) and Tang et al.…”

“…Recent advancements in sequencing technologies have culminated in multiple publications presenting genome assemblies for various diploid and polyploid potato varieties (Table 1; Kyriakidou et al, 2020;Pham et al, 2020;Yang et al, 2020;Zhou et al, 2020;Freire et al, 2021;Tiwari et al, 2021;Sun et al, 2022). Finally, two pangenome assembly were obtained through the implementation of long-read sequencing technology: Hoopes et al (2022) encompassed six potato varieties tailored for distinct marketsfresh ('Colomba', 'Spunta'), chip processing ('Atlantic'), frozen processing ('Castle Russet'), and starch markets ('Altus', 'Avenger'), developing the first pan-genome of polyploid potato varieties.…”