BEGIN:VCALENDAR VERSION:2.0 PRODID:-//wp-events-plugin.com//7.2.3.1//EN TZID:Europe/Paris X-WR-TIMEZONE:Europe/Paris BEGIN:VEVENT UID:1854@i2m.univ-amu.fr DTSTART;TZID=Europe/Paris:20170706T140000 DTEND;TZID=Europe/Paris:20170706T160000 DTSTAMP:20241209T085221Z URL:https://www.i2m.univ-amu.fr/evenements/comparative-genomics-study-for- identification-of-gene-acquisitions-in-megavirales/ SUMMARY:Sourabh Jain (Unité de recherche sur les maladies infectieuses et tropicales émergentes): Comparative genomics study for identification of gene acquisitions in Megavirales DESCRIPTION:Sourabh Jain: Discovery of giant viruses with giant genome size and surprising genomic features raises different question about their ori gin 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\, p rovide useful classification of MVs\, but they give little insight on the remaining un-conserved and variable gene content of accessory genomes. Thu s\, many phylogenetic studies have pointed out decisive role of HGTs and g enetic exchanges on evolution of MVs\, but\, majority of them are based on closely related MV families. However\, exact proportion of instances of g enes 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 e volutionary events like HGT in MVs to decipher genomic composition and gen ome mosaicism of distantly related MV families. To investigate the contrib ution of HGTs in distantly related MV families\, we have determined gene d istributions and gene phylogenies for the 86 complete MV ORFomes classifie d in 6 defined and 4 putative families\, in context of their homologs from other domains of life. At first\, we prepared an automated phylogenetic w orkflow MimiLook\, which deduces orthologous groups (OGs) from ORFomes of MVs and constructs phylogeny by performing alignment generation\, alignmen t editing and BLASTP searching across NCBI nr protein sequence database. F inally\, this tool detects statistically validated events of gene acquisit ions with the help of T-REX algorithm.\nWe found 4577 clusters of ortholog us 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 infer red to have transferred from eukaryotes\, 106 to have transferred from bac teria 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 assoc iation of MVs with more than one cellular domain). Interestingly\, 129 gen e families were identified to be involved in gene transfers from MVs to ot her cellular domains. We applied a similar procedure to the 7\,898 non-ort hologous proteins to detect transfer events and putative donors and identi fied 259 instances of HGT from non-orthologous proteins\, of which 135 cas es were from eukaryotes\, 82 cases from bacteria\, 11 cases from Phages an d other viruses\, 31 cases where MVs are transferring protein to other cel lular domains. Instances of HGT were found to be depicting donor specifici ty\, as viruses of vertebrates/invertebrates (Poxviridae\, Ascoviridae and Iridoviridae) acquired genes from donors like Euteleostomii\, Eutheria\, Baculoviridae and proteobacteria\; algal viruses (Phycodnaviridae) and pro tozoan viruses (pandoravirus\, Mimiviridae\, pithovirus\, and Marseillevir idae) were found to be acquiring genes majorly from cellular donors like D ictyostellium\, Mammeillales\, Firmicutes\, Clostridiales\, Klebsormidium\ , Rozella allomycis\, Ooomycetes and Phytophthora.\nIn conclusion\, clear distinction can be seen in the genome mosaicism of distantly related Megav irale families\, where they evolved via genome specificity and family spec ific gene acquisitions from their respective ecological niche. Evolution o f Megavirale families can be evidently based on phylogenetic analysis of f ew core genes as well as similarities of their gene contents\, but\, knowi ng that the horizontal gene transfer play a major role on the gene content s of Megavirales\, it could be unforeseen to decipher the evolution of all Megavirale families by this approach.\n\nKeywords : Megavirales\; Horizon tal gene transfer\; MimiLook\; Comparative genomics\; phylogeny.\n\n*Jury Members:\n- Dr. Pierre Pontarotti (EBM\, AMU\, Marseille)\, directeur de t hèse\n- Prof. Didier Raoult (IHU\, Marseille)\, co-directeur de thèse\n- Prof. Patrick Forterre (Institute Pasteur\, Paris)\n- Prof. Jean Louis Me ge (Faculty of Medicine\, AMU\, Marseille)\n- Dr. Franck Panabieres (INRA\ , Nice)\n\nLien : theses.fr CATEGORIES:Soutenance de thèse END:VEVENT BEGIN:VTIMEZONE TZID:Europe/Paris X-LIC-LOCATION:Europe/Paris BEGIN:DAYLIGHT DTSTART:20170326T030000 TZOFFSETFROM:+0100 TZOFFSETTO:+0200 TZNAME:CEST END:DAYLIGHT END:VTIMEZONE END:VCALENDAR