This approach yielded breakpoint predictions with single base resolution for a ~11 kb amplification harboring the SUL1 gene, providing insights into the mechanisms that may have facilitated the expansion underlying this adaptive rearrangement.
With this new pipeline, it is now possible to perform whole-genome DNA methylation analysis at single base resolution for a large number of samples for understanding how DNA methylation and its changes are involved in development, differentiation, and disease pathogenesis.
Using this approach, we were able to build approximately 20,000 high-quality PAS clusters (72% to 78% of the total mapped PolyA clusters) that allowed us to map 3'UTR ends at single base resolution for approximately 6,000, 2,000, and 1,200 genes in our intestine and two muscle datasets, respectively.
Applied to the data of the genome of the evolved strain, this approach yielded upstream and downstream breakpoint predictions with single-base resolution for the SUL1 amplification.
In particular, full-length cDNAs with one-base resolution for TSSs enabled the identification of consensus motifs in promoter sequences and demonstrated clear distributions of identified motifs.
In this study, we performed unbiased whole-genome BS-seq for the mantles of two individual oysters to generate DNA methylomes at single-base resolution for this model mollusc.
Our study presented two genome-wide DNA methylomes at single-base resolution for the mantle tissues of the Pacific oyster C. gigas, and provided a comprehensive investigation of the characteristics of DNA methylation in this species.
The procedures we used were tested with respect to efficiency and specificity of on-surface sequence capture, and the ability to discover genetic variation in coding and non-coding regions comparing the genotypes with single-base resolution for selected 3.5 Mb MHC sequence.
The exception was found in the 10 base resolution analysis for C. jejuni, where GenomiPhi and Repli-G exchanged position; while significant, the difference between the Repli-G and GenomiPhi samples in this instance was slight (0.005).
Finally, our study provides a high quality, single base resolution resource for further study into the complex genetics of obesity across human chromosome 16q12.2, and a general methodology for targeted sequencing and analysis of variation across large genomic regions in general.
