Kerr Stephanie C, Gaiti Federico, Tanurdzic Milos
School of Biological Sciences, The University of Queensland, St Lucia, QLD, Australia.
New York Genome Center and Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
Methods Mol Biol. 2019;1933:265-275. doi: 10.1007/978-1-4939-9045-0_16.
The ability to identify and quantify transcribed sequences from a multitude of organisms using high-throughput RNA sequencing has revolutionized our understanding of genetics and plant biology. However, a number of computational tools used in these analyses still require a reference genome sequence, something that is seldom available for non-model organisms. Computational tools employing de Bruijn graphs to reconstruct full-length transcripts from short sequence reads allow for de novo transcriptome assembly. Here we provide detailed methods for generating and annotating de novo transcriptome assembly from plant RNA-seq data.
利用高通量RNA测序技术识别和量化多种生物体转录序列的能力，彻底改变了我们对遗传学和植物生物学的理解。然而，这些分析中使用的许多计算工具仍然需要参考基因组序列，而对于非模式生物来说，这种序列很少能够获得。采用德布鲁因图从短序列读取中重建全长转录本的计算工具允许进行从头转录组组装。在这里，我们提供了从植物RNA-seq数据生成和注释从头转录组组装的详细方法。
