Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome.

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Version: Final published version
License: CC BY 4.0
Serval ID
serval:BIB_6469004280EE
Type
Article: article from journal or magazin.
Collection
Publications
Title
Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome.
Journal
Bioinformatics
Author(s)
Piližota I., Train C.M., Altenhoff A., Redestig H., Dessimoz C.
ISSN
1367-4811 (Electronic)
ISSN-L
1367-4803
Publication state
Published
Issued date
01/04/2019
Peer-reviewed
Oui
Volume
35
Number
7
Pages
1159-1166
Language
english
Notes
Publication types: Journal Article
Publication Status: ppublish
Abstract
As the time and cost of sequencing decrease, the number of available genomes and transcriptomes rapidly increases. Yet the quality of the assemblies and the gene annotations varies considerably and often remains poor, affecting downstream analyses. This is particularly true when fragments of the same gene are annotated as distinct genes, which may cause them to be mistaken as paralogs.
In this study, we introduce two novel phylogenetic tests to infer non-overlapping or partially overlapping genes that are in fact parts of the same gene. One approach collapses branches with low bootstrap support and the other computes a likelihood ratio test. We extensively validated these methods by (i) introducing and recovering fragmentation on the bread wheat, Triticum aestivum cv. Chinese Spring, chromosome 3B; (ii) by applying the methods to the low-quality 3B assembly and validating predictions against the high-quality 3B assembly; and (iii) by comparing the performance of the proposed methods to the performance of existing methods, namely Ensembl Compara and ESPRIT. Application of this combination to a draft shotgun assembly of the entire bread wheat genome revealed 1221 pairs of genes that are highly likely to be fragments of the same gene. Our approach demonstrates the power of fine-grained evolutionary inferences across multiple species to improving genome assemblies and annotations.
An open source software tool is available at https://github.com/DessimozLab/esprit2.
Supplementary data are available at Bioinformatics online.
Pubmed
Web of science
Open Access
Yes
Create date
10/09/2018 13:35
Last modification date
20/08/2019 15:20
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