TABLE 1.
Summary of recombination signals detectable in ssDNA virus full-genome data sets
| Host | Family | Data set | Data set
|
No. of eventsa | Probability of <90 (<80) | Hot spot | Cold spot | |
|---|---|---|---|---|---|---|---|---|
| Name | No. | |||||||
| Animals | Unassigned | Anellovirus | TTV | 7 | 67 | 99 (87) | IR-ORF2-ORF4 | CP |
| TTMV | 8 | 21 | 100 (100) | IR-ORF4 | ||||
| Circoviridae | Circovirus/PCV | PCV | 9 | 16 | 0 (0) | |||
| Circovirus/BF | BF | 10 | 17 | 45 (18) | IR-beginning of Rep | CP | ||
| Circovirus/goose | Goose | 11 | 1 | 0 (0) | ||||
| Gyrovirus | Gyro | 12 | 1 | 0 (0) | ||||
| Parvoviridae | Dependovirus/parvovirus | Merged | 13 + 15 | 35* | 86 (29) | IR | ||
| Dependovirus | Dependo | 13 | 17 | 78 (33) | ||||
| Erythrovirus | Erythro | 14 | 2 | 100 (0) | ||||
| Parvovirus | Parvo | 15 | 13 | 100 (33) | ||||
| Bacteria | Microviridae | Microvirus | Micro | 16 | 38 | 45 (27) | Spike-RepA | G-CP |
| Plants | Geminiviridae | Mastrevirus | Mastre | 17 | 37 | 66 (11) | LIR-SIR-repB-end of CP | CP-repA |
| Begomovirus | Begomo | 18 | 245 | 100 (84) | IR-Rep | CP-V2-C2-C3 | ||
| DNA-B | Merged | 19→23 | 67* | 79 (63) | IR | BV1-BC1 | ||
| Old World | 19 | 17 | 100 (11) | |||||
| EACMV | 20 | 10 | 14 (14) | |||||
| Asia 1 | 21 | 9 | 71 (57) | |||||
| Asia 2 | 22 | 6 | 33 (33) | |||||
| New world | 23 | 41 | 100 (100) | |||||
| DNA-Beta | Merged | 24→26 | 52* | 92 (71) | IR | ORF | ||
| beta1 | 24 | 25 | 100 (90) | |||||
| beta2 | 25 | 20 | 80 (50) | |||||
| beta3 | 26 | 11 | 100 (67) | |||||
| DNA-1 | dna1 | 27 | 38 | 100 (75) | Rep | Beginning of Rep | ||
| Nanoviridae | Babuvirus/nanovirus | Merged babu nano CP | 32 + 33 | 9* | 100 (80) | CP-IR | IR | |
| Babuvirus | babu1 | 28 | 4 | 100 (100) | ||||
| babu2 | 29 | 3 | ||||||
| babu3 | 30 | 1 | ||||||
| babu4 | 31 | 0 | ||||||
| babu5 | 32 | 2 | 100 (0) | |||||
| Nanovirus | nano | 33 | 7 | 100 (100) | ||||
a
*, partial genome data set. Multiple testing correction was more severe in the merged data sets than in the separated ones. As a consequence of this, the number of recombination events in the merged data sets is not simply the sum of events detected in the separated data sets.