Abstract:The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large-scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their chloroplasts, the phylogenetic tree that can be inferred by their core genes is not necessarily well supported, due to the possible occurrence of "problematic" genes (i.e., homoplasy, incomplete lineage sorting, horizontal gene transfers, etc.) which may blur the phylogeneti… Show more
“…7 ). Indeed, with these bacteria, we have not to find the most supported tree based on the largest subset of core genes, as aligning the whole complete genomes leads to a well supported tree: it is not possible to improve the results, which is nice as the core genome is many times greater than in the chloroplast case (and so, it is not sure that the heuristic approach presented in our previous articles [ 32 , 38 , 39 ] can succeed to find the optima). Fig.…”
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.
“…7 ). Indeed, with these bacteria, we have not to find the most supported tree based on the largest subset of core genes, as aligning the whole complete genomes leads to a well supported tree: it is not possible to improve the results, which is nice as the core genome is many times greater than in the chloroplast case (and so, it is not sure that the heuristic approach presented in our previous articles [ 32 , 38 , 39 ] can succeed to find the optima). Fig.…”
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.
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.
In this article, we propose a semi-automated method to rebuild genome ancestors of chloroplasts by taking into account gene duplication. Two methods have been used in order to achieve this work: a naked eye investigation using homemade scripts, whose results are considered as a basis of knowledge, and a dynamic programming based approach similar to Needleman-Wunsch. The latter fundamentally uses the Gestalt pattern matching method of sequence matcher to evaluate the occurrences probability of each gene in the last common ancestor of two given genomes. The two approaches have been applied on chloroplastic genomes from Apiales, Asterales, and Fabids orders, the latter belonging to Pentapetalae group. We found that Apiales species do not undergo indels, while they occur in the Asterales and Fabids orders. A series of experiments was then carried out to extensively verify our findings by comparing the obtained ancestral reconstruction results with the latest released approach called MLGO (Maximum Likelihood for Gene-Order analysis).
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