The Major Phylogeny based Realms of Viruses are Riboviria, Monodnaviria, Duplodnaviria and Viridnaviria . I propose 2 more realms including 1. Helicaviria : for Helical capsid containing Archaea Viruses and 2. Insectovirea : for an Insect Infecting Group. All of these entities either arose from or had their evolution influenced by multiple mobile “genetic” elements including viroids, ribozymes, prions, transposons, insertion sequences, plasmids, other realms of viruses, and GTAs.

Framework : Origin and Morphogenesis of Mobile Genetic Elements

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.

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.

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 ancestor. The evolutionary paths of structural elements (capsids, tails, vertex complexes, and packaging apparti) 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 vs transportation systems), element addiction/dependency systems (ie. toxin/anti-toxin systems), and anti-host defense components.

My Morphogenetic evolution model treasure map created in 2012Origin and Evolution Theories:

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. dsRNA elements originated from prokayotic CRISPR systems

4.  Retroid RNA/DNA elements originated in Eubacteria or Archaea
vs they originated in a Precellular World

5. Large DNA Viruses and Plasmids originated Pre-LUCA free living life forms / genetic additions of Pre-LUCA free living life forms vs are Post LUCA derived elements such as derived of spores

6. . Small DNA viruses arose from recombinations of DNA plasmids and RNA viruses.

7. New Virus Orders and Types can originate from recombinations of prior virus Types

8. Satellite elements co-evolve with their host elements to create new element types.

9. Plasmids originate from a Superintegron system either pre or post LUCA (This system involves IS elements, transposons, operons, CRISPR, and retrons)

Eukaryotic Elements – Theories on origin include the above along with more detailed models for specific elements and hosts. These elements provide clues to the evolution of LECA ( Last Eukaryotic Common Ancestor ) as well as the major eukaryotic phylla.

1. Eukayotic NCLD viruses originated Pre-FECA from common ancestors of prokaryotic Caudivirales

2. + ssRNA Picorna-like viruses originate from a Post LUCA /pre LECA World. They infect, recombine, horizontally transfer and coevolve in their hosts.

3. 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 ? )

4.Multipartite + ssRNA plant ourmiaviruses from dsRNA Narnovirus + ssRNA Tobusmavirus,

5. some ssDNA viruses originate from a ssRNA Tombusmavirus + ssDNA Nano/Circovirus

6. ssDNA Geminiviruses in plants originate from phytoplasma ssDNA plasmids( pMV158) + tombusviridae ssRNA tobacco necrosis virus like capsid (? involving fungal vector)

7 .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.

8. Plant endomaviridae dsRNA elements originated from ss RNA alpha-like viruses

9. Hepatitis B virus/HBV evolved from deletions in an ancestor to Type-C retroviruses

10. HIV-1 originated from a recombination of different strains of the SIV and zoonotic horizontal transfer 

II Mobile Genetic Element Evolution, Content, and Structure