Alternative splicing impacts the rice stripe virus response transcriptome

被引：2
作者：
Li, Shanshan [1 ,2 ]
Guo, Wenbin [3 ]
Wang, Chen [1 ,2 ]
Tang, Yao [1 ,2 ]
Li, Lulu [2 ]
Zhang, Hehong [2 ]
Li, Yanjun [2 ]
Wei, Zhongyan [2 ]
Chen, Jianping [1 ,2 ]
Sun, Zongtao [2 ]
机构：
[1] Nanjing Agr Univ, Coll Plant Protect, Nanjing 210095, Peoples R China
[2] Ningbo Univ, Inst Plant Virol, State Key Lab Managing Biot & Chem Threats Qual &, Key Lab Biotechnol Plant Protect MOA China & Zhej, Ningbo 315211, Peoples R China
[3] James Hutton Inst, Informat & Computat Sci, Dundee DD2 5DA, Scotland
来源：
VIROLOGY | 2023年 / 587卷
关键词：
Rice stripe virus (RSV); Transcriptome; Alternative splicing (AS); Genome-wide; Differentially expressed genes (DEGs); Differentially alternative spliced (DAS); Differential transcript usage (DTU); STRESS; GENE; PROTEIN; DEFENSE; ACTIVATION; INFECTION; INSIGHTS; IMMUNITY; SALINITY; FUNGAL;
D O I：
10.1016/j.virol.2023.109870
中图分类号：
Q93 [微生物学];
学科分类号：
071005 ; 100705 ;
摘要：
Alternative splicing (AS) is an important form of post transcriptional modification present in both animals and plants. However, little information was obtained about AS events in response to plant virus infection. In this study, we conducted a genome-wide transcriptome analysis on AS change in rice infected by a devastating virus, Rice stripe virus (RSV). KEGG analysis was performed on the differentially expressed (DE) genes and differentially alternative spliced (DAS) genes. The results showed that DE genes were significantly enriched in the pathway of interaction with plant pathogens. The DAS genes were mainly enriched in basal metabolism and RNA splicing pathways. The heat map clustering showed that DEGs clusters were mainly enriched in regulation of transcription and defense response while differential transcript usage (DTU) clusters were strongly enriched in mRNA splicing and calcium binding. Overall, our results provide a fundamental basis for gene-wide AS changes in rice after RSV infection.
引用
收藏
页数：9
相关论文
共 81 条
[1]   CONTROLLING THE FALSE DISCOVERY RATE - A PRACTICAL AND POWERFUL APPROACH TO MULTIPLE TESTING [J].
BENJAMINI, Y ;
HOCHBERG, Y .
JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY, 1995, 57 (01) :289-300
[2]   Mechanisms of alternative pre-messenger RNA splicing [J].
Black, DL .
ANNUAL REVIEW OF BIOCHEMISTRY, 2003, 72 :291-336
[3]   Alternative Splicing in Angiogenesis [J].
Bowler, Elizabeth ;
Oltean, Sebastian .
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2019, 20 (09)
[4]   The Rice Serine/Arginine Splicing Factor RS33 Regulates Pre-mRNA Splicing during Abiotic Stress Responses [J].
Butt, Haroon ;
Bazin, Jeremie ;
Prasad, Kasavajhala V. S. K. ;
Awad, Nourelislam ;
Crespi, Martin ;
Reddy, Anireddy S. N. ;
Mahfouz, Magdy M. .
CELLS, 2022, 11 (11)
[5]   Oryza sativa salt-induced RING E3 ligase 2 (OsSIRP2) acts as a positive regulator of transketolase in plant response to salinity and osmotic stress [J].
Chapagain, Sandeep ;
Park, Yong Chan ;
Kim, Ju Hee ;
Jang, Cheol Seong .
PLANTA, 2018, 247 (04) :925-939
[6]   fastp: an ultra-fast all-in-one FASTQ preprocessor [J].
Chen, Shifu ;
Zhou, Yanqing ;
Chen, Yaru ;
Gu, Jia .
BIOINFORMATICS, 2018, 34 (17) :884-890
[7]   An alternatively spliced heat shock transcription factor, OsHSFA2dI, functions in the heat stress-induced unfolded protein response in rice [J].
Cheng, Q. ;
Zhou, Y. ;
Liu, Z. ;
Zhang, L. ;
Song, G. ;
Guo, Z. ;
Wang, W. ;
Qu, X. ;
Zhu, Y. ;
Yang, D. .
PLANT BIOLOGY, 2015, 17 (02) :419-429
[8]   The JAZ family of repressors is the missing link in jasmonate signalling [J].
Chini, Andrea ;
Fonseca, S. ;
Fernandez, G. ;
Adie, B. ;
Chico, J. M. ;
Lorenzo, O. ;
Garcia-Casado, G. ;
Lopez-Vidriero, I. ;
Lozano, F. M. ;
Ponce, M. R. ;
Micol, J. L. ;
Solano, R. .
NATURE, 2007, 448 (7154) :666-+
[9]  
Cho WK, 2013, PLANT PATHOLOGY J, V29, P223
[10]   Biology and molecular biology of viruses in the genus Tenuivirus [J].
Falk, BW ;
Tsai, JH .
ANNUAL REVIEW OF PHYTOPATHOLOGY, 1998, 36 :139-163
123456789