On the Ability to Reconstruct Ancestral Genomes from Mycobacterium Genus

Guyeux, Christophe; Al-Nuaimi, Bashar; AlKindy, Bassam; Couchot, Jean-François; Salomon, Michel

doi:10.1007/978-3-319-56148-6_57

Cited by 4 publications

(4 citation statements)

References 47 publications

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“…Only a successful and accurate sequence alignment leads to a genealogically interrelated tree [19]. Furthermore, it may assist in the detection of mutations or recombination events in pairs of closely related genomes [10].…”

Section: Preprocessing and Multiple Sequence Alignmentmentioning

confidence: 99%

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Phylogenetic Tree Construction of Gamma Coronavirus Genera and SARS-CoV-2

Khudair Abbas Al-Khafaji,

Bashar Talib Al-Nuaimi

2024

Acad. Sci. J.

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The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), has spread worldwide. Therefore, this study aimed to build a phylogenetic tree of complete genomes of SARS-CoV-2 and other species of Gamma coronavirus to explore the possibility of finding the evolutionary relationships between them and wished to analyze them in order to forecast the best trees illustrating the sequences' evolutionary relationships and obtain a well-supported phylogenetic tree by using the Neighbor-Joining (NJ) and Maximum Likelihood (ML) methods after performing multiple sequence alignment (MSA). This study utilized 16 isolates of Gamma coronavirus species and SARS-CoV-2 retrieved from the NCBI (National Center for Biotechnology Information) database for this investigation. The experimental outcomes when applying the two methods to the same dataset show that a well-supported and trustworthy phylogenetic tree was obtained with a bootstrapping value of 100% for all branches of the tree when applying the ML method. Additionally, a well-supported and fast-constructing phylogenetic tree was obtained through the NJ method for all branches except one, where the bootstrapping value appeared to be 56%. The research was conducted in 2022 at the College of Science, Diyala University.

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Section: Preprocessing and Multiple Sequence Alignmentmentioning

confidence: 99%

“…The current evolutionary methods need to be rethought to be more accurate reflections of reality [10].…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic Tree Construction of Gamma Coronavirus Genera and SARS-CoV-2

Khudair Abbas Al-Khafaji,

Bashar Talib Al-Nuaimi

2024

Acad. Sci. J.

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“…This research work is an extension of an article presented to the 5th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2017, [ 11 ]). Its main objective is to show that, if we focus on strongly related bacterial chromosomes, the reconstruction of their most recent common ancestors is possible in practice.…”

Section: Introductionmentioning

confidence: 99%

On the reconstruction of the ancestral bacterial genomes in genus Mycobacterium and Brucella

et al. 2018

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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.

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“…For biologists it is vital to know the evolutionary history of the species they study. Evolutionary histories are among other things needed to find the reservoir/initial infection for some disease (e.g., Gao et al, 1999;Lessler et al, 2016), or to learn about the evolution of genes, giving us insight in how they work (e.g., Shindyalov et al, 1994;Yu et al, 2015;Joy et al, 2016;Guyeux et al, 2017;Atas et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Heading in the right direction? Using head moves to traverse phylogenetic network space

Janssen¹

2018

Preprint

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Head moves are a type of rearrangement moves for phylogenetic networks. They have mostly been studied as part of more encompassing types of moves, such as rSPR moves. Here, we study head moves as a type of moves on themselves. We show that the tiers (k > 0) of phylogenetic network space are connected by local head moves. Then we show tail moves and head moves are closely related: sequences of tail moves can be converted to sequences of head moves and vice versa, changing the length by at most a constant factor. Because the tiers of network space are connected by rSPR moves, this gives a second proof of the connectivity of these tiers. Furthermore, we show that these tiers have small diameter by reproving the connectivity a third time. As the head move neighbourhood is in general small, this makes head moves a good candidate for local search heuristics. Finally we prove that finding the shortest sequence of head moves between two networks is NP-hard.

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On the Ability to Reconstruct Ancestral Genomes from Mycobacterium Genus

Cited by 4 publications

References 47 publications

Phylogenetic Tree Construction of Gamma Coronavirus Genera and SARS-CoV-2

Phylogenetic Tree Construction of Gamma Coronavirus Genera and SARS-CoV-2

On the reconstruction of the ancestral bacterial genomes in genus Mycobacterium and Brucella

Heading in the right direction? Using head moves to traverse phylogenetic network space

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