DOI: 10.5061/dryad.8384
title: Data from: Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in phylogenetic trees of phylogenetic marker genes

description: 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. 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.
description: Wu_2011_DataStalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in phylogenetic trees of phylogenetic marker genes. Dongying Wu, Martin Wu, Aaron Halpern, Doug Rusch, Shibu Yooseph, Marvin Frazier, J. Craig Venter, Jonathan A. Eisen. Supplementary Data: (1) recA data: recA.tgz. recA.tgz contains the following files: recA_GOS.pep -- Amino acid sequences for GOS RecAs, recA_ref.pep -- Amino acid sequences for RecAs from NRAA and genome sequences, recA_cluster.txt -- Lek clusters of RecA sequences (Table 1), recA.ali -- Original alignment for the RecA tree (Figure 1), recA.trim.ali -- Trimmed RecA alignment that the RecA tree is built upon (Figure 1), recA.tre -- RecA tree in Newick format (Figure 1), recA_GOS_pepID_assemblyID.map -- The assembly IDs of the recA encoding GOS assemblies (Table 2), recA_linked.pep -- The Amino Acid sequences of the genes that share assemblies with the GOS novel recA (Table 2). (2) rpoB data: rpoB.tgz. rpoB.tgz contains the following files: rpoB_GOS.pep -- Amino acid sequences for GOS RpoBs, rpoB_ref.pep -- Amino acid sequences for RpoBs from NRAA and genome sequences, rpoB_cluster.txt -- Lek clusters of RpoB sequences (Table 3), rpoB.tre.ali -- Original alignment for the RpoB tree (Figure 3), rpoB.tre.trim -- Trimmed RpoB alignment that the RpoB tree is built upon (Figure 3), rpoB.tre -- RpoB tree in Newick format (Figure 3). (3) ss-rRNA data: ssu.tgz. ssu.tgz contains the following files: SSU_GOSreads.fa -- GOS ss-rRNA sequences, SSU_GOSreads_deepbrach.fa -- Potential GOS deep-branching ss-rRNA. (4) Lek Clustering Program: lek.tgz. lek.tgz contains scripts for the Lek clustering protocol. Instructions can be found in the included README file.