[metagenomics-jclub] Upcoming journal club meeting

[Adina Chuang Howe]

Hi all,

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.

Best,
Adina

Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering,
and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees

Dongying Wu1<http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff1>,
Martin Wu1<http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff1>
,4<http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff4>,
Aaron Halpern2<http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff2>
,3<http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff3>,
Douglas B. Rusch2<http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff2>
,3<http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff3>,
Shibu Yooseph2<http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff2>
,3<http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff3>,
Marvin Frazier2<http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff2>
,3<http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff3>,
J. Craig Venter2<http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff2>
,3<http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff3>,
Jonathan A. Eisen1<http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#aff1>
*<http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#cor1>
Abstract  Background

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.
Methodology/Principal Findings

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 *recA* and
*rpoB*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 *recA* and *rpoB* gene families.
Analysis of available sequence data likely from the same genomes as these
novel *recA* and *rpoB* homologs was then used to further characterize the
possible organismal source of the novel sequences.
Conclusions/Significance

Of the novel *recA* and *rpoB* 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.1<http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018011#>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.
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