As expected, the replicate Prochlorococcus SAGs A and B displayed large variations in local sequencing coverage (Figure 1a).
When Illumina sequencing data were combined with the 454 reads, the fraction of genome recovered increased to 99.6% and 91.1% for SAGs A and B, respectively (Table S2).
Eight loci were selected based on coverage depths observed in 454-FLX libraries of SAGs A and B. Specific primers were designed to quantify these loci, while primers matching 454-FLX adapter sequences were used to quantify the entire library.
The procedure was first tested by comparing the relative abundance of eight loci that were distributed across the complete genome and which fell in regions found to have both high and low sequence coverage in previously sequenced libraries of SAGs A and B (Figure 3a, Figure S2).
Single-cell genome libraries were sequenced to an average depth of ∼40X with 454-FLX, but the representation of specific loci ranged from 0 to >2,500X, with a median coverage of 8.6X and 7.5X for SAGs A and B, respectively (Table S2).
After that, the album sags a bit.
