Identification of hub genes in digestive system of mandarin fish (Siniperca chuatsi) fed with artificial diet by weighted gene co-expression network analysis.

Yawei Shen; Lingyuan Song; Tiantian Chen; Hewei Jiang; Guokun Yang; Yanmin Zhang; Xindang Zhang; Kah Kheng Lim; Xiaolin Meng; Jinliang Zhao; Xiaowu Chen

doi:10.1016/j.cbd.2023.101112

Identification of hub genes in digestive system of mandarin fish (Siniperca chuatsi) fed with artificial diet by weighted gene co-expression network analysis.

Yawei Shen, Lingyuan Song, Tiantian Chen, Hewei Jiang, Guokun Yang, Yanmin Zhang, Xindang Zhang, Kah Kheng Lim, Xiaolin Meng, Jinliang Zhao, Xiaowu Chen

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

Abstract

Mandarin fish (Siniperca chuatsi) is a carnivorous freshwater fish and an economically important species. The digestive system (liver, stomach, intestine, pyloric caecum, esophagus, and gallbladder) is an important site for studying fish domestication. In our previous study, we found that mandarin fish undergoes adaptive changes in histological morphology and gene expression levels of the digestive system when subjected to artificial diet domestication. However, we are not clear which hub genes are highly associated with domestication. In this study, we performed WGCNA on the transcriptomes of 17 tissues and 9 developmental stages and combined differentially expressed genes analysis in the digestive system to identify the hub genes that may play important functions in the adaptation of mandarin fish to bait conversion. A total of 31,657 genes in 26 samples were classified into 23 color modules via WGCNA. The modules midnightblue, darkred, lightyellow, and darkgreen highly associated with the liver, stomach, esophagus, and gallbladder were extracted, respectively. Tan module was highly related to both intestine and pyloric caecum. The hub genes in liver were cp, vtgc, c1in, c9, lect2, and klkb1. The hub genes in stomach were ghrl, atp4a, gjb3, muc5ac, duox2, and chia2. The hub genes in esophagus were mybpc1, myl2, and tpm3. The hub genes in gallbladder were dyst, npy2r, slc13a1, and slc39a4. The hub genes in the intestine and pyloric caecum were slc15a1, cdhr5, btn3a1, anpep, slc34a2, cdhr2, and ace2. Through pathway analysis, modules highly related to the digestive system were mainly enriched in digestion and absorption, metabolism, and immune-related pathways. After domestication, the hub genes vtgc and lect2 were significantly upregulated in the liver. Chia2 was significantly downregulated in the stomach. Slc15a1, anpep, and slc34a2 were significantly upregulated in the intestine. This study identified the hub genes that may play an important role in the adaptation of the digestive system to artificial diet, which provided novel evidence and ideas for further research on the domestication of mandarin fish from molecular level.

Original language	English (US)
Pages (from-to)	101112
Journal	Comparative biochemistry and physiology. Part D, Genomics & proteomics
Volume	47
DOIs	https://doi.org/10.1016/j.cbd.2023.101112
State	Published - Jul 27 2023

Bibliographical note

KAUST Repository Item: Exported on 2023-08-01
Acknowledgements: This research was supported by the Earmarked fund for CARS (CARS-46), the Key National and Special Project of Blue Granary Science and Technology Innovation (2020YFD0900400), the Scholarship from China Scholarship Council (202008967002), the Training plan for applied talents integrating industry and education – Collage of Future Technology, and the Doctoral Research Initiation Grant of Henan Normal University (5101229170829).

ASJC Scopus subject areas

Biochemistry
Genetics
Molecular Biology
Physiology

Access to Document

10.1016/j.cbd.2023.101112

Cite this

Shen, Y., Song, L., Chen, T., Jiang, H., Yang, G., Zhang, Y., Zhang, X., Lim, K. K., Meng, X., Zhao, J., & Chen, X. (2023). Identification of hub genes in digestive system of mandarin fish (Siniperca chuatsi) fed with artificial diet by weighted gene co-expression network analysis. Comparative biochemistry and physiology. Part D, Genomics & proteomics, 47, 101112. https://doi.org/10.1016/j.cbd.2023.101112

@article{54f65a1494324ffab68a60c396ae295e,

title = "Identification of hub genes in digestive system of mandarin fish (Siniperca chuatsi) fed with artificial diet by weighted gene co-expression network analysis.",

abstract = "Mandarin fish (Siniperca chuatsi) is a carnivorous freshwater fish and an economically important species. The digestive system (liver, stomach, intestine, pyloric caecum, esophagus, and gallbladder) is an important site for studying fish domestication. In our previous study, we found that mandarin fish undergoes adaptive changes in histological morphology and gene expression levels of the digestive system when subjected to artificial diet domestication. However, we are not clear which hub genes are highly associated with domestication. In this study, we performed WGCNA on the transcriptomes of 17 tissues and 9 developmental stages and combined differentially expressed genes analysis in the digestive system to identify the hub genes that may play important functions in the adaptation of mandarin fish to bait conversion. A total of 31,657 genes in 26 samples were classified into 23 color modules via WGCNA. The modules midnightblue, darkred, lightyellow, and darkgreen highly associated with the liver, stomach, esophagus, and gallbladder were extracted, respectively. Tan module was highly related to both intestine and pyloric caecum. The hub genes in liver were cp, vtgc, c1in, c9, lect2, and klkb1. The hub genes in stomach were ghrl, atp4a, gjb3, muc5ac, duox2, and chia2. The hub genes in esophagus were mybpc1, myl2, and tpm3. The hub genes in gallbladder were dyst, npy2r, slc13a1, and slc39a4. The hub genes in the intestine and pyloric caecum were slc15a1, cdhr5, btn3a1, anpep, slc34a2, cdhr2, and ace2. Through pathway analysis, modules highly related to the digestive system were mainly enriched in digestion and absorption, metabolism, and immune-related pathways. After domestication, the hub genes vtgc and lect2 were significantly upregulated in the liver. Chia2 was significantly downregulated in the stomach. Slc15a1, anpep, and slc34a2 were significantly upregulated in the intestine. This study identified the hub genes that may play an important role in the adaptation of the digestive system to artificial diet, which provided novel evidence and ideas for further research on the domestication of mandarin fish from molecular level.",

author = "Yawei Shen and Lingyuan Song and Tiantian Chen and Hewei Jiang and Guokun Yang and Yanmin Zhang and Xindang Zhang and Lim, {Kah Kheng} and Xiaolin Meng and Jinliang Zhao and Xiaowu Chen",

note = "KAUST Repository Item: Exported on 2023-08-01 Acknowledgements: This research was supported by the Earmarked fund for CARS (CARS-46), the Key National and Special Project of Blue Granary Science and Technology Innovation (2020YFD0900400), the Scholarship from China Scholarship Council (202008967002), the Training plan for applied talents integrating industry and education – Collage of Future Technology, and the Doctoral Research Initiation Grant of Henan Normal University (5101229170829).",

year = "2023",

month = jul,

day = "27",

doi = "10.1016/j.cbd.2023.101112",

language = "English (US)",

volume = "47",

pages = "101112",

journal = "Comparative biochemistry and physiology. Part D, Genomics & proteomics",

issn = "1744-117X",

publisher = "Elsevier",

}

Shen, Y, Song, L, Chen, T, Jiang, H, Yang, G, Zhang, Y, Zhang, X, Lim, KK, Meng, X, Zhao, J & Chen, X 2023, 'Identification of hub genes in digestive system of mandarin fish (Siniperca chuatsi) fed with artificial diet by weighted gene co-expression network analysis.', Comparative biochemistry and physiology. Part D, Genomics & proteomics, vol. 47, pp. 101112. https://doi.org/10.1016/j.cbd.2023.101112

Identification of hub genes in digestive system of mandarin fish (Siniperca chuatsi) fed with artificial diet by weighted gene co-expression network analysis. / Shen, Yawei; Song, Lingyuan; Chen, Tiantian et al.
In: Comparative biochemistry and physiology. Part D, Genomics & proteomics, Vol. 47, 27.07.2023, p. 101112.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - Identification of hub genes in digestive system of mandarin fish (Siniperca chuatsi) fed with artificial diet by weighted gene co-expression network analysis.

AU - Shen, Yawei

AU - Song, Lingyuan

AU - Chen, Tiantian

AU - Jiang, Hewei

AU - Yang, Guokun

AU - Zhang, Yanmin

AU - Zhang, Xindang

AU - Lim, Kah Kheng

AU - Meng, Xiaolin

AU - Zhao, Jinliang

AU - Chen, Xiaowu

N1 - KAUST Repository Item: Exported on 2023-08-01 Acknowledgements: This research was supported by the Earmarked fund for CARS (CARS-46), the Key National and Special Project of Blue Granary Science and Technology Innovation (2020YFD0900400), the Scholarship from China Scholarship Council (202008967002), the Training plan for applied talents integrating industry and education – Collage of Future Technology, and the Doctoral Research Initiation Grant of Henan Normal University (5101229170829).

PY - 2023/7/27

Y1 - 2023/7/27

N2 - Mandarin fish (Siniperca chuatsi) is a carnivorous freshwater fish and an economically important species. The digestive system (liver, stomach, intestine, pyloric caecum, esophagus, and gallbladder) is an important site for studying fish domestication. In our previous study, we found that mandarin fish undergoes adaptive changes in histological morphology and gene expression levels of the digestive system when subjected to artificial diet domestication. However, we are not clear which hub genes are highly associated with domestication. In this study, we performed WGCNA on the transcriptomes of 17 tissues and 9 developmental stages and combined differentially expressed genes analysis in the digestive system to identify the hub genes that may play important functions in the adaptation of mandarin fish to bait conversion. A total of 31,657 genes in 26 samples were classified into 23 color modules via WGCNA. The modules midnightblue, darkred, lightyellow, and darkgreen highly associated with the liver, stomach, esophagus, and gallbladder were extracted, respectively. Tan module was highly related to both intestine and pyloric caecum. The hub genes in liver were cp, vtgc, c1in, c9, lect2, and klkb1. The hub genes in stomach were ghrl, atp4a, gjb3, muc5ac, duox2, and chia2. The hub genes in esophagus were mybpc1, myl2, and tpm3. The hub genes in gallbladder were dyst, npy2r, slc13a1, and slc39a4. The hub genes in the intestine and pyloric caecum were slc15a1, cdhr5, btn3a1, anpep, slc34a2, cdhr2, and ace2. Through pathway analysis, modules highly related to the digestive system were mainly enriched in digestion and absorption, metabolism, and immune-related pathways. After domestication, the hub genes vtgc and lect2 were significantly upregulated in the liver. Chia2 was significantly downregulated in the stomach. Slc15a1, anpep, and slc34a2 were significantly upregulated in the intestine. This study identified the hub genes that may play an important role in the adaptation of the digestive system to artificial diet, which provided novel evidence and ideas for further research on the domestication of mandarin fish from molecular level.

AB - Mandarin fish (Siniperca chuatsi) is a carnivorous freshwater fish and an economically important species. The digestive system (liver, stomach, intestine, pyloric caecum, esophagus, and gallbladder) is an important site for studying fish domestication. In our previous study, we found that mandarin fish undergoes adaptive changes in histological morphology and gene expression levels of the digestive system when subjected to artificial diet domestication. However, we are not clear which hub genes are highly associated with domestication. In this study, we performed WGCNA on the transcriptomes of 17 tissues and 9 developmental stages and combined differentially expressed genes analysis in the digestive system to identify the hub genes that may play important functions in the adaptation of mandarin fish to bait conversion. A total of 31,657 genes in 26 samples were classified into 23 color modules via WGCNA. The modules midnightblue, darkred, lightyellow, and darkgreen highly associated with the liver, stomach, esophagus, and gallbladder were extracted, respectively. Tan module was highly related to both intestine and pyloric caecum. The hub genes in liver were cp, vtgc, c1in, c9, lect2, and klkb1. The hub genes in stomach were ghrl, atp4a, gjb3, muc5ac, duox2, and chia2. The hub genes in esophagus were mybpc1, myl2, and tpm3. The hub genes in gallbladder were dyst, npy2r, slc13a1, and slc39a4. The hub genes in the intestine and pyloric caecum were slc15a1, cdhr5, btn3a1, anpep, slc34a2, cdhr2, and ace2. Through pathway analysis, modules highly related to the digestive system were mainly enriched in digestion and absorption, metabolism, and immune-related pathways. After domestication, the hub genes vtgc and lect2 were significantly upregulated in the liver. Chia2 was significantly downregulated in the stomach. Slc15a1, anpep, and slc34a2 were significantly upregulated in the intestine. This study identified the hub genes that may play an important role in the adaptation of the digestive system to artificial diet, which provided novel evidence and ideas for further research on the domestication of mandarin fish from molecular level.

UR - http://hdl.handle.net/10754/693341

UR - https://linkinghub.elsevier.com/retrieve/pii/S1744117X23000576

U2 - 10.1016/j.cbd.2023.101112

DO - 10.1016/j.cbd.2023.101112

M3 - Article

C2 - 37516099

SN - 1744-117X

VL - 47

SP - 101112

JO - Comparative biochemistry and physiology. Part D, Genomics & proteomics

JF - Comparative biochemistry and physiology. Part D, Genomics & proteomics

ER -

Identification of hub genes in digestive system of mandarin fish (Siniperca chuatsi) fed with artificial diet by weighted gene co-expression network analysis.

Abstract

Bibliographical note

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this