Genome-wide analysis of alternative splicing events during response to drought stress in tomato (Solanum lycopersicum L.)

2019 ◽  
Vol 95 (3) ◽  
pp. 286-293 ◽  
Author(s):  
Hee Ju Lee ◽  
Seung Hee Eom ◽  
Jin Hyoung Lee ◽  
Seung Hwan Wi ◽  
Sung Kyeom Kim ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Drought Stress ◽  
Solanum Lycopersicum ◽  
Genome Wide Analysis ◽  
Solanum Lycopersicum L ◽  
Genome Wide ◽  
Alternative Splicing Events

scholarly journals Genome-Wide Analysis of Alternative Splicing during Host-Virus Interactions in Chicken

Viruses ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2409
Author(s):  
Weiwei Liu ◽  
Yingjie Sun ◽  
Xusheng Qiu ◽  
Chunchun Meng ◽  
Cuiping Song ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Virus Infection ◽  
Immune Gene ◽  
Genome Wide Analysis ◽  
Pathogen Invasion ◽  
Avian Virus ◽  
Genome Wide ◽  
A Genome ◽  
Model Animal ◽  
Alternative Splicing Events

The chicken is a model animal for the study of evolution, immunity and development. In addition to their use as a model organism, chickens also represent an important agricultural product. Pathogen invasion has already been shown to modulate the expression of hundreds of genes, but the role of alternative splicing in avian virus infection remains unclear. We used RNA-seq data to analyze virus-induced changes in the alternative splicing of Gallus gallus, and found that a large number of alternative splicing events were induced by virus infection both in vivo and in vitro. Virus-responsive alternative splicing events preferentially occurred in genes involved in metabolism and transport. Many of the alternatively spliced transcripts were also expressed from genes with a function relating to splicing or immune response, suggesting a potential impact of virus infection on pre-mRNA splicing and immune gene regulation. Moreover, exon skipping was the most frequent AS event in chickens during virus infection. This is the first report describing a genome-wide analysis of alternative splicing in chicken and contributes to the genomic resources available for studying host–virus interaction in this species. Our analysis fills an important knowledge gap in understanding the extent of genome-wide alternative splicing dynamics occurring during avian virus infection and provides the impetus for the further exploration of AS in chicken defense signaling and homeostasis.

scholarly journals Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize

2015 ◽  
Vol 170 (1) ◽  
pp. 586-599 ◽  
Author(s):  
Shawn R. Thatcher ◽  
Olga N. Danilevskaya ◽  
Xin Meng ◽  
Mary Beatty ◽  
Gina Zastrow-Hayes ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Drought Stress ◽  
Genome Wide Analysis ◽  
Genome Wide

scholarly journals Genome-wide analysis of alternative splicing events inHordeum vulgare: Highlighting retention of intron-based splicing and its possible function through network analysis

FEBS Letters ◽  
2015 ◽  
Vol 589 (23) ◽  
pp. 3564-3575 ◽  
Author(s):  
Bahman Panahi ◽  
Seyed Abolghasem Mohammadi ◽  
Reyhaneh Ebrahimi Khaksefidi ◽  
Jalil Fallah Mehrabadi ◽  
Esmaeil Ebrahimie
Keyword(s):  
Alternative Splicing ◽  
Network Analysis ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Alternative Splicing Events

scholarly journals Integrative Genome-wide Analysis of the Determinants of RNA Splicing in Kidney Renal Clear Cell Carcinoma

2014 ◽  
Author(s):  
Kjong-Van Lehmann ◽  
Andre Kahles ◽  
Cyriac Kandoth ◽  
William Lee ◽  
Nikolaus Schultz ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Cell Carcinoma ◽  
Clear Cell ◽  
Clear Cell Carcinoma ◽  
Renal Clear Cell Carcinoma ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Alternative Splicing Events ◽  
Splicing Patterns

We present a genome-wide analysis of splicing patterns of 282 kidney renal clear cell carcinoma patients in which we integrate data from whole-exome sequencing of tumor and normal samples, RNA-seq and copy number variation. We proposed a scoring mechanism to compare splicing pat- terns in tumor samples to normal samples in order to rank and detect tumor-specific isoforms that have a potential for new biomarkers. We identified a subset of genes that show introns only observable in tumor but not in normal samples, ENCODE and GEUVADIS samples. In order to improve our understanding of the underlying genetic mechanisms of splicing variation we performed a large-scale association analysis to find links between somatic or germline variants with alternative splicing events. We identified 915 cis- and trans-splicing quantitative trait loci (sQTL) associated with changes in splicing patterns. Some of these sQTL have previously been associated with being susceptibility loci for cancer and other diseases. Our analysis also allowed us to identify the function of several COSMIC variants showing significant association with changes in alternative splicing. This demonstrates the potential significance of variants affecting alternative splicing events and yields insights into the mechanisms related to an array of disease phenotypes.

scholarly journals Genome-Wide Identification and Expression Profiling of the PDI Gene Family Reveals Their Probable Involvement in Abiotic Stress Tolerance in Tomato (Solanum lycopersicum L.)

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 23
Author(s):  
Antt Htet Wai ◽  
Muhammad Waseem ◽  
A B M Mahbub Morshed Khan ◽  
Ujjal Kumar Nath ◽  
Do Jin Lee ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Stress Tolerance ◽  
Solanum Lycopersicum ◽  
Expression Profiling ◽  
Abiotic Stress Tolerance ◽  
Dependent Manner ◽  
Solanum Lycopersicum L ◽  
Genome Wide ◽  
Protein Disulfide

Protein disulfide isomerases (PDI) and PDI-like proteins catalyze the formation and isomerization of protein disulfide bonds in the endoplasmic reticulum and prevent the buildup of misfolded proteins under abiotic stress conditions. In the present study, we conducted the first comprehensive genome-wide exploration of the PDI gene family in tomato (Solanum lycopersicum L.). We identified 19 tomato PDI genes that were unevenly distributed on 8 of the 12 tomato chromosomes, with segmental duplications detected for 3 paralogous gene pairs. Expression profiling of the PDI genes revealed that most of them were differentially expressed across different organs and developmental stages of the fruit. Furthermore, most of the PDI genes were highly induced by heat, salt, and abscisic acid (ABA) treatments, while relatively few of the genes were induced by cold and nutrient and water deficit (NWD) stresses. The predominant expression of SlPDI1-1, SlPDI1-3, SlPDI1-4, SlPDI2-1, SlPDI4-1, and SlPDI5-1 in response to abiotic stress and ABA treatment suggested they play regulatory roles in abiotic stress tolerance in tomato in an ABA-dependent manner. Our results provide new insight into the structure and function of PDI genes and will be helpful for the selection of candidate genes involved in fruit development and abiotic stress tolerance in tomato.

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