Isoform Sequencing Provides Insight Into Freezing Response of Common Wheat (Triticum aestivum L.)

Abstract

The objective of the study is to reveal the freezing tolerance mechanisms of wheat by combining the emerging single-molecule real-time (SMRT) sequencing technology PacBio Sequel and Illumina sequencing. Commercial semiwinter wheat Zhoumai 18 was exposed to −6 • C for 4 h at the four-leave stage. Leaves of the control group and freezing-treated group were used to perform cDNA library construction. PacBio SMRT sequencing yielded 51,570 high-quality isoforms from leaves of control sample of Zhoumai 18, encoded by 20,366 gene loci. In total, 73,695 transcript isoforms, corresponding to 23,039 genes, were identified from the freezing-treated leaves. Compared with transcripts from the International Wheat Genome Sequencing Consortium RefSeq v1.1, 57,667 novel isoforms were discovered, which were annotated 21,672 known gene loci, as well as 3,399 novel gene loci. Transcriptome characterization including alterative spliced events, alternative polydenylation sites, transcription factors, and fusion transcripts were also analyzed. Freezing-responsive genes and signals were uncovered and proved that the ICE-ERF-COR pathway and ABA signal transduction play a vital role in the freezing response of wheat. In this study, PacBio sequencing and Illumina sequencing were applied to investigate the freezing tolerance in common wheat, and the transcriptome results provide insights into the molecular regulation mechanisms under freezing treatment.

Transcription-associated metabolomic profiling reveals the critical role of frost tolerance in wheat

“…With the speediness evolution of sequencing tools, transcriptome sequencing technology has been extensively applied to clarify gene function by high-throughput analysis of genomic information, and provided a potent way to systematically study the relationship between genotype and phenotype in transcriptional regulation [37]. For example, it has been widely used in research wheat stress resistance to reveal differentially expressed genes in different biological processes, such as cold [38][39][40], drought [41], heat [42], and salt tolerance [43]. However, low abundance and unknown transcripts are unable to distinguish [37].…”

The Landscapes of Gluten Regulatory Network in Elite Wheat Cultivars Contrasting in Gluten Strength

“…Third-generation sequencing technology holds great potential for improved transcript detection compared to second-generation sequencing techniques such as RNA-seq. This has been demonstrated through its successful applications in a variety of plants [31][32][33][34]. The current study provided comprehensive landscapes of isoform full-length sequences, gene structures, lncRNAs, and AS events.…”

The Isolation and Full-Length Transcriptome Sequencing of a Novel Nidovirus and Response of Its Infection in Japanese Flounder (Paralichthys olivaceus)

“…The exon-intron structure of each transcript was predicted. Newly found loci and isoforms were identified by comparing them to the reference genome annotation, using the same criteria as for loci and isoform identification [24]. Alternative splicing (AS) events were analyzed using SUPPA [25].…”

“…The absolute dpsi value of 0.1 and p-value of 0.05 were set as the threshold for significantly differential alternative splice. The full-length transcript that was mapped on two or more loci in the reference genome with more than 99% alignment coverage and having the locus 100 kb apart from each other on the reference genome and a 10% alignment of each gene locus to the corresponding transcript was predicted as a fusion transcript [24].…”