Open Access Highly Accessed Methodology article

Automated alignment-based curation of gene models in filamentous fungi

Ate van der Burgt12, Edouard Severing23, Jérôme Collemare1 and Pierre JGM de Wit1*

Author Affiliations

1 Laboratory of Phytopathology, Wageningen University & Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands

2 Applied Bioinformatics, Plant Research International, Wageningen University & Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands

3 Laboratory of Genetics, Wageningen University & Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands

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BMC Bioinformatics 2014, 15:19  doi:10.1186/1471-2105-15-19

Published: 16 January 2014

Abstract

Background

Automated gene-calling is still an error-prone process, particularly for the highly plastic genomes of fungal species. Improvement through quality control and manual curation of gene models is a time-consuming process that requires skilled biologists and is only marginally performed. The wealth of available fungal genomes has not yet been exploited by an automated method that applies quality control of gene models in order to obtain more accurate genome annotations.

Results

We provide a novel method named alignment-based fungal gene prediction (ABFGP) that is particularly suitable for plastic genomes like those of fungi. It can assess gene models on a gene-by-gene basis making use of informant gene loci. Its performance was benchmarked on 6,965 gene models confirmed by full-length unigenes from ten different fungi. 79.4% of all gene models were correctly predicted by ABFGP. It improves the output of ab initio gene prediction software due to a higher sensitivity and precision for all gene model components. Applicability of the method was shown by revisiting the annotations of six different fungi, using gene loci from up to 29 fungal genomes as informants. Between 7,231 and 8,337 genes were assessed by ABFGP and for each genome between 1,724 and 3,505 gene model revisions were proposed. The reliability of the proposed gene models is assessed by an a posteriori introspection procedure of each intron and exon in the multiple gene model alignment. The total number and type of proposed gene model revisions in the six fungal genomes is correlated to the quality of the genome assembly, and to sequencing strategies used in the sequencing centre, highlighting different types of errors in different annotation pipelines. The ABFGP method is particularly successful in discovering sequence errors and/or disruptive mutations causing truncated and erroneous gene models.

Conclusions

The ABFGP method is an accurate and fully automated quality control method for fungal gene catalogues that can be easily implemented into existing annotation pipelines. With the exponential release of new genomes, the ABFGP method will help decreasing the number of gene models that require additional manual curation.

Keywords:
Gene model; Automated gene model curation; Sequence error; Truncated gene model; Pseudogene; Fungal genome; Cladosporium fulvum