Conversely, there were 704 A. thaliana genes with diverged gene regulation in both Populus and O. sativa and 389 genes with at least one ortholog with conserved regulation and at least one other ortholog with diverged regulation in the two other plants.
The use of multiple genomes of a same species allowed to identify genomes with diverging gene order with respect to their conspecific.
This is the first investigation to report that the total number of differential genes decreases with diverging atherosclerotic disease pattern between porcine brachial and femoral arteries.
A comparative analysis delineated two distinct gene expression programs with diverging functional trends before and following the switch (Additional file 2: Table S2).
In fact, the dinoflagellate Karenia brevis bearing haptophyte tertiary plastids possesses plastid-targeted genes with phylogenetically diverged origins [41].
Among the genes that were differentially regulated in response to varying doses of cadmium were metallothionein genes with highly diverged protein sequences, but with consensus metal-responsive elements in their promotors.
Some of these genes might correspond to sex-linked genes with highly diverged X and Y copies that assembled in separate RNA-seq contigs and might therefore be wrongly classified as X-hemizygous, or not be detected as sex-linked at all.
The lineage divergence continuum, as visualized by networks, begins with gene frequencies diverging with only older internal haplotypes shared (less frequent haplotypes arising since isolation are private), followed by a lack of haplotype sharing.
Since genes with conserved neighbourhoods and genes with diverged neighbourhoods are different subsets of genes, we also investigated the overlapping set of genes with both conserved and diverged orthologs.
The early evolutionary history of the NR1I subfamily (VDR, PXR, CAR) in vertebrates is not completely clear, but one hypothesis is that a single ancestral 'VDR/PXR' gene duplicated, with the two genes then diverging into distinct VDRs and PXRs, both of which are currently found in both mammalian and non-mammalian species [ 22].
