Weighted Gene Co-Expression Network Analysis Based on Stimulation by Lipopolysaccharides and Polyinosinic:polycytidylic Acid Provides a Core Set of Genes for Understanding Hemolymph Immune Response Mechanisms of <i>Amphioctopus fangsiao</i>
The primary influencer of aquaculture quality in <i>Amphioctopus fangsiao</i> is pathogen infection. Both lipopolysaccharides (LPS) and polyinosinic:polycytidylic acid (Poly I:C) are recognized by the pattern recognition receptor (PRR) within immune cells, a system that frequently serves...
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MDPI AG
2023-12-01
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| Series: | Animals |
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| Online Access: | https://www.mdpi.com/2076-2615/14/1/80 |
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| author | Yongjie Wang Xipan Chen Xiaohui Xu Jianmin Yang Xiumei Liu Guohua Sun Zan Li |
| author_facet | Yongjie Wang Xipan Chen Xiaohui Xu Jianmin Yang Xiumei Liu Guohua Sun Zan Li |
| author_sort | Yongjie Wang |
| collection | DOAJ |
| description | The primary influencer of aquaculture quality in <i>Amphioctopus fangsiao</i> is pathogen infection. Both lipopolysaccharides (LPS) and polyinosinic:polycytidylic acid (Poly I:C) are recognized by the pattern recognition receptor (PRR) within immune cells, a system that frequently serves to emulate pathogen invasion. Hemolymph, which functions as a transport mechanism for immune cells, offers vital transcriptome information when <i>A. fangsiao</i> is exposed to pathogens, thereby contributing to our comprehension of the species’ immune biological mechanisms. In this study, we conducted analyses of transcript profiles under the influence of LPS and Poly I:C within a 24 h period. Concurrently, we developed a Weighted Gene Co-expression Network Analysis (WGCNA) to identify key modules and genes. Further, we carried out Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses to investigate the primary modular functions. Co-expression network analyses unveiled a series of immune response processes following pathogen stress, identifying several key modules and hub genes, including <i>PKMYT1</i> and <i>NAMPT</i>. The invaluable genetic resources provided by our results aid our understanding of the immune response in <i>A. fangsiao</i> hemolymph and will further our exploration of the molecular mechanisms of pathogen infection in mollusks. |
| first_indexed | 2024-03-08T15:12:27Z |
| format | Article |
| id | doaj.art-7db12674d829491c8d8dfa31ab37801d |
| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-08T15:12:27Z |
| publishDate | 2023-12-01 |
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| record_format | Article |
| series | Animals |
| spelling | doaj.art-7db12674d829491c8d8dfa31ab37801d2024-01-10T14:50:14ZengMDPI AGAnimals2076-26152023-12-011418010.3390/ani14010080Weighted Gene Co-Expression Network Analysis Based on Stimulation by Lipopolysaccharides and Polyinosinic:polycytidylic Acid Provides a Core Set of Genes for Understanding Hemolymph Immune Response Mechanisms of <i>Amphioctopus fangsiao</i>Yongjie Wang0Xipan Chen1Xiaohui Xu2Jianmin Yang3Xiumei Liu4Guohua Sun5Zan Li6School of Agriculture, Ludong University, Yantai 264025, ChinaSchool of Agriculture, Ludong University, Yantai 264025, ChinaSchool of Agriculture, Ludong University, Yantai 264025, ChinaSchool of Agriculture, Ludong University, Yantai 264025, ChinaCollege of Life Sciences, Yantai University, Yantai 264005, ChinaSchool of Agriculture, Ludong University, Yantai 264025, ChinaSchool of Agriculture, Ludong University, Yantai 264025, ChinaThe primary influencer of aquaculture quality in <i>Amphioctopus fangsiao</i> is pathogen infection. Both lipopolysaccharides (LPS) and polyinosinic:polycytidylic acid (Poly I:C) are recognized by the pattern recognition receptor (PRR) within immune cells, a system that frequently serves to emulate pathogen invasion. Hemolymph, which functions as a transport mechanism for immune cells, offers vital transcriptome information when <i>A. fangsiao</i> is exposed to pathogens, thereby contributing to our comprehension of the species’ immune biological mechanisms. In this study, we conducted analyses of transcript profiles under the influence of LPS and Poly I:C within a 24 h period. Concurrently, we developed a Weighted Gene Co-expression Network Analysis (WGCNA) to identify key modules and genes. Further, we carried out Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses to investigate the primary modular functions. Co-expression network analyses unveiled a series of immune response processes following pathogen stress, identifying several key modules and hub genes, including <i>PKMYT1</i> and <i>NAMPT</i>. The invaluable genetic resources provided by our results aid our understanding of the immune response in <i>A. fangsiao</i> hemolymph and will further our exploration of the molecular mechanisms of pathogen infection in mollusks.https://www.mdpi.com/2076-2615/14/1/80<i>Amphioctopus fangsiao</i>hemolymphLPSPoly I:CWGCNAprotein–protein interaction networks |
| spellingShingle | Yongjie Wang Xipan Chen Xiaohui Xu Jianmin Yang Xiumei Liu Guohua Sun Zan Li Weighted Gene Co-Expression Network Analysis Based on Stimulation by Lipopolysaccharides and Polyinosinic:polycytidylic Acid Provides a Core Set of Genes for Understanding Hemolymph Immune Response Mechanisms of <i>Amphioctopus fangsiao</i> Animals <i>Amphioctopus fangsiao</i> hemolymph LPS Poly I:C WGCNA protein–protein interaction networks |
| title | Weighted Gene Co-Expression Network Analysis Based on Stimulation by Lipopolysaccharides and Polyinosinic:polycytidylic Acid Provides a Core Set of Genes for Understanding Hemolymph Immune Response Mechanisms of <i>Amphioctopus fangsiao</i> |
| title_full | Weighted Gene Co-Expression Network Analysis Based on Stimulation by Lipopolysaccharides and Polyinosinic:polycytidylic Acid Provides a Core Set of Genes for Understanding Hemolymph Immune Response Mechanisms of <i>Amphioctopus fangsiao</i> |
| title_fullStr | Weighted Gene Co-Expression Network Analysis Based on Stimulation by Lipopolysaccharides and Polyinosinic:polycytidylic Acid Provides a Core Set of Genes for Understanding Hemolymph Immune Response Mechanisms of <i>Amphioctopus fangsiao</i> |
| title_full_unstemmed | Weighted Gene Co-Expression Network Analysis Based on Stimulation by Lipopolysaccharides and Polyinosinic:polycytidylic Acid Provides a Core Set of Genes for Understanding Hemolymph Immune Response Mechanisms of <i>Amphioctopus fangsiao</i> |
| title_short | Weighted Gene Co-Expression Network Analysis Based on Stimulation by Lipopolysaccharides and Polyinosinic:polycytidylic Acid Provides a Core Set of Genes for Understanding Hemolymph Immune Response Mechanisms of <i>Amphioctopus fangsiao</i> |
| title_sort | weighted gene co expression network analysis based on stimulation by lipopolysaccharides and polyinosinic polycytidylic acid provides a core set of genes for understanding hemolymph immune response mechanisms of i amphioctopus fangsiao i |
| topic | <i>Amphioctopus fangsiao</i> hemolymph LPS Poly I:C WGCNA protein–protein interaction networks |
| url | https://www.mdpi.com/2076-2615/14/1/80 |
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