Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae
Figure 7
Representative identification of a putative translational frameshift.
A) Hybridization evidence for oligos labeled A, B, and C is shown. Expression levels are shown normalized to each oligo's mean (via a Z-score calculation) across a time course/thermal switch (37°C/26°C) experiment for Y. pestis CO92 (YPO) and Y. pestis Pestoides F (YPDSF). Green indicates down-regulation relative to the mean, and red indicates up-regulation relative to the mean. Genome annotations are labeled for YPDSF_1005 and YPO2124 corresponding to annotated coding sequences. Although oligos A and B purportedly lack a corresponding transcription for YPDSF (NA = not applicable), evidence clearly shows hybridization consistent with oligo C. B) illustrates the 210 aa translation of YPO2124 and C) illustrates the 63 aa translation of YPDSF_1005. Frame translations are shown below gene level detail with oligo evidence (black) overlaid on each gene and peptide evidence (red) overlaid on the appropriate reading frame. For YPDSF_1005, gene alignment with YPO2124 reveals two oligos upstream of the coding region. Corroborating peptide evidence was also seen upstream but in a different reading frame than the existing annotation. This evidence supports the expression of YPDSF_1005 as a frameshifted protein.