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Review
. 2008 Jun;74(12):3619-25.
doi: 10.1128/AEM.02812-07. Epub 2008 Apr 18.

Structure of the archaeal community of the rumen

Peter H Janssen  1 , Marek Kirs
Affiliations
Review

Structure of the archaeal community of the rumen

Peter H Janssen et al. Appl Environ Microbiol. 2008 Jun.
No abstract available

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Figures

FIG. 1.
FIG. 1.
Phylogenetic dendrogram of total rumen and rumen protozoan-associated archaea and selected reference sequences. Sequences of >870 nt long (138 reference sequences and 271 cloned sequences) were aligned using the EDIT4 primary sequence editor in ARB (23), and the alignments were checked and corrected to produce a master alignment. All positions were considered for the subsequent analyses. Phylogenetic dendrograms of just the 138 reference sequences and of the reference sequences plus 271 cloned sequences of >870 nt were generated in ARB using the Jukes-Cantor distance correction (17) and the neighbor-joining algorithm (38). These dendrograms were rooted with eight sequences from the Crenarchaeota. These alignments were exported from ARB, and 1,000 bootstrap data sets were generated from each in PAUP (46) using Juke-Cantor distances before 1,000 dendrograms were generated using neighbor joining. Consensus dendrograms were then generated in PAUP. These two consensus dendrograms, with bootstrap values, were used to define the clades referred to in this review. Key bootstrap values from the analysis of the larger data set have been added to the phylogenetic dendrogram illustrated. Sequences of <800 nt long (Table 1) were then inserted into the dendrogram of 271 cloned sequences of >870 nt plus 138 reference sequences using the parsimony insertion tool in ARB. For simplicity, clades are shown as shaded parallelograms, with the total number of sequences used in the dendrogram construction shown in parentheses. Sequences and clades containing sequences that originate from PCR-mediated surveys listed in Table 1 are indicated in boldface text. The scale bar indicates 0.10 inferred nucleotide substitutions per position. Mbb, Methanobrevibacter.
See this image and copyright information in PMC

References

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