david ford wrote:

John Wilkins wrote:

[snip]

Gene duplication (paralogy) is a
major source of novel functions. And there's no limit on that.

How do you account for the origination of ORFans?

This appears to explain well enough. Unless you actually have some
viable explanation, which I doubt:

Bacterial Genomes as New Gene Homes: The Genealogy of ORFans in E. coli

Vincent Daubin1 and Howard Ochman
Department of Biochemistry & Molecular Biophysics, University of
Arizona

Differences in gene repertoire among bacterial genomes are usually
ascribed to gene loss or to lateral gene transfer from unrelated
cellular organisms. However, most bacteria contain large numbers of
ORFans, that is, annotated genes that are restricted to a particular
genome and that possess no known homologs.

The uniqueness of ORFans
within a genome has precluded the use of a comparative approach to
examine their function and evolution. However, by identifying sequences
unique to monophyletic groups at increasing phylogenetic depths, we can
make direct comparisons of the characteristics of ORFans of different
ages in the Escherichia coli genome, and establish their functional
status and evolutionary rates. Relative to the genes ancestral to
-Proteobacteria and to those genes distributed sporadically in other
prokaryotic species, ORFans in the E. coli lineage are short, A+T rich,
and evolve quickly. Moreover, most encode functional proteins.

Based on
these features, ORFans are not attributable to errors in gene
annotation, limitations of current databases, or to failure of methods
for detecting homology. Rather, ORFans in the genomes of free-living
microorganisms apparently derive from bacteriophage and occasionally
become established by assuming roles in key cellular functions.

[...]
The existence of ORFans in virtually every genome has been termed a
"mystery" (Dujon 1996), and numerous explanations have been offered to
account for their occurrence and for the inability to classify these
genes into existing protein families (Fischer and Eisenberg 1999).

The most common explanation is that ORFans represent very rapidly evolving
genes, or possibly pseudogenes, undergoing rates of substitution and
rearrangements that obscure their similarity to known proteins
(Domazet-Loso and Tautz 2003).

Alternatively, these genes could be
produced de novo from noncoding sequences, which are more highly
diverged between taxa.

Furthermore, they could represent genes
transferred from organisms that have no representatives in the
databases such that no significant similarity can be detected. Then
again, ORFans might not be real genes, but simply artifacts resulting
from the algorithms used to recognize coding sequences in genomes.

It is possible that the factors responsible for the presence of ORFans
will differ among taxomonic groups. For example, in eukaryotes, the
sparse sampling of complete genome sequences may account for a large
proportion of ORFans, whereas in many bacterial groups, this
explanation is less likely because of the large numbers of genome
sequences already available.

Previous analyses of the species or strain-specific genes in bacteria
showed that such sequences tend to have lower G+C contents than genes
with a wider distribution among species. Charlebois et al. (2003),
noting that intergenic regions are often A+T rich in bacterial genomes,
interpreted the biased base composition of species-specific ORFans as
indicating that they might be either annotation artifacts or
fast-evolving genes.

In contrast, Daubin et al. (2003) viewed the
existence of unique ORFans in very closely related genomes as evidence
that these sequences arose by lateral gene transfer.
http://www.genome.org/cgi/content/full/14/6/1036

2006
http://www.biomedcentral.com/1471-2148/6/63
The origin of microbial ORFans, ORFs having no
detectable homology to other ORFs in the
databases, is one of the unexplained puzzles of the
post-genomic era.

//////////////////////////////////////////////////////////////////////////////////////////
How do you account for the origination of new genes?
http://groups.google.com/groups?selm=dford3-1164396926.582303.88630%40j72g2000cwa.googlegroups.com

david ford wrote:

John Wilkins wrote:

[snip]

Gene duplication (paralogy) is a
major source of novel functions. And there's no limit on that.

How do you account for the origination of ORFans?

http://groups-beta.google.com/group/talk.origins/browse_frm/thread/f4abdc01edc7f6d7/93ef19a39010a794?tvc=1&hl=en#93ef19a39010a794

2006
http://www.biomedcentral.com/1471-2148/6/63
The origin of microbial ORFans, ORFs having no
detectable homology to other ORFs in the
databases, is one of the unexplained puzzles of the
post-genomic era.

//////////////////////////////////////////////////////////////////////////////////////////
How do you account for the origination of new genes?
http://groups.google.com/groups?selm=dford3-1164396926.582303.88630%40j72g2000cwa.googlegroups.com