Genome-Wide Analysis of Alternative Splicing during Host-Virus Interactions in Chicken
Abstract
:1. Introduction
2. Materials and Methods
2.1. Data Sources
2.2. Read Alignment to the Reference Chicken Genome and Gene Expression Estimation
2.3. Putative Transcript Assembly and AS Event Identification
2.4. Alternative Splicing Landscapes and Differential Splicing Analysis
2.5. Functional Enrichment, Clustering, and Isoform-Level Differential Expression Analysis
2.6. 3′ UTR Analysis
2.7. Spliceosome Analysis
3. Results
3.1. Mapping Transcriptome Data to the Reference Chicken Genome
3.2. Alternative Splicing Events of Virus-Infected Chicken
3.3. Virus-Modulated Alternatively Spliced Gene Cluster Analysis
3.4. Dynamic Analyses of Alternative Polyadenylation in 3′ UTRs
3.5. Spliceosome during Virus Infection
3.6. Virus-Modulated Alternative Splicing of Splicing Factors
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Total | B1 | B2 | B3 | H1 | H2 | H3 | L1 | L2 | L3 | |
---|---|---|---|---|---|---|---|---|---|---|
Mapped Reads | ||||||||||
Unique left (%) | 299,224,346 (91.2%) | 42,058,610 (90.3%) | 42,726,173 (90.1%) | 33,598,545 (91.9%) | 24,791,424 (90.8%) | 28,441,340 (91.8%) | 29,097,409 (91.0%) | 34,714,376 (91.4%) | 31,484,844 (92.6%) | 32,311,625 (91.3%) |
Nonunique left (%) | 28,796,379 (8.8%) | 4,309,183 (9.7%) | 4,705,478 (9.9%) | 2,954,136 (8.1%) | 2,516,090 (9.2%) | 2,546,773 (8.2%) | 2,863,948 (9.0%) | 3,285,909 (8.6%) | 2,525,643 (7.4%) | 3,089,219 (8.7%) |
Unique right (%) | 285,044,438 (91.3%) | 39,971,739 (90.3%) | 41,096,311 (90.1%) | 30,961,117 (91.9%) | 23,667,626 (90.8%) | 27,053,760 (91.8%) | 27,702,817 (91.1%) | 33,141,424 (91.4%) | 30,353,878 (92.6%) | 31,095,766 (91.3%) |
Nonunique left (%) | 27,808,310 (8.7%) | 4,542,921 (9.7%) | 4,495,046 (9.9%) | 2,720,323 (8.1%) | 2,397,429 (9.2%) | 2,407,222 (8.2%) | 2,716,835 (8.9%) | 3,130,883 (8.6%) | 2,429,221 (7.4%) | 2,968,430 (8.7%) |
Overall alignment | 79.00% | 86.80% | 87.20% | 85.80% | 66.50% | 66.70% | 69.70% | 82.70% | 82.80% | 82.60% |
Total aligned pairs | 293,168,743 | 41,610,655 | 42,736,163 | 31,659,213 | 24,439,859 | 27,508,308 | 28,424,075 | 33,979,545 | 30,741,417 | 32,069,508 |
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Liu, W.; Sun, Y.; Qiu, X.; Meng, C.; Song, C.; Tan, L.; Liao, Y.; Liu, X.; Ding, C. Genome-Wide Analysis of Alternative Splicing during Host-Virus Interactions in Chicken. Viruses 2021, 13, 2409. https://doi.org/10.3390/v13122409
Liu W, Sun Y, Qiu X, Meng C, Song C, Tan L, Liao Y, Liu X, Ding C. Genome-Wide Analysis of Alternative Splicing during Host-Virus Interactions in Chicken. Viruses. 2021; 13(12):2409. https://doi.org/10.3390/v13122409
Chicago/Turabian StyleLiu, Weiwei, Yingjie Sun, Xusheng Qiu, Chunchun Meng, Cuiping Song, Lei Tan, Ying Liao, Xiufan Liu, and Chan Ding. 2021. "Genome-Wide Analysis of Alternative Splicing during Host-Virus Interactions in Chicken" Viruses 13, no. 12: 2409. https://doi.org/10.3390/v13122409
APA StyleLiu, W., Sun, Y., Qiu, X., Meng, C., Song, C., Tan, L., Liao, Y., Liu, X., & Ding, C. (2021). Genome-Wide Analysis of Alternative Splicing during Host-Virus Interactions in Chicken. Viruses, 13(12), 2409. https://doi.org/10.3390/v13122409