RNA‑seq技术在水生生物生态毒理学中的应用进展

doi:10.19586/j.2095-2341.2021.0041

生物技术进展 ›› 2021, Vol. 11 ›› Issue (4): 535-541.DOI: 10.19586/j.2095-2341.2021.0041

RNA‑seq技术在水生生物生态毒理学中的应用进展

柯杨¹(), 马瑜¹^,²(), 朱海云¹, 张育辉²

^1.陕西省微生物研究所，西安 710043
^2.陕西师范大学生命科学学院，西安 710119

收稿日期:2021-03-29 接受日期:2021-06-02 出版日期:2021-07-25 发布日期:2021-08-02
通讯作者: 马瑜
作者简介:柯杨 E-mail: keyang-bio@163.com；
基金资助:
陕西省科学院科技计划项目(2017k-05)

Application Progress of RNA‑seq Technology in Ecotoxicology of Aquatic Organisms

Yang KE¹(), Yu MA¹^,²(), Haiyun ZHU¹, Yuhui ZHANG²

^1.Microbiology Institute of Shaanxi，Xi’an 710043，China
^2.College of Life Sciences，Shaanxi Normal University，Xi’an 710119，China

Received:2021-03-29 Accepted:2021-06-02 Online:2021-07-25 Published:2021-08-02
Contact: Yu MA

摘要/Abstract

摘要：

水域是地球环境的重要组成部分，也是最易受污染的生态系统之一。水生态系统中不同营养级别的水生生物可通过摄食、接触等多种途径摄入水体中的污染物。因此，监测水域污染物对水生生物和生态系统的影响，解析污染物对不同水生生物的毒性机制，筛选敏感、有效的生物标志物对生态毒理学研究和环境风险评价具有重要意义。RNA测序（RNA sequencing，RNA?seq）技术因所需样品量少，且不需参考序列，可在整体水平上鉴定基因差异表达，成为水生生物生态毒理学研究的最佳方法之一。基于此，介绍了RNA?seq技术的基本流程与数据分析过程，对该技术在不同生态位的水生生物（如鱼类、两栖类、贝类、甲壳类等）生态毒理学中的应用展开综述，并对RNA?seq技术面临的不足、挑战及发展趋势进行探讨，以期为该技术在水生生物生态毒理学研究中的应用，尤其是水生态环境中污染物胁迫水生生物机制的阐明及污染水域生态环境恢复提供参考。

关键词: RNA?seq, 转录组学, 水生生物, 生态毒理学

Abstract:

Aquatorium is an important parts of the earth environments and one of the most vulnerable ecosystems to pollution. The aquatic organisms on different trophic levels are prone to the pollutants in aquatic system via food intake and exposure. Therefore， monitoring the impacts of pollutants in water on aquatic organisms and ecosystems， analyzing the toxicity mechanisms of pollutants on different aquatic organisms， and screening sensitive and effective biomarkers are of great significance for ecotoxicology research and environmental risk assessment. RNA sequencing （RNA?seq） technology has become one of the best methods for aquatic ecotoxicology research， for it can identify gene differential expression at the overall level with less sample volume and with no need of reference sequences. Based on this， the basic process and data analysis process of RNA?seq technology were introduced. Moreover， the application of RNA?seq in ecotoxicology of aquatic organisms with different ecological niches （such as fish， amphibians， shellfish and crustaceans） was reviewed， and the deficiency， challenges and developments trends of RNA?seq technology in toxicology research were also discussed. These were expected to provide reference for the application of RNA?seq technology in aquatic ecotoxicology， especially for the clarification of the mechanism of pollutants on aquatic organisms and the restoration of the ecological environment of pollutant aquatic systems.

Key words: RNA?seq, transcriptomics, aquatic organisms, ecotoxicology

中图分类号:

Q178.1

柯杨, 马瑜, 朱海云, 张育辉. RNA‑seq技术在水生生物生态毒理学中的应用进展[J]. 生物技术进展, 2021, 11(4): 535-541.

Yang KE, Yu MA, Haiyun ZHU, Yuhui ZHANG. Application Progress of RNA‑seq Technology in Ecotoxicology of Aquatic Organisms[J]. Current Biotechnology, 2021, 11(4): 535-541.

图/表 1

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用途	软件名称	参考文献
原始数据处理	FastQC、NGS QC	[9-10]
读序比对	Bowtie、BWA、MAQ、TopHat、STAR、GSNAP	[9]
质量控制	HTQC、Qualimap2、RNA‑SeQC、QC‑chain	[9,11-12]
序列组装	Cufflinks、TGICL、stackPACK、Velvet、transAbySS、Oases、ALLPATHS2、Trinity、SOAP denovo‑Trans、PCAP	[9,13-15] [16-17]
转录本识别	Stringtie、cufflinks、CIDANE、TransComb、iReckon	[16,18-20]
转录本定量	featureCounts、StringTie、Cufflinks、RSEM、Sailfish、kallisto	[9,21-23]
差异表达分析	Cuffdiff2、EdgeR、DEseq、Limma、Voom	[16,24]

用途	软件名称	参考文献
原始数据处理	FastQC、NGS QC	[9-10]
读序比对	Bowtie、BWA、MAQ、TopHat、STAR、GSNAP	[9]
质量控制	HTQC、Qualimap2、RNA‑SeQC、QC‑chain	[9,11-12]
序列组装	Cufflinks、TGICL、stackPACK、Velvet、transAbySS、Oases、ALLPATHS2、Trinity、SOAP denovo‑Trans、PCAP	[9,13-15] [16-17]
转录本识别	Stringtie、cufflinks、CIDANE、TransComb、iReckon	[16,18-20]
转录本定量	featureCounts、StringTie、Cufflinks、RSEM、Sailfish、kallisto	[9,21-23]
差异表达分析	Cuffdiff2、EdgeR、DEseq、Limma、Voom	[16,24]

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[2]	常文婧，赵彦艳. 激光捕获显微切割在肿瘤多组学研究中的应用进展[J]. 生物技术进展, 2020, 10(2): 130-136.
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RNA‑seq技术在水生生物生态毒理学中的应用进展

Application Progress of RNA‑seq Technology in Ecotoxicology of Aquatic Organisms

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