I Virogenesis : Theories on the origin of mobile genetic elements Viruses, plasmids and transposons are mobile genetic elements. They exist in all cellular domains as obligatory parasites , commensuals, or symbionts. Reviewing the various types in the earliest domains provides clues to their origin. Origin scenarios increase with the higher cellular complexity of their hosts. A. Prokaryotic Elements - enter the cells and chromosomes of Archaea and Eubacteria. These elements provide clues to the origin and evolution of LUCA (Last Universal Common Ancestor). They include dsDNA phages, ssDNA phages (Microviridae and Inoviridae), +ssRNA phages, Plasmids and Retrons. They currently have not been found to include -ssRNA elements, or retroviruses. Various origin and evolution theories are not necessarily mutually exclusive. The true scenario of origin depends on the class of viruses/mobile genetic elements, stage of replication, history of recombination, and the point in evolutionary time to which they are compared to their putatative ancestor. The evolutionary paths of stuctural elements (capsids, tails, vertex complexes, and packaging appartuses) has not always followed the same paths as the genetic reproduction and transcription regulation systems. There is also independent evolutionary paths for viral exiting strategies (ie. lysis and transportation systems), element addiction/dependency systems (ie. toxin/anti-toxin systems), and anti-host defense components. An in-progress Morphogenetic evolution model treasure map. Origin and EvolutionTheories: 1. Some mobile genetic elements evolved from prokarytoic outer membrane vesicles (Budding off using ESCORT III ,FTZ , and Actin-like sorting systems in prokaryotes ) 2. RNA viruses (positive strand) originated from a Pre LUCA world (ie. RNA world) 3. RNA viruses originated from a Post -LUCA world 4. dsRNA elements originted from prokayotic CRISPR systems 5, Retroid RNA/DNA elements originated in Eubacteria or Archaea 6 .Retroid RNA-DNA elements originated in a Precellular World 7. Large DNA Viruses and Plasmids are genetic regressions of Pre-LUCA free living life forms 8. Large DNA Viruses and Plasmids are genetic additions of Pre-LUCA free living life forms 9. Large DNA Viruses and Plasmids are genetic regressions of Post LUCA derived elements ie. derivatives of spores 10. Large DNA Viruses and Plasmids are genetic additions to Post LUCA derived elements. 11 . Small DNA viruses arose from recombinations of DNA plasmids and RNA viruses within cell 12. New Virus Orders and Types can originate from recombinations of prior virus Types 13. Satellite elements coevolve with their host elements to create new element types 14. Plasmids originate from a Superintegron system either pre or post LUCA (This system involves IS elements, transposons, operons, CRISPR, and retrons) B. Eukaryotic Elements - Theories on origin include the above along with more detailed models for specfic elements and hosts. These elements provide clues to the evolution of LECA ( Last Eukaryotic Common Ancestor ) as well as the major eukarytoic phylla. 15. Eukayotic NCLD viruses originated Pre-LECA from common ancestors of prokaryotic Caudivirales 16. Eukaryotic NCLD viruses evolved from prokaryotic Caudivirales after infection of LECA 17. + ssRNA Picorna-like viruses originate from a Post LUCA /pre LECA World. They infect, recombine, horizontally transfer and coevolve in their hosts. 18. multipartitie linear -ss RNA Bunyavirus in vertebrates transfered by insect vector to plants where it recombined with a plant viral protein to create an ancestral tospovirus that coevolved with its host. (Or was it the other way around ? ) 19.Multipartite + ssRNA plant ourmiaviruses from dsRNA Narnovirus + ssRNA Tobusmavirus, 20. ssDNA virus originate from a ssRNA Tombusmavirus + ssDNA Nano/Circovirus 21 ssDNA Geminiviruses in plants originate from phytoplasma ssDNA plasmids( pMV158) + tombusviridae ssRNA tobacco necrosis virus like capsid (? involving fungal vector) 22.ssDNA Circoviruses originate from bacterial ssDNA plasmids + host viral capsids and then coevolve with their hosts. or they originate from ssDNA Nanoviruses recombining with ssRNA Calicivirus/Picorna virus family in a vertebrate host. 23Plant endomaviridae dsRNA elements originated from ss RNA alpha-like viruses 24. Hepatitis B virus/HBV evolved from a deletions in an ancestor to Type-C retroviruses 25 HIV-1 originated from a recombination of different strains of the SIV and zoonotic horizontal transfer   II Mobile Genetic Element Evolution, Content, and Structure   © 2012 Foster P. Carr MD all rights reserved