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Viruses 2017, 9(4), 72; doi:10.3390/v9040072

MimiLook: A Phylogenetic Workflow for Detection of Gene Acquisition in Major Orthologous Groups of Megavirales

1
Aix-Marseille Université, Ecole Centrale de Marseille, I2M UMR 7373, CNRS équipe Evolution Biologique et Modélisation, 13284 Marseille, France
2
Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63 CNRS 7278 INSERM U1095IRD 198, Faculté de Médecine, 13284 Marseille, France
3
IHU Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo-universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, 13385 Marseille, France
These authors contributed equally to this work.
*
Authors to whom correspondence should be addressed.
Academic Editor: Eric O. Freed
Received: 28 February 2017 / Revised: 3 April 2017 / Accepted: 3 April 2017 / Published: 7 April 2017
(This article belongs to the Special Issue Viruses of Protozoa)
View Full-Text   |   Download PDF [1324 KB, uploaded 7 April 2017]   |  

Abstract

With the inclusion of new members, understanding about evolutionary mechanisms and processes by which members of the proposed order, Megavirales, have evolved has become a key area of interest. The central role of gene acquisition has been shown in previous studies. However, the major drawback in gene acquisition studies is the focus on few MV families or putative families with large variation in their genetic structure. Thus, here we have tried to develop a methodology by which we can detect horizontal gene transfers (HGTs), taking into consideration orthologous groups of distantly related Megavirale families. Here, we report an automated workflow MimiLook, prepared as a Perl command line program, that deduces orthologous groups (OGs) from ORFomes of Megavirales and constructs phylogenetic trees by performing alignment generation, alignment editing and protein-protein BLAST (BLASTP) searching across the National Center for Biotechnology Information (NCBI) non-redundant (nr) protein sequence database. Finally, this tool detects statistically validated events of gene acquisitions with the help of the T-REX algorithm by comparing individual gene tree with NCBI species tree. In between the steps, the workflow decides about handling paralogs, filtering outputs, identifying Megavirale specific OGs, detection of HGTs, along with retrieval of information about those OGs that are monophyletic with organisms from cellular domains of life. By implementing MimiLook, we noticed that nine percent of Megavirale gene families (i.e., OGs) have been acquired by HGT, 80% OGs were Megaviralespecific and eight percent were found to be sharing common ancestry with members of cellular domains (Eukaryote, Bacteria, Archaea, Phages or other viruses) and three percent were ambivalent. The results are briefly discussed to emphasize methodology. Also, MimiLook is relevant for detecting evolutionary scenarios in other targeted phyla with user defined modifications. It can be accessed at following link 10.6084/m9.figshare.4653622. View Full-Text
Keywords: megavirales; giant viruses; HGT; gene acquisition; T-REX; workflow; orthologous groups megavirales; giant viruses; HGT; gene acquisition; T-REX; workflow; orthologous groups
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

Supplementary materials

  • Supplementary File 1:

    ZIP-Document (ZIP, 2263 KB)

  • Externally hosted supplementary file 1
    Doi: 10.6084/m9.figshare.4653622
    Description: Workflow script available on this link
  • Externally hosted supplementary file 2
    Doi: 10.6084/m9.figshare.4645273
    Description: Phylogenetic trees available on this link

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MDPI and ACS Style

Jain, S.; Panda, A.; Colson, P.; Raoult, D.; Pontarotti, P. MimiLook: A Phylogenetic Workflow for Detection of Gene Acquisition in Major Orthologous Groups of Megavirales. Viruses 2017, 9, 72.

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