Our findings suggest that a combination of factors contribute to duplicate gene persistence following whole genome duplication, but that the total expression level and evenness of expression across tissues and through development before duplication are most important.
For example, genes with high expression intensities or broad expression patterns tend to evolve slowly [ 30- 37] so it is not clear with which degree each variable influences duplicate gene persistence after factoring out the role of the other.
Our findings suggest that genomic imprinting can be a factor in duplicate gene divergence, so as to induce the diversification and retention of duplicates.
A possible reason for this is the relatively smaller population size of vertebrates, in which the neutral, random genetic drift is more dominant factor in their duplicate gene loss/retention [ 8].
First, we disentangle the multiplicity of possible structures formed by duplicate transcription factors.
In particular, the WGD produced a larger number of γ subgraphs and of other DSs involving duplicate transcription factors.
For instance, duplicate transcription factors are specifically retained in plant and animal genomes and both positive selection and transcriptional divergence appear to have played a role in their diversification.
For example, if a replication initiation factor duplicate was not in sync with the expression of other components of the replication machinery, the duplicated factor would not be functional and eventually eliminated from the genome.
For performance and scalability tests with large data volumes, the 39 device descriptions and corresponding functional profiles were renamed and duplicated by factors 10, 100, and 1.000, thus resulting in four different databases.
The observation that DSs containing transcription factor nodes are more abundant and statistically enriched in the WGD is consistent with the previously reported abundance of WGD-duplicate transcription factors [ 23].
