Chicken transcriptome analysis and discovery of novel genes involved in infectious bursal disease virus infection
Infectious bursal disease (IBD) is a major concern to food security because pathogenic strain of IBD virus (vvIBDV) can cause high mortality and immunosuppression in chickens that has not been controlled till date. This study aims to study the differential expression and discover novel genes in I...
Saved in:
| 主要作者: | |
|---|---|
| 格式: | Thesis |
| 语言: | English |
| 出版: |
2018
|
| 主题: | |
| 在线阅读: | http://psasir.upm.edu.my/id/eprint/99471/1/SHARANYA%20RAVI%20-%20IR.pdf |
| 标签: |
添加标签
没有标签, 成为第一个标记此记录!
|
| id |
my-upm-ir.99471 |
|---|---|
| record_format |
uketd_dc |
| spelling |
my-upm-ir.994712023-04-04T03:51:44Z Chicken transcriptome analysis and discovery of novel genes involved in infectious bursal disease virus infection 2018-01 Ravi, Sharanya Infectious bursal disease (IBD) is a major concern to food security because pathogenic strain of IBD virus (vvIBDV) can cause high mortality and immunosuppression in chickens that has not been controlled till date. This study aims to study the differential expression and discover novel genes in IBDV infected chickens. 18 transcriptomes generated from de novo sequencing of samples from six different lines of IBDV infected and control chicken were analysed. Sequences that did not map to the reference genome of Gallus gallus were analysed for differentially expressed genes (DEG) in IBDV infected chickens. About 600 unigenes out of 10,828 were selected for VENNTURE (Venn diagram) analysis that resulted in 12 upregulated and 18 downregulated DEGs that were common to all the six lines of chicken. Annotation predicted the functions to be involved in the transcription factor activities and extra cellular binding activities which aids in the immune response. Three upregulated and four downregulated unigenes did not have any significant BLAST hits. Gene networks generated using the weighted gene correlation network analysis (WGCNA) predicted the functions of the unknown sequences to be related to interleukin 18 binding protein, mucin13 isoform XI and extracellular matrix protein, cerebellar degenerative protein, cell surface protein, ubiquitin conjugating protein. Quantitative PCR was performed on 10 genes including the unknown genes (7 genes), FoxP3 gene and two known genes that were homologues with species other than Gallus gallus to validate the differential expression. Presence of FOX P3 gene was validated by visualizing the amplification. Based on the results, four out of seven unknown were found to be in chicken and their functional prediction contributes to the resistance against the disease. Chickens - Viruses Poultry - Diseases 2018-01 Thesis http://psasir.upm.edu.my/id/eprint/99471/ http://psasir.upm.edu.my/id/eprint/99471/1/SHARANYA%20RAVI%20-%20IR.pdf text en public doctoral Universiti Putra Malaysia Chickens - Viruses Poultry - Diseases Mat Isa, Nurulfiza |
| institution |
Universiti Putra Malaysia |
| collection |
PSAS Institutional Repository |
| language |
English |
| advisor |
Mat Isa, Nurulfiza |
| topic |
Chickens - Viruses Poultry - Diseases |
| spellingShingle |
Chickens - Viruses Poultry - Diseases Ravi, Sharanya Chicken transcriptome analysis and discovery of novel genes involved in infectious bursal disease virus infection |
| description |
Infectious bursal disease (IBD) is a major concern to food security because pathogenic
strain of IBD virus (vvIBDV) can cause high mortality and immunosuppression in
chickens that has not been controlled till date. This study aims to study the differential
expression and discover novel genes in IBDV infected chickens. 18 transcriptomes
generated from de novo sequencing of samples from six different lines of IBDV
infected and control chicken were analysed. Sequences that did not map to the
reference genome of Gallus gallus were analysed for differentially expressed genes
(DEG) in IBDV infected chickens. About 600 unigenes out of 10,828 were selected
for VENNTURE (Venn diagram) analysis that resulted in 12 upregulated and 18
downregulated DEGs that were common to all the six lines of chicken. Annotation
predicted the functions to be involved in the transcription factor activities and extra
cellular binding activities which aids in the immune response. Three upregulated and
four downregulated unigenes did not have any significant BLAST hits. Gene networks
generated using the weighted gene correlation network analysis (WGCNA) predicted
the functions of the unknown sequences to be related to interleukin 18 binding protein,
mucin13 isoform XI and extracellular matrix protein, cerebellar degenerative protein,
cell surface protein, ubiquitin conjugating protein. Quantitative PCR was performed
on 10 genes including the unknown genes (7 genes), FoxP3 gene and two known genes
that were homologues with species other than Gallus gallus to validate the differential
expression. Presence of FOX P3 gene was validated by visualizing the amplification.
Based on the results, four out of seven unknown were found to be in chicken and their
functional prediction contributes to the resistance against the disease. |
| format |
Thesis |
| qualification_level |
Doctorate |
| author |
Ravi, Sharanya |
| author_facet |
Ravi, Sharanya |
| author_sort |
Ravi, Sharanya |
| title |
Chicken transcriptome analysis and discovery of novel genes involved in infectious bursal disease virus infection |
| title_short |
Chicken transcriptome analysis and discovery of novel genes involved in infectious bursal disease virus infection |
| title_full |
Chicken transcriptome analysis and discovery of novel genes involved in infectious bursal disease virus infection |
| title_fullStr |
Chicken transcriptome analysis and discovery of novel genes involved in infectious bursal disease virus infection |
| title_full_unstemmed |
Chicken transcriptome analysis and discovery of novel genes involved in infectious bursal disease virus infection |
| title_sort |
chicken transcriptome analysis and discovery of novel genes involved in infectious bursal disease virus infection |
| granting_institution |
Universiti Putra Malaysia |
| publishDate |
2018 |
| url |
http://psasir.upm.edu.my/id/eprint/99471/1/SHARANYA%20RAVI%20-%20IR.pdf |
| _version_ |
1776100339275005952 |