Replicated sequence differences observed in the mature sequence of both miR172 and miR-390 suggest the existence of multiple miR172 and miR-390 family members in cotton, and potentially, there are different miR172 and miR-390 members functioning at different DPA periods.
Strikingly, when replicating various G4 plasmid templates, an additional band of around 750 nt, corresponding to a product stalled close to the G4 site, was visible from 2.5 up to 20 min depending on the replicated G4 sequence (Fig 3C, right panels, and Supplementary Fig S3).
The structure of each signal, either singlet (S), representing a non-replicated sequence, or doublet (D), disclosing a replicated sequence, was noted.
Accordingly, the structure of the fluorescent signal of each identified region was noted: either singlet (S), denoting a non-replicated sequence, or doublet (D), disclosing a replicated sequence.
Accordingly, following hybridization, the fluorescence signals are divided into two categories, a single dot-like signal (designated: "singlet" or "S"), representing a yet non-replicated DNA sequence and a duplicated bipartite signal (designated: "doublet" or "D"), indicating a replicated sequence.
The LS coefficient, as well as the ML function value or the Maximum parsimony score, can be used as an estimate of how close the distance matrix obtained from the pseudo-replicated sequences (or the set of pseudo-replicated sequences, in the case of ML or MP) is to the space of trees.
Indeed, the average SBS or LS (original or normalized) estimates of the trees (e.g., of the trees obtained from the pseudo-replicated sequences) could be used to compute the consensus tree (see also [ 43]).
In our approach, the weights of the trees inferred from pseudo-replicates are assigned according to either the LS estimate of this tree (i.e., how well it fits the pseudo-replicated sequences) or to the average secondary bootstrap scores (SBS) of the tree (i.e., the bootstrap scores associated with the internal branches of "pseudo-replicated" trees).
These two weighting schemes can be used to correct the standard non-parametric bootstrapping procedure that assign equal weights to each of the phylogenies obtained from the pseudo-replicated sequences.
In this study, the oleaginous, CO2-tolerant microalga Scenedesmus dimorphus was combined with a wastewater-derived microbial community and grown in replicated sequencing batch photobioreactors.
