I'm not one to halve bunnies, so I'm glad I don't have that problem here. You two are somewhat ambiguous, so I guess I'll just have to wade in here. =o)
The Alchemist: You need to extricate the concept of gene duplication from that of pseudogene formation. And in no sense of the word do diploid/polyploid organisms have pseudogenomes! - (nominally) all the genes on all chromosomes are functional, aren't they?
ariels: I'm assuming you mean 'transcribed' rather than 'functional', no? But pseudogenes may or may not be transcribed; that per sé is not an identification criterion, though the inherent inability of the gene to be transcribed does mark it as such. Short range transcriptional control - ie. promoters - are the order of the day here.
Just so we're absolutely clear: pseudogenes are 'genes that aren't genes'. They are not expressed to give functional protein but they do have sequence characteristics of genes (and are in this manner identified via DNA sequencing). Pseudogenes fall into two classes:
'Dead Genes'
These possess the same
intron/
exon structure as the related functional gene BUT
mutations prevent
expression. 'Dead genes' arise as a result of conventional
gene duplication, and are thus often physically close to the live gene.
Example: human pseudo-beta globin.
These are intron-less and
promoter-less versions of functional genes. Processed pseudogenes are thought to arise by
integration of the
retrotranscribed (by the
RT of
retrotransposon-type elements)
mRNA back into the genome; correspondingly, these can be found anywhere in the
genome w.r.t. the progenitor gene - even on a different
chromosome.
Example: murine (mouse) pseudo-alpha globin.