From: Regis Zimmer
Cc: mappers iastate.edu
Subject: Re: number of avian genes
Date: Mon, 25 Nov 96 17:44 EST
As Dr. Dodgson has mentioned, there's no data to support concentration of
functional genes in the chicken microchromosomes. However, the data
available in the referred database (ChickGBASE) is based mainly in
anonymous markers (RAPDS, microsatellites, etc).
Since anonymous markers are generated by linkage analysis, and the
microchromosomes are usually small enough not to allow a significant LOD
score by linkage analysis, the only source for compreheensive data seems
to be the physical mapping (e.g. PFGE analysis or microdissection
techniques). In my oppinion significant data has demonstrated that there's
a concentration of expressed genes and CpG
islands in the microchromosomes (McQueen et al. (1996) Nature Genetics
12: 321-324; Riegert et al., (1996) PNAS 93: 1243-1248; Miller et al.
(1996) PNAS 93: 3958-3962). Of course this is
proportional to representation of the microchromosomes (25-30% of the total
chicken
genome) but it's on the edge of the maximum known concentration of genes
found in specific sequences among vertebrates. Furthermore, to support
this data evolutionary, there's letter published at Nature (1995) 377: 391
commenting on the findings that the lost in the patterns
and size of birds seems to correlate with the reduction in their genome size.
It appears that the shortening in size during evolution had protected the
chicken microchromosomes against defective mutations (deletions and
translocations).
Regis Zimmer.
On Mon, 25 Nov 1996, angenmap wrote:
> ------- Forwarded Message
>
> Date: Mon, 25 Nov 96 17:44 EST
> To: angenmapiastate.edu
> From: "Jerry.Dodgson" <22314JBDMSU.EDU>
> Subject: number of avian genes
>
> In the latest version of the avian genome map (Bumstead, Cheng, and
> Crittenden, soon to be available at http://poultry.mph.msu.edu), there is no
> evidence for clustering of expressed genes on microchromosomes (in comparison
> to anonymous markers). So I have considerable doubt about the hypothesis that
> expressed genes are predominantly located in or even heavily enriched in
> microchromosomes.
>
> Without having done any careful surveying, my impression based on studies of
> several gene families (globin, histone, actin, HMGs) is that in most cases,
> chickens have a similar number of genes to mammals, but with smaller
> intergenic regions, many fewer pseudogenes, and in some cases smaller introns.
> Thus, although the argument remains at the academic stage as Dr. Miller
> suggests, my best guess would be that birds will have a similar number of
> functional genes as do mammals (but fewer pseudogenes), but more closely
> spaced (and probably rather evenly distributed among euchromatic regions).
>
> Just one person's opinion, though.
>
> Jerry Dodgson,
> Dept. of Microbiology, Michigan State U.
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