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While most duplicates are rapidly lost from the genome, some are retained because of increased dosage requirements, the acquisition of new functions (e.g. neofunctionilization) or the splitting of the ancestral function between the duplicate copies (e.g. subfunctionilization) [ 5, 6].
Pairwise comparison of synonymous and non-synonymous substitution rates between the duplicate copies (dN/dS = 0.088) did not indicate any signs of positive selection operating on the genes following duplication.
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By contrast, the differences between paralogous IGHV gene segments within each complete duplicate block are much greater than those between the counterparts of the duplicate copies.
For each of the 122 one-to-two trios, it is possible to infer the localizations of the progenitor gene of the duplicate copies and differentiate between sublocalization and neolocalization after gene duplication (Marques et al. 2008), based on the parsimony principle.
These observations raise two questions: (1) whether 4-31 is located within a highly active genetic element and/or (2) whether the areas at the boundaries of the duplicated units are genetically very active so that exchange in these areas between the duplicated copies occurs at a high frequency.
For example, our initial sequence analysis comparing the Rattus norvegicus and Tokudaia muenninki Sry copies did not reveal any connections between the duplicated copies at either the DNA or amino acid level, indicating that Sry duplication has occurred more than once.
Moreover, several factors such as length, orientation, degree of sequence similarity and the distance between the duplicated copies may lead to differential degrees of genomic rearrangements of sequences in genome [ 45].
The CSP is responsible for deleting the duplicate copies.
This is because the Spray and Wait protocol also control the amount of the duplicate copies.
7,272 genes are classified as being segmental duplicates and 1,512 genes are classified as being tandem duplicates with the duplicate copies immediately neighboring each other [5].
A decrease of the rλ indicates differences in the evolutionary rates between the original and the duplicate copy, and a measure of such divergence is assigned as θ = 1−rλ, where θ is a coefficient of functional divergence [15].
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