Full-length transcriptome sequencing reveals the molecular mechanism of potato seedlings responding to low-temperature

Abstract

Background Potato (Solanum tuberosum L.) is one of the world's most important crops, the cultivated potato is frost-sensitive, and low-temperature severely influences potato production. However, the mechanism by which potato responds to low-temperature stress is unclear. In this research, we apply a combination of second-generation sequencing and third-generation sequencing technologies to sequence full-length transcriptomes in low-temperature-sensitive cultivars to identify the important genes and main pathways related to low-temperature resistance. Results In this study, we obtained 41,016 high-quality transcripts, which included 15,189 putative new transcripts. Amongst them, we identified 11,665 open reading frames, 6085 simple sequence repeats out of the potato dataset. We used public available genomic contigs to analyze the gene features, simple sequence repeat, and alternative splicing event of 24,658 non-redundant transcript sequences, predicted the coding sequence and identified the alternative polyadenylation. We performed cluster analysis, GO, and KEGG functional analysis of 4518 genes that were differentially expressed between the different low-temperature treatments. We examined 36 transcription factor families and identified 542 transcription factors in the differentially expressed genes, and 64 transcription factors were found in the AP2 transcription factor family which was the most. We measured the malondialdehyde, soluble sugar, and proline contents and the expression genes changed associated with low temperature resistance in the low-temperature treated leaves. We also tentatively speculate that StLPIN10369.5 and StCDPK16 may play a central coordinating role in the response of potatoes to low temperature stress. Conclusions Overall, this study provided the first large-scale full-length transcriptome sequencing of potato and will facilitate structure–function genetic and comparative genomics studies of this important crop.

Full-length transcriptome and RNA-Seq analyses reveal the resistance mechanism of sesame in response to Corynespora cassiicola

“…When plants encounter stress, AS can result in a series of defensive stress responses [ 21 ]. Recent studies have revealed that several defence genes undergo alternative splicing that is often affected by pathogen infection [ 42 ].…”

“…In the past few years, an increasing number of PacBio full-length transcriptome have been sequenced and assembled. These studies have helped us to identify numerous new genes and alternatively spliced isoforms in many species, including potato [ 21 ], sorghum [ 22 ], Larix kaempferi [ 23 ], Italian ryegrass root [ 24 ] and kiwifruit [ 25 ]. Overall, the above studies demonstrated that third-generation sequencing complements second-generation sequencing in the quantitative determination of eukaryotic transcripts and contributes to the discovery of an increasing number of alternatively spliced isoforms [ 26 ].…”

Transcriptome analysis reveals the effect of cold storage time on the expression of genes related to oxidative metabolism in Chinese black truffle

“…TFs bind DNA in a sequence-specific way to control gene transcription ( 73 ). Under stress conditions, organisms activate RNA polymerase II transcription complexes by stimulating TFs through a sequential signal transmission with the appropriate cis-acting element combination, activating the expression of particular genes and response to environmental signals ( 74 , 75 ). Previous studies showed that TFs in association regulated the expression of functionally associated genes under stress conditions, and the overexpression of these TFs either stimulated or suppressed the expression of resistance-related genes to ultimately alter an organism’s capacity to survive in stressed environments ( 76 ).…”

“…Previous studies showed that TFs in association regulated the expression of functionally associated genes under stress conditions, and the overexpression of these TFs either stimulated or suppressed the expression of resistance-related genes to ultimately alter an organism’s capacity to survive in stressed environments ( 76 ). For example, studies have confirmed that a group of TFs, including bHLH, bZIP, MYB, C2H2, ERF, NAC, and WRKY, play an important role in plant responses to low temperature stress ( 75 ). Our results showed that a total of 1,342 TFs of 43 families were differentially expressed in truffles under cold storage for 0, 15, or 30 d, respectively, with the highest level of abundance of TFs revealed in the C2H2 family, followed by zn-clus, C3H, and bZIP families of TFs.…”

Chromosome-scale genome, together with transcriptome and metabolome, provides insights into the evolution and anthocyanin biosynthesis of Rubus rosaefolius Sm. (Rosaceae)

“…The quality and content of the extracted DNA and total RNA were checked using a Qubit 2.0 fluorometer (Thermo Fisher Scientific, Waltham, MA, USA) and an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The genomic short-read library, genomic long-read library, short-read transcriptome library, and full-length transcriptome library were constructed following the standard protocol provided by the sequencer manufacturer and have been ‘described earlier [ 47 , 48 ]. The Hi-C library of R. rosaefolius was constructed following the protocols proposed by Rao et al .…”