Transcriptome Sequencing Analysis Reveals Dynamic Changes in Major Biological Functions during the Early Development of Clearhead Icefish, Protosalanx chinensis
Early development, when many important developmental events occur, is a critical period for fish. However, research on the early development of clearhead icefish is very limited, especially in molecular research. In this study, we aimed to explore the dynamic changes in the biological functions of f...
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ftdoajarticles:oai:doaj.org/article:e82972d302564dd7aed52e684bc30bd3 2023-05-15T16:42:06+02:00 Transcriptome Sequencing Analysis Reveals Dynamic Changes in Major Biological Functions during the Early Development of Clearhead Icefish, Protosalanx chinensis Xuemei Tang Shulun Jiang Henglin Wang Yanfeng Zhou Fei Peng Xizhao Zhang Yifan Zhou Shiyue Guo Yang You 2022-05-01T00:00:00Z https://doi.org/10.3390/fishes7030115 https://doaj.org/article/e82972d302564dd7aed52e684bc30bd3 EN eng MDPI AG https://www.mdpi.com/2410-3888/7/3/115 https://doaj.org/toc/2410-3888 doi:10.3390/fishes7030115 2410-3888 https://doaj.org/article/e82972d302564dd7aed52e684bc30bd3 Fishes, Vol 7, Iss 115, p 115 (2022) Protosalanx chinensis early development biological function transcriptome WGCNA Biology (General) QH301-705.5 Genetics QH426-470 article 2022 ftdoajarticles https://doi.org/10.3390/fishes7030115 2022-12-30T23:14:11Z Early development, when many important developmental events occur, is a critical period for fish. However, research on the early development of clearhead icefish is very limited, especially in molecular research. In this study, we aimed to explore the dynamic changes in the biological functions of five key periods in clearhead icefish early development, namely the YL (embryonic), PM (first day after hatching), KK (fourth day after hatching), LC (seventh day after hatching), and SL (tenth day after hatching) stages, through transcriptome sequencing and different analysis strategies. A trend expression analysis and an enrichment analysis revealed that the expression ofgenes encoding G protein-coupled receptors and their ligands, i.e., prss1_2_3 , pomc , npy , npb , sst , rln3 , crh , gh , and prl that are associated with digestion and feeding regulation gradually increased during early development. In addition, a weighted gene co-expression network analysis (WGCNA) showed that eleven modules were significantly associated with early development, among which nine modules were significantly positively correlated. Through the enrichment analysis and hub gene identification results of these nine modules, it was found that the pathways related to eye, bone, and heart development were significantly enriched in the YL stage, and the ccnd2 , seh1l , kdm6a , arf4, and ankrd28 genes that are associated with cell proliferation and differentiation played important roles in these developmental processes; the pak3 , dlx3 , dgat2, and tas1r1 genes that are associated with jaw and tooth development, TG (triacylglycerol) synthesis, and umami amino acid receptors were identified as hub genes for the PM stage; the pathways associated with aerobic metabolism and unsaturated fatty acid synthesis were significantly enriched in the KK stage, with the foxk , slc13a2_3_5 , ndufa5 , and lsc2 genes playing important roles; the pathways related to visual perception were significantly enriched in the LC stage; and the bile acid biosynthetic ... Article in Journal/Newspaper Icefish Directory of Open Access Journals: DOAJ Articles Fishes 7 3 115 |
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Directory of Open Access Journals: DOAJ Articles |
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language |
English |
topic |
Protosalanx chinensis early development biological function transcriptome WGCNA Biology (General) QH301-705.5 Genetics QH426-470 |
spellingShingle |
Protosalanx chinensis early development biological function transcriptome WGCNA Biology (General) QH301-705.5 Genetics QH426-470 Xuemei Tang Shulun Jiang Henglin Wang Yanfeng Zhou Fei Peng Xizhao Zhang Yifan Zhou Shiyue Guo Yang You Transcriptome Sequencing Analysis Reveals Dynamic Changes in Major Biological Functions during the Early Development of Clearhead Icefish, Protosalanx chinensis |
topic_facet |
Protosalanx chinensis early development biological function transcriptome WGCNA Biology (General) QH301-705.5 Genetics QH426-470 |
description |
Early development, when many important developmental events occur, is a critical period for fish. However, research on the early development of clearhead icefish is very limited, especially in molecular research. In this study, we aimed to explore the dynamic changes in the biological functions of five key periods in clearhead icefish early development, namely the YL (embryonic), PM (first day after hatching), KK (fourth day after hatching), LC (seventh day after hatching), and SL (tenth day after hatching) stages, through transcriptome sequencing and different analysis strategies. A trend expression analysis and an enrichment analysis revealed that the expression ofgenes encoding G protein-coupled receptors and their ligands, i.e., prss1_2_3 , pomc , npy , npb , sst , rln3 , crh , gh , and prl that are associated with digestion and feeding regulation gradually increased during early development. In addition, a weighted gene co-expression network analysis (WGCNA) showed that eleven modules were significantly associated with early development, among which nine modules were significantly positively correlated. Through the enrichment analysis and hub gene identification results of these nine modules, it was found that the pathways related to eye, bone, and heart development were significantly enriched in the YL stage, and the ccnd2 , seh1l , kdm6a , arf4, and ankrd28 genes that are associated with cell proliferation and differentiation played important roles in these developmental processes; the pak3 , dlx3 , dgat2, and tas1r1 genes that are associated with jaw and tooth development, TG (triacylglycerol) synthesis, and umami amino acid receptors were identified as hub genes for the PM stage; the pathways associated with aerobic metabolism and unsaturated fatty acid synthesis were significantly enriched in the KK stage, with the foxk , slc13a2_3_5 , ndufa5 , and lsc2 genes playing important roles; the pathways related to visual perception were significantly enriched in the LC stage; and the bile acid biosynthetic ... |
format |
Article in Journal/Newspaper |
author |
Xuemei Tang Shulun Jiang Henglin Wang Yanfeng Zhou Fei Peng Xizhao Zhang Yifan Zhou Shiyue Guo Yang You |
author_facet |
Xuemei Tang Shulun Jiang Henglin Wang Yanfeng Zhou Fei Peng Xizhao Zhang Yifan Zhou Shiyue Guo Yang You |
author_sort |
Xuemei Tang |
title |
Transcriptome Sequencing Analysis Reveals Dynamic Changes in Major Biological Functions during the Early Development of Clearhead Icefish, Protosalanx chinensis |
title_short |
Transcriptome Sequencing Analysis Reveals Dynamic Changes in Major Biological Functions during the Early Development of Clearhead Icefish, Protosalanx chinensis |
title_full |
Transcriptome Sequencing Analysis Reveals Dynamic Changes in Major Biological Functions during the Early Development of Clearhead Icefish, Protosalanx chinensis |
title_fullStr |
Transcriptome Sequencing Analysis Reveals Dynamic Changes in Major Biological Functions during the Early Development of Clearhead Icefish, Protosalanx chinensis |
title_full_unstemmed |
Transcriptome Sequencing Analysis Reveals Dynamic Changes in Major Biological Functions during the Early Development of Clearhead Icefish, Protosalanx chinensis |
title_sort |
transcriptome sequencing analysis reveals dynamic changes in major biological functions during the early development of clearhead icefish, protosalanx chinensis |
publisher |
MDPI AG |
publishDate |
2022 |
url |
https://doi.org/10.3390/fishes7030115 https://doaj.org/article/e82972d302564dd7aed52e684bc30bd3 |
genre |
Icefish |
genre_facet |
Icefish |
op_source |
Fishes, Vol 7, Iss 115, p 115 (2022) |
op_relation |
https://www.mdpi.com/2410-3888/7/3/115 https://doaj.org/toc/2410-3888 doi:10.3390/fishes7030115 2410-3888 https://doaj.org/article/e82972d302564dd7aed52e684bc30bd3 |
op_doi |
https://doi.org/10.3390/fishes7030115 |
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