Functional prediction of de novo uni-genes from chicken transcriptomic data following infectious bursal disease virus at 3-days post-infection.
Functional prediction of de novo uni-genes from chicken transcriptomic data following infectious bursal disease virus at 3-days post-infection.
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DOI：
10.1186/s12864-021-07690-3
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发表时间：
2021-06-19
期刊：
影响因子：
4.4
通讯作者：
Mat Isa N
中科院分区：
文献类型：
--
作者：
Azli B;Ravi S;Hair-Bejo M;Omar AR;Ideris A;Mat Isa N
传染性法氏囊病（IBD）是家禽业的一个重要经济问题，也是国家粮食安全的主要威胁之一。该病原体是一种非常强的IBD病毒的高致病性菌株，可导致鸡的高死亡率和免疫抑制。了解能够对抗这种疾病的潜在基因的重要性现在受到全球关注，以便控制未来的爆发。我们已经研究了可以阐明病毒感染后致病性的新基因，以及鸡体内可能存在的抗病基因。从IBD病毒感染的鸡中检索的一组序列没有映射到鸡参考基因组，从头组装，聚类和分析。从六个近交系鸡，我们设法组装10,828 uni-transcripts和筛选618 uni-transcripts，这是最显着的序列，已知基因，确定通过BLASTX搜索。基于差异表达基因（DEGs）分析，在所有6个自交系中鉴定出12个普遍上调和18个下调的uni基因，错误发现率q值< 0.05。然而，只有9个上调和13个下调的uni基因具有针对非冗余和Swiss-Prot数据库的BLAST命中。这些DEG的基因组本体富集关键词与免疫应答、细胞信号传导和凋亡相关。因此，使用加权基因相关网络分析R工具来预测没有显著BLAST命中的剩余未知单基因的功能注释。有趣的是，预测三个上调的uni基因的功能与先天免疫应答相关，而预测五个下调的uni基因与细胞表面功能相关。这些结果进一步阐明和支持了目前关于IBDV感染鸡法氏囊的病理生理学的分子知识。我们的数据显示，通常上调和下调的新的uni基因被确定为免疫和细胞外结合相关的，分别。此外，这些新的发现在改进现有的整合鸡转录组学注释方面做出了有价值的贡献，并可能为控制病毒颗粒，特别是抑制鸡IBD和其他传染病铺平道路。
Infectious bursal disease (IBD) is an economically very important issue to the poultry industry and it is one of the major threats to the nation’s food security. The pathogen, a highly pathogenic strain of a very virulent IBD virus causes high mortality and immunosuppression in chickens. The importance of understanding the underlying genes that could combat this disease is now of global interest in order to control future outbreaks. We had looked at identified novel genes that could elucidate the pathogenicity of the virus following infection and at possible disease resistance genes present in chickens. A set of sequences retrieved from IBD virus-infected chickens that did not map to the chicken reference genome were de novo assembled, clustered and analysed. From six inbred chicken lines, we managed to assemble 10,828 uni-transcripts and screened 618 uni-transcripts which were the most significant sequences to known genes, as determined by BLASTX searches. Based on the differentially expressed genes (DEGs) analysis, 12 commonly upregulated and 18 downregulated uni-genes present in all six inbred lines were identified with false discovery rate of q-value < 0.05. Yet, only 9 upregulated and 13 downregulated uni-genes had BLAST hits against the Non-redundant and Swiss-Prot databases. The genome ontology enrichment keywords of these DEGs were associated with immune response, cell signalling and apoptosis. Consequently, the Weighted Gene Correlation Network Analysis R tool was used to predict the functional annotation of the remaining unknown uni-genes with no significant BLAST hits. Interestingly, the functions of the three upregulated uni-genes were predicted to be related to innate immune response, while the five downregulated uni-genes were predicted to be related to cell surface functions. These results further elucidated and supported the current molecular knowledge regarding the pathophysiology of chicken’s bursal infected with IBDV. Our data revealed the commonly up- and downregulated novel uni-genes identified to be immune- and extracellular binding-related, respectively. Besides, these novel findings are valuable contributions in improving the current existing integrative chicken transcriptomics annotation and may pave a path towards the control of viral particles especially towards the suppression of IBD and other infectious diseases in chickens.
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