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This article is part of the supplement: Ninth Annual MCBIOS Conference. Dealing with the Omics Data Deluge

Open Access Proceedings

Computational workflow for analysis of gain and loss of genes in distantly related genomes

Andrey Ptitsyn1* and Leonid L Moroz12

Author affiliations

1 Whitney Laboratory for Marine Biosciences, University of Florida; 9505 Ocean Shore Blvd. Saint Augustine FL 32080, USA

2 Dept of Neuroscience, University of Florida; Gainesville, FL 32610, USA

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Citation and License

BMC Bioinformatics 2012, 13(Suppl 15):S5  doi:10.1186/1471-2105-13-S15-S5

Published: 11 September 2012



Early evolution of animals led to profound changes in body plan organization, symmetry and the rise of tissue complexity including formation of muscular and nervous systems. This process was associated with massive restructuring of animal genomes as well as deletion, acquisition and rapid differentiation of genes from a common metazoan ancestor. Here, we present a simple but efficient workflow for elucidation of gene gain and gene loss within major branches of the animal kingdom.


We have designed a pipeline of sequence comparison, clustering and functional annotation using 12 major phyla as illustrative examples. Specifically, for the input we used sets of ab initio predicted gene models from the genomes of six bilaterians, three basal metazoans (Cnidaria, Placozoa, Porifera), two unicellular eukaryotes (Monosiga and Capsospora) and the green plant Arabidopsis as an out-group. Due to the large amounts of data the software required a high-performance Linux cluster. The final results can be imported into standard spreadsheet analysis software and queried for the numbers and specific sets of genes absent in specific genomes, uniquely present or shared among different taxons.

Results and conclusions

The developed software is open source and available free of charge on Open Source principles. It allows the user to address a number of specific questions regarding gene gain and gene loss in particular genomes, and user-defined groups of genomes can be formulated in a type of logical expression. For example, our analysis of 12 sequenced genomes indicated that these genomes possess at least 90,000 unique genes and gene families, suggesting enormous diversity of the genome repertoire in the animal kingdom. Approximately 9% of these gene families are shared universally (homologous) among all genomes, 53% are unique to specific taxa, and the rest are shared between two or more distantly related genomes.