Institut de Mathématiques de Marseille, UMR 7373


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6 juillet 2017: 1 événement

  • Agenda des soutenances MEB

    Jeudi 6 juillet 14:00-16:00 - Sourabh JAIN - I2M, Marseille

    Comparative genomics study for identification of gene acquisitions in Megavirales

    Résumé : Soutenance de thèse
    Discovery of giant viruses with giant genome size and surprising genomic features raises different question about their origin and evolution. The diversity of Megavirales (MVs) imposes difficulties in collectively evaluating their phylogenetic relationships. While small subset of conserved core genes and phylogenomic analyses based on them, provide useful classification of MVs, but they give little insight on the remaining un-conserved and variable gene content of accessory genomes. Thus, many phylogenetic studies have pointed out decisive role of HGTs and genetic exchanges on evolution of MVs, but, majority of them are based on closely related MV families. However, exact proportion of instances of genes acquired horizontally varies greatly with the methodologies used for their detection of interpretation of phylogenies prepared. Therefore, it is necessary to adopt some systematic searching for detecting reticulate evolutionary events like HGT in MVs to decipher genomic composition and genome mosaicism of distantly related MV families. To investigate the contribution of HGTs in distantly related MV families, we have determined gene distributions and gene phylogenies for the 86 complete MV ORFomes classified in 6 defined and 4 putative families, in context of their homologs from other domains of life. At first, we prepared an automated phylogenetic workflow MimiLook, which deduces orthologous groups (OGs) from ORFomes of MVs and constructs phylogeny by performing alignment generation, alignment editing and BLASTP searching across NCBI nr protein sequence database. Finally, this tool detects statistically validated events of gene acquisitions with the help of T-REX algorithm.
    We found 4577 clusters of orthologus groups (OGs), out of it, 91% of OGs are found to be family specific (i.e. represented by species classified in one MV family only), whereas, only 9% are represented by proteins from 2 or more MV families. In step 2 of our analysis, we found 414 OGs with detected HGT event. 174 were inferred to have transferred from eukaryotes, 106 to have transferred from bacteria and 9 gene families to have transferred from cellular domains other than eukaryotes or bacteria (archaea, and viruses, including phages). 52 OGs were detected as cases of sympatric transfers (gene transfer by association of MVs with more than one cellular domain). Interestingly, 129 gene families were identified to be involved in gene transfers from MVs to other cellular domains. We applied a similar procedure to the 7,898 non-orthologous proteins to detect transfer events and putative donors and identified 259 instances of HGT from non-orthologous proteins, of which 135 cases were from eukaryotes, 82 cases from bacteria, 11 cases from Phages and other viruses, 31 cases where MVs are transferring protein to other cellular domains. Instances of HGT were found to be depicting donor specificity, as viruses of vertebrates/invertebrates (Poxviridae, Ascoviridae and Iridoviridae) acquired genes from donors like Euteleostomii, Eutheria, Baculoviridae and proteobacteria ; algal viruses (Phycodnaviridae) and protozoan viruses (pandoravirus, Mimiviridae, pithovirus, and Marseilleviridae) were found to be acquiring genes majorly from cellular donors like Dictyostellium, Mammeillales, Firmicutes, Clostridiales, Klebsormidium, Rozella allomycis, Ooomycetes and Phytophthora.
    In conclusion, clear distinction can be seen in the genome mosaicism of distantly related Megavirale families, where they evolved via genome specificity and family specific gene acquisitions from their respective ecological niche. Evolution of Megavirale families can be evidently based on phylogenetic analysis of few core genes as well as similarities of their gene contents, but, knowing that the horizontal gene transfer play a major role on the gene contents of Megavirales, it could be unforeseen to decipher the evolution of all Megavirale families by this approach.
    Keywords : Megavirales ; Horizontal gene transfer ; MimiLook ; Comparative genomics ; phylogeny.
    Jury Members :
    - Dr. Pierre Pontarotti (EBM, AMU, Marseille), directeur de thèse
    - Prof. Didier Raoult (IHU, Marseille), co-directeur de thèse
    - Prof. Patrick Forterre (Institute Pasteur, Paris)
    - Prof. Jean Louis Mege (Faculty of Medicine, AMU, Marseille)
    - Dr. Franck Panabieres (INRA, Nice)

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6 juillet 2017: 2 événements

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