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

2023-09Journal article Restricted access
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dc.contributor.authorShen, Yawei
dc.contributor.authorSong, Lingyuan
dc.contributor.authorChen, Tiantian
dc.contributor.authorJiang, Hewei
dc.contributor.authorYang, Guokun
dc.contributor.authorZhang, Yanmin
dc.contributor.authorZhang, Xindang
dc.contributor.authorLim, Kah Kheng
dc.contributor.authorMeng, Xiaolin
dc.contributor.authorZhao, Jinliang
dc.contributor.authorChen, Xiaowu
dc.date.accessioned2023-10-26T13:45:46Z
dc.date.available2023-10-26T13:45:46Z
dc.date.issued2023-09
dc.description.abstractMandarin 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.pt_PT
dc.description.sponsorshipKey National and Special Project of Blue Granary Science and Technology Innovation 202008967002, China Scholarship Council 5101229170829, Training plan for applied talents integrating industry and education - Collage of Future Technology 2020YFD0900400,pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.doi10.1016/j.cbd.2023.101112pt_PT
dc.identifier.eissn1878-0407
dc.identifier.urihttp://hdl.handle.net/10400.1/20098
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherElsevierpt_PT
dc.subjectSiniperca chuatsipt_PT
dc.subjectDigestive systempt_PT
dc.subjectDomesticationpt_PT
dc.subjectWeighted gene co-expression network analysispt_PT
dc.titleIdentification of hub genes in digestive system of mandarin fish (Siniperca chuatsi) fed with artificial diet by weighted gene co-expression network analysispt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.citation.startPage101112pt_PT
oaire.citation.titleComparative Biochemistry and Physiology Part D: Genomics and Proteomicspt_PT
oaire.citation.volume47pt_PT
person.familyNameShen
person.givenNameYawei
person.identifierAAS-4934-2021
person.identifier.ciencia-id8D16-9F74-17F9
person.identifier.orcid0000-0003-2595-7995
person.identifier.scopus-author-id57203162642
rcaap.rightsrestrictedAccesspt_PT
rcaap.typearticlept_PT
relation.isAuthorOfPublication202ed846-cd19-419b-b48b-4dbb036d5c3e
relation.isAuthorOfPublication.latestForDiscovery202ed846-cd19-419b-b48b-4dbb036d5c3e

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