MimiLook: A Phylogenetic Workflow for Detection of Gene Acquisition in Major Orthologous Groups of Megavirales
Abstract
:1. Introduction
2. A General Overview of Workflow
2.1. Complete ORFomes
2.2. Detection of Orthologous Groups
2.3. Search for Homologs and Curation of Blast Output
2.4. Alignment Generation, Alignment Editing and Tree Preparation
2.5. Detection of Horizontal Gene Transfer Event
2.6. Plotting OGs and Evolutionary Scenarios on Reference Megavirale Family Tree
3. Implementation
4. Results of MimiLook Analysis in the Proposed Order Megavirales
5. Discussion and Future Perspective
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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ORF Name | Source of Transfer [40] | OG ID | Evolutionary Scenario Detected | Putative Donor/Receptor |
---|---|---|---|---|
OtV1_33/OsV5_33 | Eukaryote | OG_02476 | Transfer from eukaryote | Magnoliophyta |
OtV1_113/OsV5_131 | Eukaryote | OG_04266 | Transfer from eukaryote | Pyrenomonadales |
OsV5_125 | Virus | OG_00455 | Specific to Megavirales | - |
OsV5_218 | Eukaryote | OG_00469 | Specific to Megavirales | - |
OtV2_3 | Bacteria | OG_00262 | Shared origin with bacteria | - |
OtV2_29 | Bacteria | OG_04066 | Transfer from bacteria | Clostridiales |
OtV2_30 | Bacteria | OG_00775 | Transfer from bacteria | Alphaproteobacteria |
OtV2_40 | Ambiguous | OG_02248 | Transfer from phages | Phages (Myoviridae) |
OtV2_78/OlV1_89 | Bacteria | OG_00556 | Transfer from bacteria | Helicobacter (Proteobacteria) |
OtV2_158/OlV1_172 | Eukaryote | OG_02251 | Shared origin with eukaryote | - |
OtV2_165 | Bacteria | OG_02131 | Specific to Megavirales | MV specific |
OtV2_167 | Ambiguous | OG_02177 | Shared origin with bacteria | - |
OtV2_179 | Virus | OG_04069 | Shared origin with phages | - |
OtV2_193/OlV1_206 | Eukaryote | OG_02255 | Specific to Megavirales | MV specific |
OtV2_201/OlV1_213 | Host | OG_02256 | Transfer from eukaryote | Saccharomycetes |
OtV2_202/OlV1_214 | Ambiguous | OG_02257 | Probable transfer | Probable transfer from Rickettsiaceae (bacteria) |
OtV2_222/OlV1_234 | Host | OG_01016 | Transfer from eukaryote | Mamiellales |
OlV1_190 | Eukaryote | OG_02481 | Sympatric transfer | Transfer from Bacteria; Gene with eukaryotes |
OlV1_236 | Host | OG_01062 | Specific to Megavirales | MV-specific |
MpV1_8 | Host | OG_04280 | Shared origin with eukaryote | - |
MpV1_9 | Host | OG_04281 | Transfer from eukaryote | Mamiellales |
MpV1_201 | Bacteria | OG_00262 | Transfer from bacteria | Enterobacteriales (independent acquisition) |
MpV1_203 | Virus | OG_00202 | Transfer from Megavirales | Insectomime virus and Port-Miou virus |
Ny2A_137/AR158_126 | Ambiguous | OG_00853 | Sympatric transfer | Transfer from Chlorella variabilis; Outside bacteria |
Ny2A_359 | Ambiguous | OG_00554 | Ambiguous | Ambiguous (mix of bacteria and bacteriophages) |
Ny2A_543/AR158_487 | Ambiguous | OG_00554 | Ambiguous | Ambiguous (mix of bacteria and bacteriophages) |
Ny2A_542/AR158_486 | Virus | OG_03082 | Shared origin with phages | - |
Chiliensis_647 | Ambiguous | OG_01369 | Transfer from Megavirales | Brucellaceae (bacteria) |
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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. https://doi.org/10.3390/v9040072
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(4):72. https://doi.org/10.3390/v9040072
Chicago/Turabian StyleJain, Sourabh, Arup Panda, Philippe Colson, Didier Raoult, and Pierre Pontarotti. 2017. "MimiLook: A Phylogenetic Workflow for Detection of Gene Acquisition in Major Orthologous Groups of Megavirales" Viruses 9, no. 4: 72. https://doi.org/10.3390/v9040072