Integrated analysis of genes and long non-coding RNAs in trachea transcriptome to decipher the host response during Newcastle disease challenge in different breeds of chicken
Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved..
Newcastle disease is a highly infectious economically devastating disease caused by Newcastle disease Virus in Chicken (Gallus gallus). Leghorn and Fayoumi are two breeds which show differential resistance patterns towards NDV. This study aims to identify the differentially expressed genes and lncRNAs during NDV challenge which could play a potential role in this differential resistance pattern. A total of 552 genes and 1580 lncRNAs were found to be differentially expressing. Of them, 52 genes were annotated with both Immune related pathways and Gene ontologies. We found that most of these genes were upregulated in Leghorn between normal and challenged chicken but several were down regulated between different timepoints after NDV challenge, while Fayoumi showed no such downregulation. We also observed that higher number of positively correlating lncRNAs was found to be downregulated along with these genes. This shows that although Leghorn is showing higher number of differentially expressed genes in challenged than in non-challenged, most of them were downregulated during the disease between different timepoints. With this we hypothesize that the downregulation of immune related genes and co-expressing lncRNAs could play a significant role behind the Leghorn being comparatively susceptible breed than Fayoumi. The computational pipeline is available at https://github.com/Venky2804/FHSpipe.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2023 |
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| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:253 |
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| Enthalten in: |
International journal of biological macromolecules - 253(2023), Pt 5 vom: 31. Dez., Seite 127183 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Vanamamalai, Venkata Krishna [VerfasserIn] |
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| Links: |
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| Themen: |
Differential expression analysis |
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| Anmerkungen: |
Date Completed 24.11.2023 Date Revised 24.11.2023 published: Print-Electronic Citation Status MEDLINE |
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| doi: |
10.1016/j.ijbiomac.2023.127183 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM36287252X |
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| 100 | 1 | |a Vanamamalai, Venkata Krishna |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Integrated analysis of genes and long non-coding RNAs in trachea transcriptome to decipher the host response during Newcastle disease challenge in different breeds of chicken |
| 264 | 1 | |c 2023 | |
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| 500 | |a Date Completed 24.11.2023 | ||
| 500 | |a Date Revised 24.11.2023 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved. | ||
| 520 | |a Newcastle disease is a highly infectious economically devastating disease caused by Newcastle disease Virus in Chicken (Gallus gallus). Leghorn and Fayoumi are two breeds which show differential resistance patterns towards NDV. This study aims to identify the differentially expressed genes and lncRNAs during NDV challenge which could play a potential role in this differential resistance pattern. A total of 552 genes and 1580 lncRNAs were found to be differentially expressing. Of them, 52 genes were annotated with both Immune related pathways and Gene ontologies. We found that most of these genes were upregulated in Leghorn between normal and challenged chicken but several were down regulated between different timepoints after NDV challenge, while Fayoumi showed no such downregulation. We also observed that higher number of positively correlating lncRNAs was found to be downregulated along with these genes. This shows that although Leghorn is showing higher number of differentially expressed genes in challenged than in non-challenged, most of them were downregulated during the disease between different timepoints. With this we hypothesize that the downregulation of immune related genes and co-expressing lncRNAs could play a significant role behind the Leghorn being comparatively susceptible breed than Fayoumi. The computational pipeline is available at https://github.com/Venky2804/FHSpipe | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Differential expression analysis | |
| 650 | 4 | |a Functional annotation | |
| 650 | 4 | |a Gene-lncRNA co-expression analysis | |
| 650 | 4 | |a Long non-coding RNAs | |
| 650 | 4 | |a Newcastle disease | |
| 650 | 4 | |a Trachea transcriptome | |
| 650 | 7 | |a RNA, Long Noncoding |2 NLM | |
| 700 | 1 | |a E, Priyanka |e verfasserin |4 aut | |
| 700 | 1 | |a T R, Kannaki |e verfasserin |4 aut | |
| 700 | 1 | |a Sharma, Shailesh |e verfasserin |4 aut | |
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