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Introduction of the native P. falciparum MSP142 gene sequence into E. coli resulted in a dramatic shift in codon usage frequencies within this region (compare first and second lines, respectively).
Thus, the shift in codon usage toward rare codons is not a general property of spontaneous mutations in the analyzed set of 19 ASD-associated genes (Table 1).
The shift in codon usage seemed to follow a gradient from early diverging photosynthetic to late diverging photosynthetic or heterotrophic taxa along the branches.
The same latter eight alleles showed a deletion of two amino acids, leading to a shortened amino acid sequence, but not to a frame shift in codon translation.
Thus the shift in codon usage likely occurred ancestrally in the lineage leading to all extant members of this willistoni-saltans lineage.
Thus, the observed shift in codon usage associated with AVs is unlikely to be due to chance [P SH ≤ SH_r) = 0.007].
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The distribution of shifts in codon usage for random mutations (SH_r) is shown in Figure 1.
Shifts in codon usage are usually considered to be caused by changes in functional constraints and in gene expression levels.
But again, this would seem to be insufficient to account for greater shifts in codon usage for some amino acids and not others.
In summary, shifts in codon usage between the species seem not biased by expression level per se but possibly by evolutionary forces requiring specific expression levels in a certain (thermal) environment.
While major shifts in codon preferences are unlikely between closely related species, changes in evolutionary parameters, particular in effective population sizes, are relatively common even over short evolutionary time scales [ 5].
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