Transcript annotation of Chinese sturgeon (Acipenser sinensis) using Iso-seq and RNA-seq data. - National Genomics Data Center (CNCB-NGDC)

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Transcript annotation of Chinese sturgeon (Acipenser sinensis) using Iso-seq and RNA-seq data.

Xiaolin Liao, Libin Zhang, Hua Tian, Bo Yang, Ezhou Wang, Bin Zhu

Author Information

Xiaolin Liao: Key Laboratory of Ecological Impacts of Hydraulic-Projects and Restoration of Aquatic Ecosystem, Ministry of Water Resources, Institute of Hydroecology, Ministry of Water Resources and Chinese Academy of Sciences, Wuhan, 430079, China. xliao@mail.ihe.ac.cn.
Libin Zhang: College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China. libinzhang@hust.edu.cn.
Hua Tian: Key Laboratory of Ecological Impacts of Hydraulic-Projects and Restoration of Aquatic Ecosystem, Ministry of Water Resources, Institute of Hydroecology, Ministry of Water Resources and Chinese Academy of Sciences, Wuhan, 430079, China.
Bo Yang: Key Laboratory of Ecological Impacts of Hydraulic-Projects and Restoration of Aquatic Ecosystem, Ministry of Water Resources, Institute of Hydroecology, Ministry of Water Resources and Chinese Academy of Sciences, Wuhan, 430079, China.
Ezhou Wang: Key Laboratory of Ecological Impacts of Hydraulic-Projects and Restoration of Aquatic Ecosystem, Ministry of Water Resources, Institute of Hydroecology, Ministry of Water Resources and Chinese Academy of Sciences, Wuhan, 430079, China.
Bin Zhu: Key Laboratory of Ecological Impacts of Hydraulic-Projects and Restoration of Aquatic Ecosystem, Ministry of Water Resources, Institute of Hydroecology, Ministry of Water Resources and Chinese Academy of Sciences, Wuhan, 430079, China.

PMID: 36823216 DOI: 10.1038/s41597-023-02014-4

Chinese sturgeon (Acipenser sinensis) is a critically endangered fish inhabiting the Yangtze River and Chinese coastal waters. Numerous research projects and conservation efforts have focused on artificial propagation and release to restore this endangered species. However, genomic and full-length transcriptomic sequencing of Chinese sturgeon has rarely been reported. In this study, a total of 10 Chinese sturgeon tissues were used for PacBio Iso-seq and RNA-seq analyses. A total of 19,538 full-length transcripts were obtained with sizes from 51 bp to 7,033 bp. Moreover, cluster analysis of gene families and phylogenetic analysis of 14 species were performed. Furthermore, lncRNAs and coding sequence (CDS) were identified in all Chinese sturgeon tissues. Finally, gene expression profiles and differentially expressed genes (DEGs) were analyzed among 10 tissues in Chinese sturgeon. Taken together, full-length transcripts and the gene expression profile from Chinese sturgeon tissues will provide gene sequences and expression information for future functional genomic study and be very helpful for comprehensive understanding of the genetic mechanism of endangerment in Chinese sturgeon.

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Animals

Endangered Species

Fishes

Phylogeny

RNA-Seq

Transcriptome

Dataset Journal Article

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Transcriptome Analyses Reveal Expression Profiles of Morphologically Undifferentiated and Differentiated Gonads of Yangtze Sturgeon .Transcriptomic annotation of the Chungtien schizothoracin (Ptychobarbus chungtienensis) using Iso-seq and RNA-seq data.Integrating Iso-seq and RNA-seq data for the reannotation of the greater amberjack genome.Expression Profiles of Housekeeping Genes and Tissue-Specific Genes in Different Tissues of Chinese Sturgeon ().