ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2019
Characterization and analysis of the transcriptome in Gymnocypris selincuoensis on the Qinghai-Tibetan Plateau using single-molecule long-read sequencing and RNA-seq.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed.
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- Population Structure, Growth Characteristics, Resource Dynamics, and Management Strategies ofBiology · 2025Article
- Exploitation of Key Regulatory Modules and Genes for High-Salt Adaptation in Schizothoracine by Weighted Gene Co-Expression Network Analysis.Animals : an open access journal from MDPI · 2024Article
- Characterization of transcriptome changes in saline stress adaptation on Leuciscus merzbacheri using PacBio Iso-Seq and RNA-Seq.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
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- PacBio Full-Length Transcriptome of a TetraploidAnimals : an open access journal from MDPI · 2023Article
- Transcriptomic Analysis of Large Yellow Croaker (Veterinary sciences · 2022Article
- Dynamic Transcriptional Landscape of Grass Carp (International journal of molecular sciences · 2022Article
- Genetic Variation inAnimals : an open access journal from MDPI · 2022Article
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- Screening and Validation of p38 MAPK Involved in Ovarian Development ofFrontiers in veterinary science · 2022Article
- Transcriptome profiling reveals gene regulation programs underlying tail development in the Ornamented Pygmy frogFrontiers in bioscience (Landmark edition) · 2021Article
- Characterization and complexity of transcriptome in Gymnocypris przewalskii using single-molecule long-read sequencing and RNA-seq.DNA research : an international journal for rapid publication of reports on genes and genomes · 2021Article
- Global tissue transcriptomic analysis to improve genome annotation and unravel skin pigmentation in goldfish.Scientific reports · 2021Article
- PacBio Single-Molecule Long-Read Sequencing Provides New Light on the Complexity of Full-Length Transcripts in Cattle.Frontiers in genetics · 2021Article
- PacBio Iso-Seq Improves the Rainbow Trout Genome Annotation and Identifies Alternative Splicing Associated With Economically Important Phenotypes.Frontiers in genetics · 2021Article
- Comparative transcriptome analysis of scaled and scaleless skins in Gymnocypris eckloni provides insights into the molecular mechanism of scale degeneration.BMC genomics · 2020Article
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- Characterization and analysis of full-length transcriptomes from two grasshoppers, Gomphocerus licenti and Mongolotettix japonicus.Scientific reports · 2020Article
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The lakes on the Qinghai-Tibet Plateau (QTP) are the largest and highest lake group in the world. Gymnocypris selincuoensis is the only cyprinid fish living in lake Selincuo, the largest lake on QTP. However, its genetic resource is still blank, limiting studies on molecular and genetic analysis. In this study, the transcriptome of G. selincuoensis was first generated by using PacBio Iso-Seq and Illumina RNA-seq. A full-length (FL) transcriptome with 75,435 transcripts was obtained by Iso-Seq with N50 length of 3,870 bp. Among all transcripts, 75,016 were annotated to public databases, 64,710 contain complete open reading frames and 2,811 were long non-coding RNAs. Based on all- vs.-all BLAST, 2,069 alternative splicing events were detected, and 80% of them were validated by reverse transcription polymerase chain reaction (RT-PCR). Tissue gene expression atlas showed that the number of detected expressed transcripts ranged from 37,397 in brain to 19,914 in muscle, with 10,488 transcripts detected in all seven tissues. Comparative genomic analysis with other cyprinid fishes identified 77 orthologous genes with potential positive selection (Ka/Ks > 0.3). A total of 56,696 perfect simple sequence repeats were identified from FL transcripts. Our results provide valuable genetic resources for further studies on adaptive evolution, gene expression and population genetics in G. selincuoensis and other congeneric fishes.
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