Deep spatiotemporal transcriptome analysis provides new insights into early development of koi carp (Cyprinus carpio var. koi)

Luo, Ming; Shi, Xiulan; Guo, Jing; Lin, Kueiyu Joshua; Zhu, Wenbin; Fu, Jianjun; Wang, Lanmei; Dong, Zaijie

doi:10.1016/j.aquaculture.2023.739767

Cited by 4 publications

(1 citation statement)

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“…The steps of transcriptome and miRNA sequencing were referred to the previous research methods of Luo et al [ 46 , 47 ]. Transcriptome sequencing mainly includes data quality control, comparison with the reference genome, transcript assembly, quantification of gene expression, differential gene analysis and functional annotation; the detailed steps are listed in Supplementary file 3 .…”

Section: Methodsmentioning

confidence: 99%

Integrated transcriptome and microRNA analysis reveals molecular responses to high-temperature stress in the liver of American shad (Alosa sapidissima)

Liu,

Liang,

et al. 2024

BMC Genomics

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Background Fish reproduction, development and growth are directly affected by temperature, investigating the regulatory mechanisms behind high temperature stress is helpful to construct a finer molecular network. In this study, we systematically analyzed the transcriptome and miRNA information of American shad (Alosa sapidissima) liver tissues at different cultivation temperatures of 24 ℃ (Low), 27 ℃ (Mid) and 30 ℃ (High) based on a high-throughput sequencing platform. Results The results showed that there were 1594 differentially expressed genes (DEGs) and 660 differentially expressed miRNAs (DEMs) in the LowLi vs. MidLi comparison group, 473 DEGs and 84 DEMs in the MidLi vs. HighLi group, 914 DEGs and 442 DEMs in the LowLi vs. HighLi group. These included some important genes and miRNAs such as calr, hsp90b1, hsp70, ssa-miR-125a-3p, ssa-miR-92b-5p, dre-miR-15a-3p and novel-m1018-5p. The DEGs were mainly enriched in the protein folding, processing and export pathways of the endoplasmic reticulum; the target genes of the DEMs were mainly enriched in the focal adhesion pathway. Furthermore, the association analysis revealed that the key genes were mainly enriched in the metabolic pathway. Interestingly, we found a significant increase in the number of genes and miRNAs involved in the regulation of heat stress during the temperature change from 24 °C to 27 °C. In addition, we examined the tissue expression characteristics of some key genes and miRNAs by qPCR, and found that calr, hsp90b1 and dre-miR-125b-2-3p were significantly highly expressed in the liver at 27 ℃, while novel-m0481-5p, ssa-miR-125a-3p, ssa-miR-92b-5p, dre-miR-15a-3p and novel-m1018-5p had the highest expression in the heart at 30℃. Finally, the quantitative expression trends of 10 randomly selected DEGs and 10 DEMs were consistent with the sequencing data, indicating the reliability of the results. Conclusions In summary, this study provides some fundamental data for subsequent in-depth research into the molecular regulatory mechanisms of A. sapidissima response to heat stress, and for the selective breeding of high temperature tolerant varieties.

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Section: Methodsmentioning

confidence: 99%