Hello Max, This is a good question. Here are some comments from our lead scientist working with the zebrafish genomic data:
> I don't know if these regions are characterised. There was whole > genome duplication in a zebrafish ancester, but additionally there are > problems with the assembly that led to false duplications. The > assembly started out being made from sequenced DNA from 1000 embryos > which were thought to be homogeneous and turned out to be more > heterogeneous than thought. This resulted in a number of misjoins, > misassemblies and artifciail duplications. I know that the latest Zv8 > assembly should be a big improvement on the previous one but there > are still problems and I don't know to what extent these have been > cleaned up. The zebrafish genome assembly project website is here and > has some information about this: > http://www.sanger.ac.uk/Projects/D_rerio/ > > I think that the best place to ask would be: [email protected]. > The people at Sanger would be the experts on this particular assembly. > > Rachel Maximilian Haeussler wrote: > Hi Donna, > > your discussion with Xianjun reminds me of requests from Zebrafish and > Medaka genome browser users here that I repeatedly heard: Why are > there so many self-chainable non-coding regions? I remember the "into > the heart of darkness"-paper from Gill but he didn't really propose an > explanation, as far as I remember. At 100-200 copies, the regions can > hardly be repeats. Many of the examples I've been looking at are not > conserved across species, so they don't look very "important" either. > You told me that you increased your thresholds in the newer human > assemblies to reduce the number of these features so I guess you don't > consider them functional. But do you have any explanation for the many > self-hits? > > cheers > Max > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
