recent publication from the Donnelly group comparing using GENCODE or Refeq annotation when predicting variants effects.
Choice of transcripts and software has a large effect on variant annotation
Genome Medicine 2014, 6:26 doi:10.1186/gm543
Genome-Wide Comparison of Medieval & Modern M. #leprae, reveals ~1600 #pseudogenes, w/ slightly more in modern strain
http://www.sciencemag.org/content/341/6142/179.abstract
QT:{{”
Most bacteria will have some pseudogenes in their genome, maybe, you know, in Mycobacterium tuberculosis, for instance a close relative, there are 4,000 genes
present and perhaps 20 pseudogenes. In Mycobacterium leprae, there are 1,600 real
genes and as many pseudogenes. For me, this has always been puzzling, because bacteria
generally tend to, once a function has been lost, the corresponding genes are usually
eliminated and we see the genome shrinking. This hasn’t happened in Mycobacterium
leprae, because there’s still such a huge number of pseudogenes present. And that makes
me think that maybe Mycobacterium leprae emerged in this form only very recently and
that there hasn’t therefore been sufficient time for these pseudogenes to be lost.
However, this is clearly speculation, and it needs to be tested by further experiment. For
instance, looking at older samples might be helpful because the analysis described in the
recent Science paper shows that there are more, a few more pseudogenes present in
modern strains of Mycobacterium leprae than there were in medieval European strains.
So if we could go back a few thousand years more, we might find that actually there were
a couple more functional genes at that particular point.
….
Now is there any evidence that the successive number of pseudogenes contributes to
either its slow growth or its resistance to growing in the lab or its just kind of long
standing plague on humanity?
….
Yes, I think while there’s no experimental evidence to prove that the pseudogenes are
responsible for the slow growth, I think it’s highly likely that they do contribute because
lots of very essential functions have been lost, and this means that M. leprae, for instance,
has difficulty in acquiring iron because it’s lost the genes required for iron uptake.
“}}
here are three more relevant papers about retroduplications :
http://www.nature.com/nmeth/journal/v9/n2/full/nmeth.1810.html http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003242 http://genomebiology.com/content/14/3/R22
this should partially explain the high insertion rate in worm: http://mbe.oxfordjournals.org/content/26/6/1199.full
QT:”
Of the new mutations observed in MA lines, more than half were short indel mutations, with fewer deletions than insertions (Denver, Morris, Lynch, and Thomas 2004). This finding on indels contrasts with previous work with C. elegans pseudogenes in which deletions are more common than insertions (Robertson 2000; Witherspoon and Robertson 2003) but is consistent with findings in C. elegansmicrosatellite mutation data (Frisse 1999; Denver, Morris, Kewalramani, et al. 2004; Seyfert et al. 2008).
“
Dead or Alive? Pseudoenzymes resemble #enzymes but difficult to pin down functionally http://www.sciencemag.org/content/340/6128/27.full #pseudogene
http://www.sciencemag.org/content/340/6128/27.full
Science 5 April 2013:
Vol. 340 no. 6128 p. 27
DOI: 10.1126/science.340.6128.27
NEWS FOCUS
Dead or Alive?
Pseudogenes as regulators of biological function
Essays in Biochemistry (2013) 54, 103-112
http://bioinformatics.oxfordjournals.org/content/early/2013/03/01/bioinformatics.btt104.full.pdf RCPedia: a database of retrocopied genes
Navarro, F.C.P. and Galante, P.A.F.
Bioinformatics 2013