Collections from Arizona Flagstaff, Oregonon (Eugene) and California (Sequoia Natl. Park) served as out-groups.
We applied a 50% conservation insertion deletion (indel) filter for tree calculation and members of the AprA lineage I (Meyer and Kuever, 2007b) served as out-groups.
Sequences of Priapulus caudatus (AF025927) and Halycriptus spinulosus (AF342790) for the host 18S rDNA tree and sequences of Alkalimnicola halodurans (AJ404972), Nitrococcus mobilis (L35510) and Methylohalobius crimeensis (AJ581837) served as out-groups for the symbiont 16S rDNA tree.
The tree was generated in program MEGA 5 using the neighbour-joining algorithm with the Methanosarcina sp. sequence serving as out-group.
One single O. villosa pmt sequence (Zelzate, Belgium) was cloned and sequenced to serve as out-group in phylogenetic analysis.
In order to understand the evolutionary history of the Treponema species, we collected the 31 marker genes described in [ 19] for the Treponema species, as well as for species serving as out-groups.
Moreover, analysis of gene expression data and TF DNA binding data has revealed that some TFs serve as out-hubs, thus regulating several other genes (Lee et al. 2002; Luscombe et al. 2004; Bergmann et al. 2004).
In our phylogenomic analysis Neurospora crassa served as an out group.
Since then, two events, the Beijing Olympics later that year and the Shanghai World Expo of 2010, might have served as coming-out parties for a rising China.
Two non-seed plant taxa, the moss, Physcomitrella patens (2), which also served as an out-group, and the lycopod, Selaginella kraussiana (1), were also used for these analyses.
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