Quantifying properties of ortholog phyletic retention, copy-number variation, and sequence conservation, we examined correlations with gene essentiality and functional traits.
Detailing ancestral gene relations therefore enables quantification of properties of ortholog sequence divergence, phyletic retention, and copy-number variation.
There were 3.4 times as many two-copy retention genes than that of three copy retention genes.
However, arguments can be made for all three of the main evolutionary conditions for copy retention – beneficial increased production, subfunctionalisation or neofunctionalisation [ 58].
Given this requirement of gene copy retention, the last common ancestor of P. infestans, P. parasitica, and P. capsici only experienced 281 gene duplications, whereas the Phytophthora ancestor and the today-living lineage P. infestans had 1,651 and 1,353 gene duplications, respectively.
We therefore conclude that duplication via retroposition from Drosophila X chromosomes with retention of both copies is often driven by selection for testis expression in the derived copy because the X-linked ancestral copy is silenced in spermatogenesis.
The most frequent aberration is the unbalanced gain of 17q, often due to translocation of the 17q segment to other chromosomes, combined with retention of two copies of the normal chromosome 17.
It has been shown that diversification of paralogous genes whose products are strictly involved in amino acid biosynthesis has led to functional diversification such that retention of both copies is needed to fulfill the function carried out by the original gene [4] [6], thus supporting the duplication-degeneration-complementation model proposed by Force et al. [7].
Two other fates of gene duplicates might lead to the retention of both copies within a genome.
Our data is consistent with the concept that there are two major fates of gene duplication: retention of both copies or pseudogenization of one of the transcripts.
This indicates trichomonads have a highly complex endomembrane system and provide a precedent for functional retention of additional copies of genes involved in protein trafficking in this species.
