Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands.
Laboratory of Molecular Biology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands.
Plant Physiol. 2019 Jan;179(1):38-54. doi: 10.1104/pp.18.00848. Epub 2018 Nov 6.
Single-molecule full-length complementary DNA (cDNA) sequencing can aid genome annotation by revealing transcript structure and alternative splice forms, yet current annotation pipelines do not incorporate such information. Here we present long-read annotation (LoReAn) software, an automated annotation pipeline utilizing short- and long-read cDNA sequencing, protein evidence, and ab initio prediction to generate accurate genome annotations. Based on annotations of two fungal genomes ( and ) and two plant genomes (Arabidopsis [] and ), we show that LoReAn outperforms popular annotation pipelines by integrating single-molecule cDNA-sequencing data generated from either the Pacific Biosciences or MinION sequencing platforms, correctly predicting gene structure, and capturing genes missed by other annotation pipelines.
单分子全长 cDNA 测序可以通过揭示转录结构和选择性剪接形式来辅助基因组注释，然而当前的注释管道并没有整合这些信息。在这里，我们介绍了长读注释（LoReAn）软件，这是一个利用短读和长读 cDNA 测序、蛋白质证据和从头预测来生成准确基因组注释的自动化注释管道。基于两个真菌基因组（和）和两个植物基因组（拟南芥[]和）的注释，我们表明，通过整合来自 Pacific Biosciences 或 MinION 测序平台的单分子 cDNA 测序数据，LoReAn 优于流行的注释管道，正确预测基因结构，并捕获其他注释管道错过的基因。
