Small Circular DNA : The muddy viral “playground” of recombinant, reassortant, and highly diverse viruses

@Varsani_lab

Arizona State University, USA University of Canterbury, New Zealand University of Cape Town, South Africa Arvind Varsani Viral evolution Reassortment Recombination Nucleotide substitutions Viral evolution Reassortment Recombination Nucleotide substitutions Viral evolution Reassortment Recombination Nucleotide substitutions I II

III IV V dsDNA ssDNA VI VII dsRNA ssRNA(+) ssRNA(-)

ssRNA(RT) dsDNA(RT) viruses Archaea Bacteria Diatoms Fungi Invertebrates Plants Vertebrates Unknown

Anelloviridae – circular (~2.1 - 3.8kb) Bacillidnaviridae - circular (~4.5 - 6kb) – circular (~1.6 - 2.3kb) – circular (~2.7kb; monopartite, bipartite, associated with α/β satellites) Genomovirdae – circular (1.8 -2.3 kb) ssDNA Inoviridae – circular (~5.8 - 8.7kb) – circular (~4.5 - 6kb) – circular (~1.2kb; multicomponent viruses; associated with satellites) – linear (~3.7 - 6kb) Pleolipoviridae* – circular ssDNA; circular dsDNA or liner dsDNA (7-16kb) Smacoviridae* - circular (2.3 - 2.9kb) ssDNA viruses Chimerism in Rep Nucleotide substitutions PPV: CPV: Parvoviruses PCV BFDV: BBTV: FBNYV: TYLCV: EACMV: SSRV: MSV: Geminiviruses - 2: ~3 ~3 x ~2 x ~ ~2 x ~3 x ~ ~ ~ ~3 ~2 1 1 x 1 x 3 x 1 x x x 10 10 10 10 10 10 10 10 10 10 ------4 4 3 3 4 3 4 3 4 4 subs/site/year subs/site/year subs/site/year subs/site/year subs/site/year subs/site/year subs/site/year subs/site/year - - 8 8 x 10 5 5 x 10 - - 5 subs/site/year (VP1;5 subs/site/year NS1) 5 subs/site/year (VP1;5 subs/site/year NS1 ) Recombination Geminiviruses Recombination Recombination Recombination Genome plasticity Gemimiviruses Pseudo-recombination Reassortment Reassortment Recombination Secondary structure Secondary structure • • • • Base accumulate preferentially Short sites genomic substitution Synonymous sites selection Purifying - - paired sites tend to tend sites paired term evolution experiments experiments evolution term is apparently is apparently complementarily coevolve complementarily rates are unusually unusually are rates at unpaired sites unpaired strongest - mutations at paired low tend to to tend at paired - nucleotide nucleotide Circoviruses Beak and feather disease disease feather and Beak Circoviruses Trafficking and evolution Beak and feather disease virus disease feather and Beak Genomoviruses Genomoviruses “Archived” viruses Reps of ssDNA viruses Origin of ssDNA viruses CRESS DNA virus CPs Sampling sequence space CRESSDNAviruses Acknowledgements Tomasz Ng Terry Simone Ribeiro Pierre Lefeuvre Philippe Mike Tisza Mart John Eric Eric Delwart Dionne Shepherd Darren Martin Darius Chris Buck Collaborators van van der Walt Krupovic Thomas Kazlauskas Kazlauskas Piaseck Roumagnac – CDC – – – NIH NIH – – Blood – – University of University Cape – University ofUniversity Institut – – CIRAD EMBRAPA – Wrocław – Kapa University of University Cape Town sysytems Vilnius University – CIRAD Pasteur Biosystems University Queensland Institute Town Simona Kraberger Rafaela Fontenele Male Maketalena Laurel Julian Daisy Stainton Brejnev Muhire Anisha students Aderito & staff lab Varsani Dayaram Monjane