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These analyses allow inference of significant patterns and events in microbial carotenoid evolution.
This phylogenetic structure therefore forms a valid framework to address more specific questions concerning microbial carotenoid evolution.
Furthermore, whereas some studies demarcate phylogenetic lineages of microbial carotenoid evolution, they do so without proper consideration of the bootstrap support for their presented phylogenies [34], [35] and in one case misidentified Paracoccus zeaxanthinifaciens as Flavobacterium sp. ATCC 21588, the only member of the Bacteroidetes included [35].
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Microbial carotenoid diversity and evolution has hitherto been analyzed primarily from structural and biosynthetic perspectives, with the few phylogenetic analyses of microbial carotenoid biosynthetic proteins using either used limited datasets or lacking methodological rigor.
In nearly all cases the ratio of two-state parsimony-informative sites to all polymorphic sites (q) was <0.35 (average q = 0.24) with low associated P values (data not shown), indicating that homologous recombination was not detected by this method, and therefore likely plays only a minor role in microbial carotenoid biosynthetic pathway evolution.
Given the recent accumulation of microbial genome sequences, a reappraisal of microbial carotenoid biosynthetic diversity and evolution from the perspective of comparative genomics is warranted to validate and complement models of microbial carotenoid diversity and evolution based upon structural and biosynthetic data.
As a microbial carotenoid, torulene possesses potential health-promoting effects in human.
Comparative genomics were used to identify and analyze in silico microbial carotenoid biosynthetic pathways.
First, the overall phylogenetic structure of carotenoid biosynthesis is determined by considering the phylogenetic distribution of microbial carotenoid structural diversity and how it relates to phylogenies of core carotenoid biosynthetic proteins.
Comparative genomics analyses of microbial carotenoid biosynthetic proteins indicate a much greater taxonomic diversity then that identified based on structural and biosynthetic data, and divides microbial carotenoid biosynthesis into several, well-supported phylogenetic lineages not evident previously.
According to the phylogenetic analyses presented thus far, horizontal transfer is a major diversifying mechanism in microbial carotenoid biosynthesis.
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