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Such a high divergence, for these families, deserves to be considered significant, possibly hinting at very divergent organismal lineages, and/or reflecting a major genetic plasticity for these functionally important, apparently ancient gene families.
A) For each of three GC% levels, three replicate reference/sample pairs were generated using INDELible v1.03 at low divergence and three replicate pairs were generated at high divergence, for a total of 18 reference/sample pairs; each sequence was ca. 10001000 bp in length.
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The minimum evolution phylogenetic trees also presented much longer branches and consequently higher divergence for the sequences belonging to cluster 2 and 7 in comparison with the others (Additional file 6: Figure S3).
We have observed a higher divergence for HM code of duplicate genes in the category of trans-targeted genes than that of controlling genes, suggesting that the change of trans-regulators binding to duplicate genes may affect the pattern of HM code in both promoter and ORF regions, and thus accelerating the divergence of histone modification code between duplicate genes.
(1) Being the Y a male-specific chromosome, and given that the mutation rate is higher in males than in females [ 48], we would expect higher divergence for Y-chromosome than for autosomal microsatellites; our data are contrary to this expectation.
Although miRNA precursor sequences show high divergence except for miRNAs and miRNAs* regions, we found a predicted homolog for osa-miR159a.2 osa-miR159a.2ches in maize located 21 nucleotides upstream from the predicted maize miR159.
Our relaxed molecular clock estimates revealed high divergence times for the Sundadanio and Paedocypris clades and provide a first temporal framework for the evolution of miniaturization among cyprinids.
We observed a single peak in both simulations, with high divergence and variance for the scenario of ancient IS acquisition and burst (scenario 1) and low divergence and variance for the scenario of recent IS acquisition and burst (scenario 2) (fig. 1).
A significant and positive correlation between read length and variant call accuracy was also demonstrated for both SNPs and indels in high divergence treatments, and for SNPs in low divergence treatments, although the impact of this relationship was relatively small (Table 2).
This may explain the relatively high divergence times (17MYA for rice/rice duplicates and 34MYA in sorghum) calculated by Paterson et al. [ 26] In this context, a similar duplication in the Brachypodium distachyon genome is expected.
Increasing average read length of a read pool also resulted in a greater decrease in average length of mapped reads across all damage levels and at both low and high divergence (Pr <<0.001 for linear regression), such that average lengths of mapped reads at 40/60/80 bp expected size were 40.05/59.99/79.44 and 40.03/59.92/79.16 bp for low and high divergence read pools, respectively.
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