非模式生物转录组研究

doi:10.3724/SP.J.1005.2013.00955

遗传 ›› 2013, Vol. 35 ›› Issue (8): 955-970.doi: 10.3724/SP.J.1005.2013.00955

非模式生物转录组研究

刘红亮, 郑丽明, 刘青青, 权富生, 张涌

西北农林科技大学动物医学院, 农业部动物生物技术重点实验室, 杨凌712100

收稿日期:2013-01-27 修回日期:2013-03-15 出版日期:2013-08-20 发布日期:2013-08-25
通讯作者: 权富生 E-mail:quanfusheng@nwsuaf.edu.cn
基金资助:
十二五国家科技计划课题(863项目)(编号：2011AA100303)资助

Studies on the transcriptomes of non-model organisms

LIU Hong-Liang, ZHENG Li-Ming, LIU Qing-Qing, QUAN Fu-Sheng, ZHANG Yong

Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A F University, Yangling 712100, China

Received:2013-01-27 Revised:2013-03-15 Online:2013-08-20 Published:2013-08-25

摘要/Abstract

摘要：

转录组代表细胞或组织内全部的RNA转录本(RNA transcripts), 反映不同生命阶段、不同组织类型、不同生理状态以及不同环境条件下表达的基因。转录组研究可以从整体水平上反映细胞中基因表达情况及其调控规律。非模式生物(Non-model organism)具有许多模式生物不具备的特征, 其转录组研究对解决基因进化、遗传育种以及生态等诸多方面的问题具有重要意义。但由于非模式生物缺乏参考基因组信息, 传统的转录组研究方法操作复杂, 实验周期长, 花费大, 使得其转录组研究进展缓慢。新一代高通量RNA测序技术(RNA-seq)完全改变了转录组学的研究模式, 迅速成为研究非模式生物转录组的先进技术。文章详细论述了近年来利用RNA-seq技术进行非模式生物转录组研究的进展情况, 从样品准备、高通量DNA测序以及生物信息学分析等方面介绍了利用RNA-seq技术研究非模式生物转录组的一般流程及方法, 并对其中有待进一步研究的问题进行了展望。

关键词: 转录组, RNA-seq, 非模式生物

Abstract:

The transcriptome represents the whole complement of RNA transcripts in cells or tissues and reflects the expressed genes at various life stages, tissue types, physiological states, and environmental conditions. Transcriptome analysis provides a comprehensive understanding of gene expression and its regulation. Non-model organism has many interesting traits of which model organisms lack, and the study of its transcriptome has great significance in solving the questions of genetic evolution, genetic breeding, ecology and so on. Because of absence of reference genome information, and traditional transcriptome research methods which are complicated to operate, long experimental period and costly, slow progress has been made in the research of non-model organism transcriptome. Fortunately, RNA sequencing (RNA-seq), the next-generation sequencing technology, has completely changed the way of transcriptome study, becoming an advanced technology on the investigation of non-model organism transcriptome. In this paper, we give a summary of the non-model organism transcriptome research using RNA-seq in recent years and briefly describe its general flow and principles from aspects of sample preparation, high throughput DNA sequencing, and bioinformatics analysis. Finally, questions that are still open and awaiting further research are also discussed.

Key words: transcriptome, non-model organism, RNA-seq

刘红亮郑丽明刘青青权富生张涌. 非模式生物转录组研究[J]. 遗传, 2013, 35(8): 955-970.

LIU Hong-Liang, ZHENG Li-Ming, LIU Qing-Qing, QUAN Fu-Sheng, ZHANG Yong. Studies on the transcriptomes of non-model organisms[J]. HEREDITAS, 2013, 35(8): 955-970.

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