David Coil edited Results and Discussion.md  almost 9 years ago

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**Phylogeny and Genome analysis**  Phylogenetic analysis was performed using the full length (1482bp) 16S rDNA sequence from the genome assembly, not the shorter (1350bp) version from Sanger sequencing. The Coronado(T) 16S rDNA sequence showed only 95% less than 95.5%  identity to the phylogenetically closest relative, _Porphyrobacter sanquineus_, and other _Porphyrobacter_ species but  identity was is  even lower throughout the rest of to other genera in  the tree. family.  Given the low 16S rDNA identity to other members of the family, we did not perform DNA-DNA hybridization as this would have been uninformative \cite{Stackebrandt_1994} \cite{Tindall_2010}. As discussed above, a large-scale taxonomic revision of the family is most likely in order given the lack of monophyly observed for most genera in the tree (Figure 2).For example, Coronado(T) is the basal member of a clade containing mostly _Porphyrobacter_ that has strong bootstrap support, but is polyphyletic with respect to both _Erythromicrobium_ and _Erythrobacter_. And, this clade falls within a well-supported polyphyletic clade of _Erythrobacter_. Based on this tree, we chose to compare Coronado(T) to the three genera in Table 1.  FIX THIS  For example, Coronado(T) is the basal member of a clade containing mostly _Porphyrobacter_ that has strong bootstrap support, but is polyphyletic with respect to both _Erythromicrobium_ and _Erythrobacter_. And, this clade falls within a well-supported polyphyletic clade of _Erythrobacter_.   Based on the different phylogenetic trees, we chose to compare Coronado(T) to the five other _Porphyrobacter_ species listed in Table 1.  Analysis of the draft genome of strain Coronado(T) was used to complement the physical characterizations typical of the family _Erythrobacteraceae_. _Erythrobacteraceae_ and the genus _Porphyrobacter_.  For example, Coronado(T) does not contain any of the numerous genes involved in bacteriochlorophyll biosynthesis, rendering protein extraction/spectrophotometry unnecessary. Conversly, while no flagella were observed by TEM, this strain appears to possess the required genes making it likely that the flagella were lost in sample preparation or that their expression is condition-dependent. **Polar lipid, respitory lipoquinone, and fatty acid methyl esters**  The major cellular fatty acids of strain Coronado(T) are C18:1\(\omega\)7cis (56.6%) and C16:0 (20.3%). Other fatty acids found in significant amounts (>1%) are 2-OH-C14:0 (4.8%), C16:1\(\omega\)5cis (1.1%), C16:1\(\omega\)7cis (9.8%), C17:1\(\omega\)6cis (2%), C18:1\(\omega\)5cis (1.1%), and C18:0 (1.2%). The fatty acid profile of strain Coronado(T) fits generally within the ranges described for members of the most closely related genera (_Erythrobacter_, _Porphyrobacter_ and _Erythromicrobium_, comparison data from \cite{Hiraishi_2002}). The two exceptions to this are a slightly higher level of C14:0 than average and a much higher level of C16:0 than average. However, it is difficult to compare across studies since variation in growth conditions can significantly influence the fatty acid profile.  The major respiratory quinone is ubiquinone 10 (92%), as it is for all members of the _Erythrobacteraceae_ family. The predominant polar lipid is phosphatidylglycerol, with significant amounts of sphingoglycolipid and phosphatidylethanolamine. Smaller amounts of diphosphatidylglycerol, phosphatidylcholine, and two unidentified phospholipids were also observed (Figure 3).