Background Mobile Genetic Elements (MGEs) are selfish DNA integrated in the genomes. Their detection ismainly based on consensus-like searches by scanning the investigated genome against the sequenceof an already identified MGE. Mobilomics aims at discovering all the MGEs in a genome and understandingtheir dynamic behavior: The data for this kind of investigation can be provided by comparativegenomics of closely related organisms. The amount of data thus involved requires a strongcomputational effort, which should be alleviated.Results Our approach proposes to exploit the high similarity among homologous chromosomes of differentstrains of the same species, following a progressive comparative genomics philosophy. We introducea software tool based on our new fast algorithm, called REGENDER, which is able to identify theconserved regions between chromosomes. Our case study is represented by a unique recently availabledataset of 39 different strains of S.cerevisiae, which REGENDER is able to compare in few minutes.By exploring the non-conserved regions, where MGEs are mainly retrotransposons called Tys, andmarking the candidate Tys based on their length, we are able to locate a priori and automatically all the already known Tys and map all the putative Tys in all the strains. The remaining putativemobile elements (PMEs) emerging from this intra-specific comparison are sharp markers of interspecificevolution: indeed, many events of non-conservation among different yeast strains correspondto PMEs. A clustering based on the presence/absence of the candidate Tys in the strains suggests anevolutionary interconnection that is very similar to classic phylogenetic trees based on SNPs analysis,even though it is computed without using phylogenetic information.Conclusions The case study indicates that the proposed methodology brings two major advantages: (a) it does notrequire any template sequence for the wanted MGEs and (b) it can be applied to infer MGEs also forlow coverage genomes with unresolved bases, where traditional approaches are largely ineffective.
via BioMed Central - Latest Articles http://www.biomedcentral.com/1471-2105/14/102/abstract
via BioMed Central - Latest Articles http://www.biomedcentral.com/1471-2105/14/102/abstract
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