One novel feature in our sequencing approach was to complement the high coverage data from the HiSeq 2000 sequencers with longer reads from the MiSeq, at low coverage, to support the assembly process.
Only the 16S rRNA gene was considered in our sequencing analysis which did not capture eukaryotes in the analysis, so profiles of chlorophyll were also examined.
Furthermore, we have never observed recombinant genotypes in our sequencing data [33].
The Broad Institute's KZN-V4207 sequence has a large-scale inversion of ∼2.5 Mb; however, this inversion was not observed in our sequencing data.
These miRNAs showed downregulation in our sequencing analysis and hsa-miR-195 downregulation was comfirmed by Real-Time qPCR in this study.
Furthermore, 223 of the known miRNAs we identified and characterized in our sequencing datasets were not represented on even the most comprehensive microarray.
In our sequencing protocol the clones are selected at high coverage but each clone is sequenced only to a low coverage CovR between 1.5x and 2.0x.
In our sequencing protocol, clones are randomly selected from the genome at a relatively high coverage CovG ranging from 7.5x to 10.0x.
Direct evidence for insensitivity of our method for de novo mutations comes from the high reproducibility of fitness estimates between replicates and the fact that we never observed any new mutations in our sequencing [33].
The majority of the 21- and 22 nt V-sRNAs and S-sRNAs recovered in our sequencing pool showed a strong bias for sequences beginning with a 5'-U, indicative of their association with AGO1.
Although we were able to identify five sequences that were evolutionary conserved in terms of sequence similarity, microsynteny between genomes, and predicted RNA secondary structure, only one of them had evidence of expression in our sequencing libraries (Figure 1A, Supplemental Figures S4b S4e).
