Transcriptome profiling reveals candidate cleft palate-related genes in cultured Chinese sturgeons (Acipenser sinensis)

Jing Yang; Yacheng Hu; Kan Xiao; Xueqing Liu; Chun Tan; Binzhong Wang; Hejun Du

doi:10.1016/j.gene.2018.05.016

Transcriptome profiling reveals candidate cleft palate-related genes in cultured Chinese sturgeons (Acipenser sinensis)

Gene. 2018 Aug 5:666:1-8. doi: 10.1016/j.gene.2018.05.016. Epub 2018 May 5.

Authors

Jing Yang¹, Yacheng Hu², Kan Xiao³, Xueqing Liu³, Chun Tan⁴, Binzhong Wang⁵, Hejun Du⁶

Affiliations

¹ Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, Hubei 443100, China; Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang, Hubei 443100, China. Electronic address: yang_jing7@ctg.com.cn.
² Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, Hubei 443100, China; Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang, Hubei 443100, China. Electronic address: hu_yacheng@ctg.com.cn.
³ Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, Hubei 443100, China; Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang, Hubei 443100, China.
⁴ Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, Hubei 443100, China; Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang, Hubei 443100, China. Electronic address: tan_chun@ctg.com.cn.
⁵ Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, Hubei 443100, China; Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang, Hubei 443100, China. Electronic address: wang_binzhong@ctg.com.cn.
⁶ Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, Hubei 443100, China; Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang, Hubei 443100, China. Electronic address: du_hejun@ctg.com.cn.

PMID: 29733966
DOI: 10.1016/j.gene.2018.05.016

Abstract

The Chinese sturgeon (Acipenser sinensis) is an anadromous fish distributed in the Yangtze River and the East China Sea. In this study, we report the novel finding of cleft palates in Chinese sturgeons derived from artificial fertilization. To explore the genetic basis of palate malformation in A. sinensis, Illumina RNA-seq technology was used to analyze the transcriptome data of farmed Chinese sturgeons with normal palates and cleft-palates. Raw reads were obtained and assembled into 808,612 unigenes, with an average length of 509.33 bp and an N50 of 574 bp. Sequence similarity analyses against four public databases (Nr, UniProt, KEGG, and COGs) found 158,642 unigenes that could be annotated. GABAergic synapses and TGF-β signal pathways were the two most enriched pathways with high Rich Factors in the analyses of differentially expressed genes. In these two signal pathways, six genes (GABRA4, GS, GNS, S6K, PITX2, and BMP8) were found as candidate cleft-palate genes in Chinese sturgeon. These findings contribute to our understanding of cleft palate genetics in sturgeon, while simultaneously adding to our knowledge about craniofacial development.

Keywords: Chinese sturgeon; Cleft palate; RNA-seq; Transcriptome.

MeSH terms

Animals
Aquaculture
China
Cleft Palate / genetics
Cleft Palate / metabolism
Cleft Palate / veterinary*
Fish Diseases / genetics*
Fish Diseases / metabolism
Fish Proteins / genetics
Fish Proteins / metabolism
Fishes / genetics*
Fishes / metabolism
Gene Expression Profiling
Molecular Sequence Annotation
Transcriptome*

Substances

Fish Proteins