Table 3. Genome Sequencing Results from 52-fragment Phage Plaquesa.
| plaque # | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| position | reference | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 |
| mutations to remove pre-existing BsmBI sitesb | |||||||||||
| 2137 | G | A | A | A | A | A | A | A | A | A | A |
| 2641 | C | T | T | T | T | T | T | T | T | T | T |
| 10867 | C | T | T | T | T | T | T | T | T | T | T |
| 12767 | G | A | A | A | A | A | A | A | A | A | A |
| 15366 | T | A | A | A | A | A | A | A | A | A | A |
| 18262 | G | A | A | A | A | A | A | A | A | A | A |
| 18983 | G | A | A | A | A | A | A | A | A | A | A |
| 20752 | C | T | T | T | T | T | T | T | T | T | T |
| 22582 | G | A | A | A | A | A | A | A | A | A | A |
| 24596 | T | A | A | A | A | A | A | A | A | A | A |
| 24734 | T | A | A | A | A | A | A | A | A | A | A |
| 31347 | T | A | A | A | A | A | A | A | A | A | A |
| 32694 | C | G | G | G | G | G | G | G | G | G | G |
| 33108 | C | T | T | T | T | T | T | T | T | T | T |
| 33396 | T | A | A | A | A | A | A | A | A | A | A |
| 35247 | C | T | T | T | T | T | T | T | T | T | T |
| novel SNPsc | |||||||||||
| 7609 | T | G | |||||||||
| 14378 | A | G | |||||||||
| 26773 | G | T | |||||||||
a
Phage genomic DNA was isolated from the phage plaques of the 52-fragment assembly reactions (plaques 1–5 from 5 h reactions and plaques 6–10 from 15 h reactions) and sequenced using nanopore sequencing. Mutations differentiating the genomic sequences of the reconstituted phages compared to the reference T7 strain (GenBank: V01146.1) are shown.
b
Assembly reactions were designed to create phage genomes with 16 silent mutations to permit assembly with the BsmBI-type IIS restriction enzyme. All assembled genomes contained these mutations.
c
SNPs appeared in several of the assembled genomes; however, these mutations were not within 40 base pairs of assembly junction sites. More information on these mutations can be found in Tables S8, S9, and S10.