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

Ma, Xiaoli; Su, Baofeng; Tian, Yuan; Backenstose, Nathan J. C.; Ye, Zhi; Moss, Anthony G.; Duong, Thuy-Yen; Wang, Xu; Dunham, Rex A.

doi:10.3390/ijms21155535

Submit to this Journal Review for this Journal Edit a Special Issue

Article Menu

...

Open AccessArticle

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

Xiaoli Ma

^1,2

Baofeng Su

^1,2

Yuan Tian

¹,

Nathan J. C. Backenstose

^1,2,3,

^1,2,4,

⁵

⁶

^2,7,8,*

and

Rex A. Dunham

^1,2,*

School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA

Alabama Agricultural Experiment Station, Auburn, AL 36849, USA

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)

View Full-Text Download PDF

Browse Figures

Citation Export

Abstract

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

▼ Show Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited

Supplementary Material

Supplementary File 1:
Supplementary (ZIP, 9469 KiB)

Share and Cite

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

Find Other Styles

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Metrics

Abstract views Pdf views Html views

Article Menu

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

Abstract

Supplementary Material

Share and Cite

Article Metrics

Article Access Statistics

Article Access Map by Country/Region

Further Information

Guidelines

MDPI Initiatives

Follow MDPI