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

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

doi:10.1038/s41597-023-02014-4

Cited by 6 publications

(4 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Iso-seq has been successfully used to discover diverse novel isoforms and annotates full-length isoforms from start to end in a wide variety of species 10 . Many studies have combined Iso-seq and short-read RNA-seq to enhance the accuracy and obtain a more comprehensive understanding of diverse isoform expression quantification 11 , 12 . Thus, there is a need for an integrated application using Iso-seq and RNA-seq to explore the complexity of transcriptomes in the greater amberjack.…”

Section: Background and Summarymentioning

confidence: 99%

Integrating Iso-seq and RNA-seq data for the reannotation of the greater amberjack genome

Zhao,

Chen,

et al. 2024

Sci Data

View full text Add to dashboard Cite

The greater amberjack is a very important fishery species with high commercial value, and it is distributed worldwide. Transcriptome-based studies on S. dumerili have been limited by an inadequate reference genome and a lack of well-annotated full-length transcripts. In this study, a total of 12 tissues from juvenile and adult fish both sexes were collected for next-generation RNA sequencing (RNA-seq) and full-length isoform sequencing (Iso-seq). For Iso-seq, a total of 163,218, 149,716, and 189,169 high-quality unique transcript sequences were obtained, with an N50 of 5,441, 5,255, and 5,939, from juvenile, adult male and adult female S. dumerili, respectively. We integrated the Iso-seq and RNA-seq data to construct a comprehensive gene annotation and systematically profiled the dynamics of gene expression across the 12 tissues. Our gene models had greater detail and accuracy than those from NCBI and Ensembl, with more precise polyA locations. These resources serve as a foundation for functional genomic studies and provide valuable insights into the molecular mechanisms underlying the development, reproduction and commercial traits of amberjack.

show abstract

Section: Background and Summarymentioning

confidence: 99%

Integrating Iso-seq and RNA-seq data for the reannotation of the greater amberjack genome

Zhao,

Chen,

et al. 2024

Sci Data

View full text Add to dashboard Cite

show abstract

“…The advent of advanced sequencing technologies, particularly global transcriptome analysis, has substantially propelled genetic investigations in fish, providing a fundamental underpinning for unraveling gene function and structure in non-model organisms without reference genome information [13][14][15] . However, a comprehensive exploration of transcriptomic and genomic landscapes in the Chungtien schizothoracin has not been fully explored, contributing to a deficiency in genetic insights crucial for understanding the adaptive mechanisms of this cherished fish.…”

Section: Background and Summarymentioning

confidence: 99%

Transcriptomic annotation of the Chungtien schizothoracin (Ptychobarbus chungtienensis) using Iso-seq and RNA-seq data

Gao,

Chong,

et al. 2024

Sci Data

View full text Add to dashboard Cite

The Chungtien schizothoracin (Ptychobarbus chungtienensis), an endangered fish species endemic to the Zhongdian Plateau, remains underexplored in terms of transcriptomic sequencing. This investigation used tissues from five distinct organs (heart, liver, spleen, kidney, and brain) of the Chungtien schizothoracin for PacBio Iso-seq and RNA-seq analyses, yielding a repertoire of 16,598 full-length transcripts spanning lengths from 363 bp to 7,157 bp. Gene family clustering and phylogenetic analysis encompassed a comprehensive set of 13 fish species, all of which were cyprinids, including the zebrafish and the examined species Ptychobarbus chungtienensis. Moreover, the identification of long non-coding RNAs (lncRNAs) and coding sequences was accomplished across all five tissues. Comprehensive analyses of gene expression profiles and differentially expressed genes among the above five tissues were performed. In summary, the obtained full-length transcripts and detailed gene expression profiles of the Chungtien schizothoracin tissues furnish crucial expression data and genetic sequences, laying the groundwork for future investigations and fostering a holistic comprehension of the adaptive mechanisms inherent in the Chungtien schizothoracin under various conditions.

show abstract

“…The Chinese sturgeon ( Acipenser sinensis ) is a critically endangered aquatic species in the Yangtze River and coastal waters of China. The Chinese sturgeon was classified as critically endangered by the IUCN (Liao et al, 2023). The major threats to Chinese sturgeon include river fragmentation, agricultural development and urbanization, and overexploitation (Chen et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Indexing serum and mucous biochemical parameters of endangered Chinese sturgeon Acipenser sinensis with implications for health assessment

Liu,

UllahKhan,

Jin

et al. 2024

Journal of Fish Biology

View full text Add to dashboard Cite

The Chinese sturgeon (Acipenser sinensis) is a critically endangered aquatic fish. Health monitoring and welfare assessments are critical for the conservation of Chinese sturgeon. In this study, biochemical parameters of serum and skin mucus in Chinese sturgeon were examined to evaluate the potential biomarkers. Serum and mucous samples were obtained from Chinese sturgeon, and the levels of total protein (TP), alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), lactate dehydrogenase (LDH), creatine kinase (CK), lactic acid (LD), acid phosphatase (ACP), lysozyme (LYZ), glucose (GLU), and cortisol were determined. The concentrations of ALT, AST, cortisol, and LYZ were significantly higher in the mucous group than those in the serum group (p < 0.05). In addition, the concentrations of ALP, ACP, LD, LDH, CK, and TP were significantly higher level in the serum group than those in the mucous group (p < 0.05). Moreover, the correlations between serum and mucous biochemical parameters were established. Statistical analysis showed a positive correlation between serum and skin mucous markers (ACP, cortisol, and LYZ). AST versus ALT in serum and mucus showed a significant positive correlation (p < 0.01). A significant positive correlation was found between cortisol and CK in mucus (p < 0.01). Moreover, LD versus LDH in serum showed a significant but weak positive correlation (p < 0.01). Principal component analysis revealed a complete separation between the serum and mucous groups, with the biomarkers that contributed the most being ALP, TP, ALT, and AST. This study provides baseline data and reference intervals for serum and mucous biochemical parameters in presumably healthy Chinese sturgeons. The current study has important implications for the development of conservation strategies and the conservation status of critically endangered species.

show abstract

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

Cited by 6 publications

References 24 publications

Integrating Iso-seq and RNA-seq data for the reannotation of the greater amberjack genome

Integrating Iso-seq and RNA-seq data for the reannotation of the greater amberjack genome

Transcriptomic annotation of the Chungtien schizothoracin (Ptychobarbus chungtienensis) using Iso-seq and RNA-seq data

Indexing serum and mucous biochemical parameters of endangered Chinese sturgeon Acipenser sinensis with implications for health assessment

Contact Info

Product

Resources

About