Orthology confers intron position conservation

BMC Genomics

Research Article

Anna Henricson¹  Erik LL Sonnhammer²  Kristoffer Forslund³ 

[1] Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77, Stockholm, Sweden;Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77, Stockholm, Sweden;Stockholm Bioinformatics Centre, Albanova, Stockholm University, SE-106 91, Stockholm, Sweden;Stockholm Bioinformatics Centre, Albanova, Stockholm University, SE-106 91, Stockholm, Sweden;

关键词: High Sequence Identity;    Gene Ontology Term;    Pair Type;    Intron Position;    Species Comparison;   

DOI  :  10.1186/1471-2164-11-412

 received in 2009-11-16, accepted in 2010-07-02,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundWith the wealth of genomic data available it has become increasingly important to assign putative protein function through functional transfer between orthologs. Therefore, correct elucidation of the evolutionary relationships among genes is a critical task, and attempts should be made to further improve the phylogenetic inference by adding relevant discriminating features. It has been shown that introns can maintain their position over long evolutionary timescales. For this reason, it could be possible to use conservation of intron positions as a discriminating factor when assigning orthology. Therefore, we wanted to investigate whether orthologs have a higher degree of intron position conservation (IPC) compared to non-orthologous sequences that are equally similar in sequence.ResultsTo this end, we developed a new score for IPC and applied it to ortholog groups between human and six other species. For comparison, we also gathered the closest non-orthologs, meaning sequences close in sequence space, yet falling just outside the ortholog cluster. We found that ortholog-ortholog gene pairs on average have a significantly higher degree of IPC compared to ortholog-closest non-ortholog pairs. Also pairs of inparalogs were found to have a higher IPC score than inparalog-closest non-inparalog pairs. We verified that these differences can not simply be attributed to the generally higher sequence identity of the ortholog-ortholog and the inparalog-inparalog pairs.Furthermore, we analyzed the agreement between IPC score and the ortholog score assigned by the InParanoid algorithm, and found that it was consistently high for all species comparisons. In a minority of cases, the IPC and InParanoid score ranked inparalogs differently. These represent cases where sequence and intron position divergence are discordant. We further analyzed the discordant clusters to identify any possible preference for protein functions by looking for enriched GO terms and Pfam protein domains. They were enriched for functions important for multicellularity, which implies a connection between shifts in intronic structure and the origin of multicellularity.ConclusionsWe conclude that orthologous genes tend to have more conserved intron positions compared to non-orthologous genes. As a consequence, our IPC score is useful as an additional discriminating factor when assigning orthology.

【 授权许可】

Unknown   
© Henricson et al; licensee BioMed Central Ltd. 2010. 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/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.