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Anthocyanins are synthesized via the flavonoid pathway, a late branch of the shikimic acid pathway [ 8].
For testing the MA model, the branch between the node corresponding to the duplication between Pg11 and Pg3 and the node corresponding to the duplication between Pg11a and Pg11c (i.e. the ancestral Pg11 gene) was considered as the late branch.
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On average, there are 6.2 clusters per genome in the late branches compared to 2 clusters per genome in the early ones (403 clusters in late-branching cyanobacteria versus 49 clusters in early-branching ones).
Two cassava varieties contrasting in plant architecture (early branching variety, rich in apices versus erect, late branching variety, poor in apices) were grown as pure stands, as a variety mixture and each intercropped independently with upland rice or Canavalia brasiliensis.
Stage 1, Inflorescence meristem stage, after initiation of primary branch (i.e. rachis and primary branch meristems); stage 2, early branching stage (panicle with elongated primary and higher order branch development); stage 3, late branching stage (i.e. panicle with elongated primary and secondary branches); stage 4, young flowers with differentiated organs.
At the end of this stage, secondary branches (white *) are initiated from PBs (5,6); stage 3: late branching stage with elongated secondary branch and spikelet meristem (SM) and floret meristem (FM) differentiation (7,8); stage 4: floret organ differentiation/development (9,10); mature stage: 11 and 12. White arrowhead: vestige of aborted rachis meristem.
While neither mature miR2118 nor 21-nt phasiRNA phasiPH12-1 were detected at the early morphological stage of panicle development (inflorescence meristem after reproductive transition, stage 1), their expression was initiated earlier in O. barthii (early branching stage, stage 2) than in O. glaberrima (late branching stage, stage 3).
We observed a marked increase of ω in early branches (ω = 0.14 compared with ω = 0.05 for late branches in MA).
However, the value of ω in late branches was likely biased by the occurrence of positive selection in Pg11, because branch models average over all sites.
From Figure 4(a), a general trend begins to take form of increasing rate variation over time; earlier branches to the left of the figure are mostly blue or purple, while late branches appear mostly red.
The opposite trend was detected for the Pg11/ pairpair, where purifying selection appeared to be actually weaker in late branches than in early branches, particularly for Pg11 (ω = 0.44).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com