Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

    We have a manual that explains all the features 

Record number 545749
Title Long-read annotation : Automated eukaryotic genome annotation based on long-read cDNA sequencing
Author(s) Cook, David E.; Valle-Inclan, Jose Espejo; Pajoro, Alice; Rovenich, Hanna; Thomma, Bart P.H.J.; Faino, Luigi
Source Plant Physiology 179 (2019)1. - ISSN 0032-0889 - p. 38 - 54.
DOI https://doi.org/10.1104/pp.18.00848
Department(s) EPS
BIOS Plant Development Systems
Laboratory of Molecular Biology
Laboratory of Phytopathology
Publication type Refereed Article in a scientific journal
Publication year 2019
Abstract

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 (Verticillium dahliae and Plicaturopsis crispa) and two plant genomes (Arabidopsis [Arabidopsis thaliana] and Oryza sativa), 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.

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