转2表达 - - 新型转录组组装管道优化用于基因表达分析
Aleksandra M Kasianova1,2, Aleksey A Penin1, Mikhail I Schelkunov1,2
1Institute for Information Transmission, Russian Academy of Sciences, Moscow, Russia.
Plant methods
|August 16, 2024
概括
Trans2express是新的混合转录组组装管道,为植物生产高质量的基因表达数据. 这种工具有助于描述转录组和分析基因表达,特别是在非模型物种中.
科学领域:
- 植物基因组学 植物基因组学
- 转录基因组序列的测序
- 生物信息学工具 生物信息学工具
背景情况:
- 对于大型复杂的植物基因组来说,新基因组组装是一个挑战.
- 转录组组装是一种替代方案,但面临着异型和不均表达等挑战.
- 现有的转录组件组装器在生产高质量的组件以供下游分析方面扎.
研究的目的:
- 开发一条可靠的管道,用于新的混合转录组组装.
- 创建一个基于Web的工具 (Trans2express) 以进行高效的转录组分析.
- 提高基因表达研究的转录组组件的质量,特别是在非模型植物中.
主要方法:
- 开发了Trans2express,一个使用rnaSPAdes进行混合转录组组装的管道.
- 实施后加工过步骤,以提高组装质量.
- 使用Illumina和牛津纳米孔数据对Arabidopsis thaliana和三个非模型植物物种进行了管道测试.
主要成果:
- Trans2express实现了高质量的转录组组,其中86.1%的Arabidopsis基因被组装成单个结合体.
- 组装的转录组与基因表达水平的基因组分析具有高度一致性.
- 对于模型和非模型植物,有效的差异基因表达分析被证明是有效的.
结论:
- Trans2express提供了一种新的混合转录组组装协议,旨在为每个基因单个转录恢复.
- 该协议和网络工具预计将在非模型植物中推进转录组特征和基因表达分析.
- Trans2express将成为研究基因表达和转录组的植物生物学家的宝贵资源.
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