Hi all,<br><br>Due to room availability, we are going to skip next week (April 6) and meet on April 13 in PSB 271 at 10 AM (the usual time). I will present the new paper from the Eisen lab which presents some "novel" phylogenetic sequences in metagenomic data (attached). After this meeting, we'll be back on our every two weeks schedule with Tracy Teal tentatively scheduled to present highlights from the Keystone Ecology meeting on April 27.<br>
<br>Best,<br>Adina <br><br><h1 rel="dc:type" href="http://purl.org/dc/dcmitype/Text"><font size="1">Stalking
the Fourth Domain in Metagenomic Data: Searching for, Discovering, and
Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees</font></h1><font size="1"></font><p class="authors"><font size="1"><span rel="dc:creator"><span>Dongying Wu</span></span><sup><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff1">1</a></sup>, <span rel="dc:creator"><span>Martin Wu</span></span><sup><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff1">1</a></sup><sup>,</sup><sup><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff4">4</a></sup>, <span rel="dc:creator"><span>Aaron Halpern</span></span><sup><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff2">2</a></sup><sup>,</sup><sup><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff3">3</a></sup>, <span rel="dc:creator"><span>Douglas B. Rusch</span></span><sup><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff2">2</a></sup><sup>,</sup><sup><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff3">3</a></sup>, <span rel="dc:creator"><span>Shibu Yooseph</span></span><sup><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff2">2</a></sup><sup>,</sup><sup><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff3">3</a></sup>, <span rel="dc:creator"><span>Marvin Frazier</span></span><sup><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff2">2</a></sup><sup>,</sup><sup><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff3">3</a></sup>, <span rel="dc:creator"><span>J. Craig Venter</span></span><sup><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff2">2</a></sup><sup>,</sup><sup><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff3">3</a></sup>, <span rel="dc:creator"><span>Jonathan A. Eisen</span></span><sup><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff1">1</a></sup><sup><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#cor1" class="fnoteref">*</a></sup></font></p>
<font size="1"></font><h2><font size="1">Abstract </font></h2>
<h3><font size="1">Background</font></h3>
<p><font size="1">Most
of our knowledge about the ancient evolutionary history of organisms
has been derived from data associated with specific known organisms
(i.e., organisms that we can study directly such as plants, metazoans,
and culturable microbes). Recently, however, a new source of data for
such studies has arrived: DNA sequence data generated directly from
environmental samples. Such metagenomic data has enormous potential in a
variety of areas including, as we argue here, in studies of very early
events in the evolution of gene families and of species.</font></p>
<h3><font size="1">Methodology/Principal Findings</font></h3>
<p><font size="1">We
designed and implemented new methods for analyzing metagenomic data and
used them to search the Global Ocean Sampling (GOS) Expedition data set
for novel lineages in three gene families commonly used in phylogenetic
studies of known and unknown organisms: small subunit rRNA and the <em>recA</em> and <em>rpoB</em>
superfamilies. Though the methods available could not accurately
identify very deeply branched ss-rRNAs (largely due to difficulties in
making robust sequence alignments for novel rRNA fragments), our
analysis revealed the existence of multiple novel branches in the <em>recA</em> and <em>rpoB</em> gene families. Analysis of available sequence data likely from the same genomes as these novel <em>recA</em> and <em>rpoB</em> homologs was then used to further characterize the possible organismal source of the novel sequences.</font></p>
<h3><font size="1">Conclusions/Significance</font></h3>
<p><font size="1">Of the novel <em>recA</em> and <em>rpoB</em>
homologs identified in the metagenomic data, some likely come from
uncharacterized viruses while others may represent ancient paralogs not
yet seen in any cultured organism. A third possibility is that some come
from novel cellular lineages that are only distantly related to any
organisms for which sequence data is currently available.<span class="note public" title="User Annotation"><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#" class="bug public" id="annAnchor1" title="Click to preview this note"><span>1</span></a>
If there exist any major, but so-far-undiscovered, deeply branching
lineages in the tree of life, we suggest that methods such as those
described herein currently offer the best way to search for them.</span></font> </p>