Systematic discovery of unannotated genes in 11 yeast species using a database of orthologous genomic segments

BMC Genomics

Research Article

Seán S ÓhÉigeartaigh¹  Kevin P Byrne¹  Kenneth H Wolfe¹  David Armisén¹ 

[1]Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland

关键词: Lactis;    Intergenic Region;    Yeast Species;    Genomic Segment;    Yeast Genome;   

DOI  :  10.1186/1471-2164-12-377

 received in 2011-04-19, accepted in 2011-07-26,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundIn standard BLAST searches, no information other than the sequences of the query and the database entries is considered. However, in situations where two genes from different species have only borderline similarity in a BLAST search, the discovery that the genes are located within a region of conserved gene order (synteny) can provide additional evidence that they are orthologs. Thus, for interpreting borderline search results, it would be useful to know whether the syntenic context of a database hit is similar to that of the query. This principle has often been used in investigations of particular genes or genomic regions, but to our knowledge it has never been implemented systematically.ResultsWe made use of the synteny information contained in the Yeast Gene Order Browser database for 11 yeast species to carry out a systematic search for protein-coding genes that were overlooked in the original annotations of one or more yeast genomes but which are syntenic with their orthologs. Such genes tend to have been overlooked because they are short, highly divergent, or contain introns. The key features of our software - called SearchDOGS - are that the database entries are classified into sets of genomic segments that are already known to be orthologous, and that very weak BLAST hits are retained for further analysis if their genomic location is similar to that of the query. Using SearchDOGS we identified 595 additional protein-coding genes among the 11 yeast species, including two new genes in Saccharomyces cerevisiae. We found additional genes for the mating pheromone a-factor in six species including Kluyveromyces lactis.ConclusionsSearchDOGS has proven highly successful for identifying overlooked genes in the yeast genomes. We anticipate that our approach can be adapted for study of further groups of species, such as bacterial genomes. More generally, the concept of doing sequence similarity searches against databases to which external information has been added may prove useful in other settings.

【 授权许可】

Unknown   
© ÓhÉigeartaigh et al; licensee BioMed Central Ltd. 2011. 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.