Here we present a method for comparing shared protein families across a large set of Aspergillus species.
The Aspergillus is one of the most diverse and important industrial and agricultural filamentous fungus. It has been found in various environments including extreme conditions and shows a surprising capacity for environmental adaptation while producing a variety of secondary metabolites. The phenotypic diversity seen in species of Aspergillus must, as all other biological diversity, be the product of evolution, including positive selection, horizontal gene transfers, and gene rearrangement. Here we discuss the genomic diversity among 37 species by investigating three different patterns in genes.
- The pan-genome comprises all gene present in one or more species and are expected to code for genetic abilities such as environmental adaptation factors and growth abilities, assuming these are not species specific.
- The core-genome is the collection of genes present in all 37 species with or without isoenzymes and are expected to encode essential cellular functions needed for all species. The more diverse the set of investigated species, the smaller the core genome becomes, as they share less biological functions.
- Species unique genes are found in only one species with or without isoenzymes. These genes are expected to be involved in environmental adaptation and speciation. Through these different views, we will discuss the possible evolutionary events that have made Aspergillus species so diverse.
Identifying orthologs (genes present in different species but originated from a single common ancestor) and paralogs (genes present in the same species created by a duplication event) is a big part of understanding the difference between species both evolutionary but also genetically. It is used in studies on population genetics, comparative genomics, evolutionary biology, biodiversity, genome annotation and the identification of taxonomically restricted sequences [Li2003].
- [Li2003] Li, L., Stoeckert, C. J., and Roos, D. S. (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes., Genome Res. 13, 2178–89.