BackgroundTo reconstruct the evolution history of DNA sequences, novel models of increasing complexity regarding the number of free parameters taken into account in the sequence evolution, as well as faster and more accurate algorithms, and statistical and computational methods, are needed. More particularly, as the principal forces that have led to major structural changes are genome rearrangements (such as translocations, fusions, and so on), understanding their underlying mechanisms, among other things via the ancestral genome reconstruction, are essential. In this problem, since finding the ancestral genomes that minimize the number of rearrangements in a phylogenetic tree is known to be NP-hard for three or more genomes, heuristics are commonly chosen to obtain approximations of the exact solution. The aim of this work is to show that another path is possible.ResultsVarious algorithms and software already deal with the difficult nature of the problem of reconstruction of the ancestral genome, but they do not function with precision, in particular when indels or single nucleotide polymorphisms fall into repeated sequences. In this article, and despite the theoretical NP-hardness of the ancestral reconstruction problem, we show that an exact solution can be found in practice in various cases, encompassing organelles and some bacteria. A practical example proves that an accurate reconstruction, which also allows to highlight homoplasic events, can be obtained. This is illustrated by the reconstruction of ancestral genomes of two bacterial pathogens, belonging in Mycobacterium and Brucella genera.ConclusionsBy putting together automatically reconstructed ancestral regions with handmade ones for problematic cases, we show that an accurate reconstruction of ancestors of the Brucella genus and of the Mycobacterium tuberculosis complex is possible. By doing so, we are able to investigate the evolutionary history of each pathogen by computing their common ancestors. They can be investigated extensively, by studying the gene content evolution over time, the resistance acquisition, and the impacts of mobile elements on genome plasticity.
The aim of this study is to investigate the relation that can be found between the phylogeny of a large set of complete chloroplast genomes, and the evolution of gene content inside these sequences. Core and pan genomes have been computed on de novo annotation of these 845 genomes, the former being used for producing well-supported phylogenetic tree while the latter provides information regarding the evolution of gene contents over time. It details too the specificity of some branches of the tree, when specificity is obtained on accessory genes. After having detailed the material and methods, we emphasize some remarkable relation between well-known events of the chloroplast history, like endosymbiosis, and the evolution of gene contents over the phylogenetic tree.
Abstract. Technical signs of progress during the last decades has led to a situation in which the accumulation of genome sequence data is increasingly fast and cheap. The huge amount of molecular data available nowadays can help addressing new and essential questions in Evolution. However, reconstructing evolution of DNA sequences requires models, algorithms, statistical and computational methods of ever increasing complexity. Since most dramatic genomic changes are caused by genome rearrangements (gene duplications, gain/loss events), it becomes crucial to understand their mechanisms and reconstruct ancestors of the given genomes. This problem is known to be NPcomplete even in the "simplest" case of three genomes. Heuristic algorithms are usually executed to provide approximations of the exact solution. We state that, even if the ancestral reconstruction problem is NP-hard in theory, its exact resolution is feasible in various situations, encompassing organelles and some bacteria. Such accurate reconstruction, which identifies too some highly homoplasic mutations whose ancestral status is undecidable, will be initiated in this work-in-progress, to reconstruct ancestral genomes of two Mycobacterium pathogenetic bacterias. By mixing automatic reconstruction of obvious situations with human interventions on signaled problematic cases, we will indicate that it should be possible to achieve a concrete, complete, and really accurate reconstruction of lineages of the Mycobacterium tuberculosis complex. Thus, it is possible to investigate how these genomes have evolved from their last common ancestors.
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