[metagenomics-jclub] Papers for MetaJclub meeting Wednesday

[Adina Chuang Howe]

A few weeks ago I went to a talk by David Ussery from Denmark's equivalent
of JGI -- he gave a talk on looking for a "protein core" among available
sequenced genomes which has recently been published in the attached (2010)
paper.  It was interesting enough that I thought I'd present his paper to
the group on Wednesday.


Best, Adina


============

There are now more than 1000 sequenced prokaryotic genomes deposited in
public databases and available for analysis. Currently, although the
sequence databases GenBank, DNA Database of Japan and EMBL are synchronized
continually, there are slight differences in content at the genomes level
for a variety of logistical reasons, including differences in format and
loading errors, such as those caused by file transfer protocol
interruptions. This means that the 1000th genome will be different in the
various databases. Some of the data on the highly accessed web pages are
inaccurate, leading to false conclusions for example about the largest
bacterial genome sequenced. Biological diversity is far greater than many
have thought. For example, analysis of multiple Escherichia coli genomes has
led to an estimate of around 45 000 gene families - more genes than are
recognized in the human genome. Moreover, of the 1000 genomes available, not
a single protein is conserved across all genomes. Excluding the members of
the Archaea, only a total of four genes are conserved in all bacteria: two
protein genes and two RNA genes.


http://www.ncbi.nlm.nih.gov/pubmed/20093288
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