We further provide evidence for strong positive, but significantly different, selection rates acting on all copy classes of NB-LRR duplicates, illustrating the impact of gene and genome duplication to the diversification of plant key traits across approximately 100 MA of genome evolution.
With this understanding of the impact of duplicated reads, we analyzed the set of recurrently over-represented genes to see if they sequenced biologically interesting categories of genes.
Therefore, with a known phylogeny, butterflies are a useful group of organisms for examining the impact of duplicate genes on phylogenetic reconstruction and divergence time estimation.
To assess the impact of retaining duplicate di-tags we detected significant interactions in HiCUP-processed CHi-C datasets using the CHiCAGO pipeline (five datasets were processed: Samples 1 and 2 are described previously and Samples 3, 4 and 5 were generated from mouse embryonic stem cells and have the Gene Expression Omnibus accession GSM1888519).
The impact of the reannotated duplicated genes is major regarding the intra- and interspecies evolution analysis (tables 1 and 2 and fig. 1).
To test these hypotheses, I estimated the impact of gene duplication and metabolic function upon intraspecific gene expression variation of segmental and tandem duplicated genes within Arabidopsis thaliana.
We also examine the impact of the extent of the duplication event by comparing SSD duplicate genes with WGD duplicate genes.
For our study of the impact of gene duplication on protein complexes, we separated paralogs into two distinct, non-overlapping classes: genes that were duplicated at the WGD event, and non-WGD duplicates detectable by sequence similarity.
To evaluate the selective constraints on the evolution of these duplicated genes, we used improved branch-site models [ 13] to examine the impact of positive selection at specific sites for each recently duplicated gene.
The aim of this study was to assess the impact of applying different methods for duplicate isolate removal on the MRSA rates.
In this study, both datasets were filtered to minimize the impact of the identified GC bias and exclude the artificial duplicate sequences.
