We define replication start timing (i.e., firing timing at origin loci or initial passive replication timing at non-origin loci), average replication timing (or half-completion timing), and (full-) completion timing as T0, T50, and T100, respectively.
These loci were also frequently identifiable after GISH labeling, without the use of the rDNA probe pTa71, appearing with a brighter green (to T. dubius origin loci) or yellow fluorescence (Figure 2).
We postulate that many of the conserved MIRNA genes arose through the latter two routes, and have lost sequence relatedness to their genetic origin loci due to drift of foldback arm sequences outside of the miRNA/miRNA-complementary regions (Figure 4).
On the other hand, siRNAs usually silence related targets or even their own origin loci, acting in cis.
As can be seen in Figures 4E 4G and Figure S1, the relevant proteins showed strong association with the origin loci.
In each cell, both origin loci were marked and their replication time in multiple individual cells was determined.
We examined the replication and segregation of the chromosomal origin (ori) locus, under the same conditions, using epifluorescence imaging of a strain carrying a fluorescently-tagged version of the ParB centromere-binding protein.
Even in the 2603-33A individual, with extremely reduced numbers of 45S rRNA genes of T. dubius origin, the locus accounts for 97% of the rRNA transcripts (see also Table 3).
Additional file 1: Sample name, origin and locus genotyped for each sample used in this study.
This further suggests a possible common origin of locus 2 and the plasmid.
