Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Liao X

PROVIDER: S-EPMC9950146 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature

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

Liao Xiaolin X Zhang Libin L Tian Hua H Yang Bo B Wang Ezhou E Zhu Bin B

Scientific data 20230223 1

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-l ...[more]

PMID: 36823216

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Project description:In this study, the effects of different feeding frequencies on the growth and the expression of genes in the GH/IGF axis were assessed in juvenile Chinese sturgeon. The newly hatched Chinese sturgeons were bred for 38 days at three different feeding frequencies groups (feeding frequency of two times a day, TWD; three times a day, THD; and four times a day, FOD), and the expression levels of the GH/IGF axis responses to feeding frequency were determined by quantitative real-time PCR. In addition, the full-length of the Coding Sequences of IGF I and IGF II genes (489-bp and 660-bp, respectively), were cloned and analyzed from Chinese sturgeon the first time. Multiple sequence alignments of IGFs revealed that Chinese sturgeon are high sequence identity to IGFs from other species. The phylogenetic relationships based on the IGF I and IGF II amino acid sequences were consistent with the traditional classification. After 38 days of growth, the three different feeding frequencies groups of Chinese sturgeon had no significant difference of body length, body weight, specific growth rate, the survival rate, the rate of weight gain and the condition factor. However, the relative expression of Chinese sturgeon GH in the pituitary decreased with increasing feeding frequency. The relative expression of Chinese sturgeon GHR in liver and skeletal muscle was deceased with increasing feeding frequency, while the relative expression of GHR in stomach and intestines at THD group was significantly higher than that of at TWD group and FOD group (p < 0.05). The relative expression of Chinese sturgeon IGF I in liver increased significantly with increasing feeding frequency (p < 0.05). The relative expression of IGF I in stomach and skeletal muscle was similar at the three groups. The relative expression of IGF I in intestines was significantly higher at FOD group than at TWD group and THD group (p < 0.05). The relative expression of Chinese sturgeon IGF II in liver at TWD group was significantly higher than that at THD group and FOD group (p < 0.05). However, the relative expression of IGF II in stomach, intestines and skeletal muscle at THD group was higher than that at TWD group and FOD group. Based on these previous studies that liver IGF I is regarded as a biomarker of growth performance, this result suggested that the juvenile Chinese sturgeon is better for growth when feeding four times daily compared to twice and thrice daily.

Project description:BackgroundThe Chinese sturgeon (Acipenser sinensis) is endangered through anthropogenic activities including over-fishing, damming, shipping, and pollution. Controlled reproduction has been adopted and successfully conducted for conservation. However, little information is available on the reproductive regulation of the species. In this study, we conducted de novo transcriptome assembly of the gonad tissue to create a comprehensive dataset for A. sinensis.ResultsThe Illumina sequencing platform was adopted to obtain 47,333,701 and 47,229,705 high quality reads from testis and ovary cDNA libraries generated from three-year-old A. sinensis. We identified 86,027 unigenes of which 30,268 were annotated in the NCBI non-redundant protein database and 28,281 were annotated in the Swiss-prot database. Among the annotated unigenes, 26,152 and 7,734 unigenes, respectively, were assigned to gene ontology categories and clusters of orthologous groups. In addition, 12,557 unigenes were mapped to 231 pathways in the Kyoto Encyclopedia of Genes and Genomes Pathway database. A total of 1,896 unigenes, potentially differentially expressed between the two gonad types, were found, with 1,894 predicted to be up-regulated in ovary and only two in testis. Fifty-five potential gametogenesis-related genes were screened in the transcriptome and 34 genes with significant matches were found. Besides, more paralogs of 11 genes in three gene families (sox, apolipoprotein and cyclin) were found in A. sinensis compared to their orthologs in the diploid Danio rerio. In addition, 12,151 putative simple sequence repeats (SSRs) were detected.ConclusionsThis study provides the first de novo transcriptome analysis currently available for A. sinensis. The transcriptomic data represents the fundamental resource for future research on the mechanism of early gametogenesis in sturgeons. The SSRs identified in this work will be valuable for assessment of genetic diversity of wild fish and genealogy management of cultured fish.

Dataset Information

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

Publications

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

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