Evaluation and integration of functional annotation pipelines for newly sequenced organisms: the potato genome as a test case

BMC Plant Biology

Research Article

Ron Shamir¹  David Amar¹  Sanjeev K Sharma²  Pete E Hedley²  Tatyana Goldberg³  Oren Tzfadia⁴  Erik Andreasson⁵  Erik Alexandersson⁵  Itziar Frades⁵  Estelle Proux-Wera⁶  Agnieszka Danek⁷ 

[1] Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel;Cell and Molecular Sciences, The James Hutton Institute, Aberdeen, Scotland, UK;Department for Bioinformatics and Computational Biology, Technical University of Munich, Arcisstraße 21, 80333, Munich, Germany;Department of Plant Science, The Weizmann Institute of Science, Rehovot, Israel;Deptartment of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden;Deptartment of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden;Current affiliation: SciLifeLab, Stockholm University, Universitetsvägen 10, 114 18, Stockholm, Sweden;Institute of Informatics, Silesian University of Technology, Akademicka 2A, 44-100, Gliwice, Poland;

关键词: Functional annotation;    Gene ontology;    Gene co-expression;    Potato;    Genomics;   

DOI  :  10.1186/s12870-014-0329-9

 received in 2014-06-12, accepted in 2014-11-10,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundFor most organisms, even if their genome sequence is available, little functional information about individual genes or proteins exists. Several annotation pipelines have been developed for functional analysis based on sequence, ‘omics’, and literature data. However, researchers encounter little guidance on how well they perform. Here, we used the recently sequenced potato genome as a case study. The potato genome was selected since its genome is newly sequenced and it is a non-model plant even if there is relatively ample information on individual potato genes, and multiple gene expression profiles are available.ResultsWe show that the automatic gene annotations of potato have low accuracy when compared to a “gold standard” based on experimentally validated potato genes. Furthermore, we evaluate six state-of-the-art annotation pipelines and show that their predictions are markedly dissimilar (Jaccard similarity coefficient of 0.27 between pipelines on average). To overcome this discrepancy, we introduce a simple GO structure-based algorithm that reconciles the predictions of the different pipelines. We show that the integrated annotation covers more genes, increases by over 50% the number of highly co-expressed GO processes, and obtains much higher agreement with the gold standard.ConclusionsWe find that different annotation pipelines produce different results, and show how to integrate them into a unified annotation that is of higher quality than each single pipeline. We offer an improved functional annotation of both PGSC and ITAG potato gene models, as well as tools that can be applied to additional pipelines and improve annotation in other organisms. This will greatly aid future functional analysis of ‘-omics’ datasets from potato and other organisms with newly sequenced genomes. The new potato annotations are available with this paper.

【 授权许可】

Unknown   
© Amar et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.