PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species

Yang, Jingli; Lv, Wanqiu; Shao, Lipei; Fu, Yanrui; Liu, Haimei; Yang, Chengjun; Chen, Aihua; Xie, Xieyu; Wang, Zhiwei; Li, Chenghao

doi:10.3389/fpls.2021.737004

Cited by 9 publications

(9 citation statements)

References 54 publications

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“…This led to more increment of transcriptome diversity and complexity in SLH and probably contributed to its adaptation to cold stressful condition. Previous reports also had showed that AS events were regulated by multiple environmental stress and were largely associated with cold stress resistance in plants ( Li et al., 2020b ; John et al., 2021 ; Yang et al., 2021 ). In agreement with other plant species, the predominant AS events were IR in peanut.…”

Section: Discussionmentioning

confidence: 88%

Full-length transcriptome sequencing provides insights into alternative splicing under cold stress in peanut

Wang,

Liu,

Ouyang

et al. 2024

Front. Plant Sci.

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IntroductionPeanut (Arachis hypogaea L.), also called groundnut is an important oil and cash crop grown widely in the world. The annual global production of groundnuts has increased to approximately 50 million tons, which provides a rich source of vegetable oils and proteins for humans. Low temperature (non-freezing) is one of the major factors restricting peanut growth, yield, and geographic distribution. Since the complexity of cold-resistance trait, the molecular mechanism of cold tolerance and related gene networks were largely unknown in peanut.MethodsIn this study, comparative transcriptomic analysis of two peanut cultivars (SLH vs. ZH12) with differential cold tolerance under low temperature (10°C) was performed using Oxford Nanopore Technology (ONT) platform.Results and discussionAs a result, we identified 8,949 novel gene loci and 95,291 new/novel isoforms compared with the reference database. More differentially expressed genes (DEGs) were discovered in cold-sensitive cultivar (ZH12) than cold-tolerant cultivar (SLH), while more alternative splicing events were found in SLH compared to ZH12. Gene Ontology (GO) analyses of the common DEGs showed that the “response to stress”, “chloroplast part”, and “transcription factor activity” were the most enriched GO terms, indicating that photosynthesis process and transcription factors play crucial roles in cold stress response in peanut. We also detected a total of 708 differential alternative splicing genes (DASGs) under cold stress compared to normal condition. Intron retention (IR) and exon skipping (ES) were the most prevalent alternative splicing (AS) events. In total, 4,993 transcription factors and 292 splicing factors were detected, many of them had differential expression levels and/or underwent AS events in response to cold stress. Overexpression of two candidate genes (encoding trehalose-6-phosphatephosphatases, AhTPPs) in yeast improves cold tolerance. This study not only provides valuable resources for the study of cold resistance in peanut but also lay a foundation for genetic modification of cold regulators to enhance stress tolerance in crops

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Section: Discussionmentioning

confidence: 88%

Full-length transcriptome sequencing provides insights into alternative splicing under cold stress in peanut

Wang,

Liu,

Ouyang

et al. 2024

Front. Plant Sci.

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“…AS mainly involve SFs interacting with RNA-binding proteins at regulatory sites known as silencers or enhancers. 42 SFs promote or inhibit splicing events by recognizing splicing regulatory sites on precursor RNA and recruiting and assembling spliceosomes. 43 SFs have become a new class of oncoproteins.…”

Section: Discussionmentioning

confidence: 99%

Immunotherapeutic Significance of a Prognostic Alternative Splicing Signature in Bladder Cancer

Chen

Liao

et al. 2022

Technol Cancer Res Treat

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Objectives: Bladder cancer is the fourth most common malignancy in men in the United States. Aberrant alternative splicing (AS) events are involved in the carcinogenesis, but the association between AS and bladder cancer remains unclear. This study aimed to construct an AS-based prognostic signature and elucidate the role of the tumor immune microenvironment (TIME) and the response to immunotherapy and chemotherapy in bladder cancer. Methods: Univariate Cox regression analysis was performed to detect prognosis-related AS events. The least absolute shrinkage and selection operator (LASSO) and multivariate Cox analyses were employed to build prognostic signatures. Kaplan–Meier survival analysis, multivariate Cox regression analysis, and receiver operating characteristic (ROC) curves were conducted to validate the prognostic signatures. Then, the Estimation of Stromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE) and tumor immune estimation resource (TIMER) databases were searched and the single-sample gene set enrichment analysis (ssGSEA) algorithm and CIBERSORT method were performed to uncover the context of TIME in bladder cancer. The Tumor Immune Dysfunction and Exclusion (TIDE) web tool and pRRophetic algorithm were used to predict the response to immunotherapy and chemotherapy. Finally, we constructed a correlation network between splicing factors (SFs) and survival-related AS events. Results: A total of 4684 AS events were significantly associated with overall survival in patients with bladder cancer. Eight prognostic signatures of bladder cancer were established, and a clinical survival prediction model was built. In addition, the consolidated prognostic signature was closely related to immune infiltration and the response to immunotherapy and chemotherapy. Furthermore, the correlation identified EIF3A, DDX21, SDE2, TNPO1, and RNF40 as hub SFs, and function analysis found ubiquitin-mediated proteolysis is correlated most significantly with survival-associated AS events. Conclusion: Our findings highlight the prognostic value of AS for patients with bladder cancer and reveal pivotal players of AS events in the context of TIME and the response to immunotherapy and chemotherapy, which may be important for patient management and treatment.

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“…It increases the chances for discovering new genes and detecting AS events, APA, as well as lncRNAs. The combined application of second- and third-generation sequencing technologies has emerged as a powerful tool in transcriptomics research, successfully revealing transcriptome and gene structure information in multiple plant species [ 22 – 25 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide characterization of post-transcriptional processes related to wood formation in Dalbergia odorifera

Jiao,

Xu,

Wang

et al. 2024

BMC Genomics

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Background Alternative polyadenylation (APA), alternative splicing (AS), and long non-coding RNAs (lncRNAs) play regulatory roles in post-transcriptional processes in plants. However, little is known about their involvement in xylem development in Dalbergia odorifera, a valuable rosewood species with medicinal and commercial significance. We addressed this by conducting Isoform Sequencing (Iso-Seq) using PacBio’s SMRT technology and combined it with RNA-seq analysis (RNA sequencing on Illumina platform) after collecting xylem samples from the transition zone and the sapwood of D. odorifera. Results We identified 14,938 full-length transcripts, including 9,830 novel isoforms, which has updated the D. odorifera genome annotation. Our analysis has revealed that 4,164 genes undergo APA, whereas 3,084 genes encounter AS. We have also annotated 118 lncRNAs. Furthermore, RNA-seq analysis identified 170 differential alternative splicing (DAS) events, 344 genes with differential APA site usage (DE-APA), and 6 differentially expressed lncRNAs in the transition zone when compared to the sapwood. AS, APA, and lncRNAs are differentially regulated during xylem development. Differentially expressed APA genes were enriched for terpenoid and flavonoid metabolism, indicating their role in the heartwood formation. Additionally, DE-APA genes were associated with cell wall biosynthesis and terpenoid metabolism, implying an APA’s role in wood formation. A DAS gene (involved in chalcone accumulation) with a significantly greater inclusion of the last exon in the transition zone than in the sapwood was identified. We also found that differentially expressed lncRNAs targeted the genes related to terpene synthesis. Conclusions This study enhances our understanding of the molecular regulatory mechanisms underlying wood formation in D. odorifera, and provides valuable genetic resources and insights for its molecular-assisted breeding.

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PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species

Cited by 9 publications

References 54 publications

Full-length transcriptome sequencing provides insights into alternative splicing under cold stress in peanut

Full-length transcriptome sequencing provides insights into alternative splicing under cold stress in peanut

Immunotherapeutic Significance of a Prognostic Alternative Splicing Signature in Bladder Cancer

Genome-wide characterization of post-transcriptional processes related to wood formation in Dalbergia odorifera

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