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Open AccessArticle

Deep Transcriptomic Analysis Reveals the Dynamic Developmental Progression during Early Development of Channel Catfish (Ictalurus punctatus)

1
School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
2
Alabama Agricultural Experiment Station, Auburn, AL 36849, USA
3
Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
4
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
5
Department of Biological Science, Auburn University, Auburn, AL 36849, USA
6
College of Aquaculture and Fisheries, Can Tho University, Can Tho City 94000, Vietnam
7
Department of Pathobiology, Auburn University, Auburn, AL 36849, USA
8
HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2020, 21(15), 5535; https://doi.org/10.3390/ijms21155535
Received: 31 May 2020 / Revised: 21 July 2020 / Accepted: 29 July 2020 / Published: 2 August 2020
(This article belongs to the Special Issue Regulation of Gene Expression During Embryonic Development)
The transition from fertilized egg to larva in fish is accompanied with various biological processes. We selected seven early developmental stages in channel catfish, Ictalurus punctatus, for transcriptome analysis, and covered 22,635 genes with 590 million high-quality RNA-sequencing (seq) reads. Differential expression analysis between neighboring developmental timepoints revealed significantly enriched biological categories associated with growth, development and morphogenesis, which was most evident at 2 vs. 5 days post fertilization (dpf) and 5 vs. 6 dpf. A gene co-expression network was constructed using the Weighted Gene Co-expression Network Analysis (WGCNA) approach and four critical modules were identified. Among candidate hub genes, GDF10, FOXA2, HCEA and SYCE3 were involved in head formation, egg development and the transverse central element of synaptonemal complexes. CK1, OAZ2, DARS1 and UBE2V2 were mainly associated with regulation of cell cycle, growth, brain development, differentiation and proliferation of enterocytes. IFI44L and ZIP10 were critical for the regulation of immune activity and ion transport. Additionally, TCK1 and TGFB1 were related to phosphate transport and regulating cell proliferation. All these genes play vital roles in embryogenesis and regulation of early development. These results serve as a rich dataset for functional genomic studies. Our work reveals new insights of the underlying mechanisms in channel catfish early development. View Full-Text
Keywords: early development; channel catfish; RNA sequencing; WGCNA early development; channel catfish; RNA sequencing; WGCNA
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MDPI and ACS Style

Ma, X.; Su, B.; Tian, Y.; Backenstose, N.J.C.; Ye, Z.; Moss, A.G.; Duong, T.-Y.; Wang, X.; Dunham, R.A. Deep Transcriptomic Analysis Reveals the Dynamic Developmental Progression during Early Development of Channel Catfish (Ictalurus punctatus). Int. J. Mol. Sci. 2020, 21, 5535. https://doi.org/10.3390/ijms21155535

AMA Style

Ma X, Su B, Tian Y, Backenstose NJC, Ye Z, Moss AG, Duong T-Y, Wang X, Dunham RA. Deep Transcriptomic Analysis Reveals the Dynamic Developmental Progression during Early Development of Channel Catfish (Ictalurus punctatus). International Journal of Molecular Sciences. 2020; 21(15):5535. https://doi.org/10.3390/ijms21155535

Chicago/Turabian Style

Ma, Xiaoli; Su, Baofeng; Tian, Yuan; Backenstose, Nathan J.C.; Ye, Zhi; Moss, Anthony G.; Duong, Thuy-Yen; Wang, Xu; Dunham, Rex A. 2020. "Deep Transcriptomic Analysis Reveals the Dynamic Developmental Progression during Early Development of Channel Catfish (Ictalurus punctatus)" Int. J. Mol. Sci. 21, no. 15: 5535. https://doi.org/10.3390/ijms21155535

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