Studies of mutations in model experimental systems, and of gene sequence variation in natural viral populations, are clarifying the mechanisms that produce “quasispecies,” even though the concept seems to be still largely misunderstood. Likewise a great range of symbiotic, commensal, and satellite relationships are found among plant viruses, and again the diversity of the relationships, of the virus groups involved, and of the resulting phenotypes, emphasizes that viruses of plants are polyphyletic. The diverse measures adopted by viruses to suppress RNA silencing and to aid their spread through plants indicate that such mechanisms have evolved independently on several occasions. This has required viruses to adopt specific mechanisms to aid their systemic spread within plants.

Plants have a rigid cellular structure with the cells connected by plasmodesmata too narrow for virions to pass through. The RNA-silencing system seems to provide the primary plant defense against viruses, and although RNA-silencing mechanisms are present in all eukaryotes, they are most developed in plants where they also modulate the expression of plant genes. Plants, animals and other organisms present viruses with very different environments, both structurally and biochemically, and this may be the reason why so few virus groups span host kingdoms, but a few do, and studies of these reveal the shared and unique constraints and opportunities provided by different types of host, and also the diverse ways that viruses overcome the constraints. The ways in which these studies provide the intellectual framework for research into the life of viruses continues to expand.

Gene sequencing was invented in the 1980s, enabling the evolutionary relationships of organisms to be studied in detail. Fernando García-Arenal, in Origin and Evolution of Viruses (Second Edition), 2008 ABSTRACT

Gene sequence definition biology