Candidatus Halobonum tyrrellensis strain G22, phylogenetic trees

<p>These are the phylogenetic trees associated with this genome annoucement (http://genomea.asm.org/content/1/6/e01001-13.full). The trees shows the placement of Ca. Halobonum tyrrellensis G22 within the Halobacteria</p> <p>- HaloG22_16S_v2, is a phylogenetic tree based on the 16S rRNA gene. Alignment was done using Mafft and tree built using FastTree.</p> <p>- HaloG22_v6, contains a phylogenetic tree based on protein markers. The software PhyloPhlan was used to generate this tree</p> <p> </p> <p></p

KS domain classification.

<p>KS domain classification.</p

Phylogeny based domain classification.

<p>A) KS domain phylogeny. Polyphyletic groups are distinguished by letters. B) C domain phylogeny.</p

Screen shot of the NaPDoS webpage.

<p>Screen shot of the NaPDoS webpage.</p

Metabolic connectivity graph showing community distribution of protein family clusters.

<p>Cohesive populations are shown as similarly colored nodes and vectors according to numbers of shared features, based on unsupervised protein family clustering of 12 habitat-specific genomes.</p

Phylogenetic distribution of protein BLAST matches for assembled population genomes and unclassified scaffolds.

<p>Taxonomic distribution of non-self matches versus the Genbank nr database were calculated using the DarkHorse algorithm at a filter threshold setting of 0.05, including only alignments covering at least 70% of both query and target sequences with an e-value of 1e-5 or better.</p

Consensus population genome properties.

§<p>Marker gene detection details are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061692#pone.0061692.s006" target="_blank">Table S6</a>.</p>*<p>Parenthetical values indicate cases where locally elevated depth of coverage suggests that assembly software may have compressed multiple 16S gene copies into a single locus.</p

Assembly-Driven Community Genomics of a Hypersaline Microbial Ecosystem

<div><p>Microbial populations inhabiting a natural hypersaline lake ecosystem in Lake Tyrrell, Victoria, Australia, have been characterized using deep metagenomic sampling, iterative <i>de novo</i> assembly, and multidimensional phylogenetic binning. Composite genomes representing habitat-specific microbial populations were reconstructed for eleven different archaea and one bacterium, comprising between 0.6 and 14.1% of the planktonic community. Eight of the eleven archaeal genomes were from microbial species without previously cultured representatives. These new genomes provide habitat-specific reference sequences enabling detailed, lineage-specific compartmentalization of predicted functional capabilities and cellular properties associated with both dominant and less abundant community members, including organisms previously known only by their 16S rRNA sequences. Together, these data provide a comprehensive, culture-independent genomic blueprint for ecosystem-wide analysis of protein functions, population structure, and lifestyles of co-existing, co-evolving microbial groups within the same natural habitat. The “assembly-driven” community genomic approach demonstrated in this study advances our ability to push beyond single gene investigations, and promotes genome-scale reconstructions as a tangible goal in the quest to define the metabolic, ecological, and evolutionary dynamics that underpin environmental microbial diversity.</p></div

Relative abundance of microbial population groups.

<p>Colors correspond to taxonmically related microbial populations, including both assembled genome sequences and non-genomic scaffolds containing less abundant variant sequences. Percentage calculations include total number of assembled nucleotides in reads associated with each group, normalized for the group's average genome size. Percentage of unclassified sequences was calculated using an estimated genome size of 3 MB, the approximate abundance-weighted average for all other groups. Known viral and plasmid sequences, representing approximately 0.2% of assembled nucleotides, have been excluded from these calculations.</p

NaPDoS bioinformatic pipeline.

<p>The web interface to this pipeline is divided 3 consecutive steps. Nucleic acid sequences are translated into predicted amino acids and genomic sequences are screened using Hidden Markov Models (HMM). For protein and small nucleic acid sequences a BLAST search is performed against curated reference database examples to identify matches to known PKS/NRPS pathways. Selected candidate sequences plus the BLAST results are trimmed and inserted into a manually curated reference alignment, keeping the original reference alignment intact. This alignment is used to build a tree.</p