Duarte Gustavo T, Volkova Polina Yu, Geras'kin Stanislav A
Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.
Russian Institute of Radiology and Agroecology, Obninsk, Russia.
Bio Protoc. 2021 Feb 5;11(3):e3912. doi: 10.21769/BioProtoc.3912.
RNA sequencing (RNA-seq) has opened up the possibility of studying virtually any organism at the whole transcriptome level. Nevertheless, the absence of a sequenced and accurately annotated reference genome may be an obstacle for applying this technique to non-model organisms, especially for those with a complex genome. While transcriptome assembly can circumvent this problem, it is often computationally demanding. Furthermore, the transcriptome annotation and Gene Ontology enrichment analysis without an automatized system is often a laborious task. Here we describe step-by-step the pipeline that was used to perform the transcriptome assembly, annotation, and Gene Ontology analysis of Scots pine (), a gymnosperm species with complex genome. Using only free software available for the scientific community and running on a standard personal computer, the pipeline intends to facilitate transcriptomic studies for non-model species, yet being flexible to be used with any organism.
RNA测序（RNA-seq）开启了在全转录组水平上研究几乎任何生物体的可能性。然而，缺乏经过测序和准确注释的参考基因组可能会成为将该技术应用于非模式生物的障碍，尤其是对于那些基因组复杂的生物。虽然转录组组装可以规避这个问题，但它通常对计算要求很高。此外，没有自动化系统的转录组注释和基因本体富集分析往往是一项艰巨的任务。在这里，我们逐步描述了用于对欧洲赤松（一种基因组复杂的裸子植物物种）进行转录组组装、注释和基因本体分析的流程。该流程仅使用科学界可用的免费软件，并在标准个人计算机上运行，旨在促进对非模式物种的转录组学研究，并且具有灵活性，可用于任何生物体。
