Whole-Genome Reciprocal BLAST Analysis Reveals that Planctomycetes Do Not Share an Unusually Large Number of Genes with Eukarya and Archaea

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Abstract
The genome sequences of Rhodopirellula baltica , formerly Pirellula sp. strain 1, Blastopirellula marina , Gemmata obscuriglobus , and Kuenenia stuttgartiensis were used in a series of pairwise reciprocal best-hit analyses to evaluate the contested evolutionary position of Planctomycetes . Contrary to previous reports which suggested that R. baltica had a high percentage of genes with closest matches to Archaea and Eukarya , we show here that these Planctomycetes do not share an unusually large number of genes with the Archaea or Eukarya , compared with other Bacteria . Thus, best-hit analyses may assign phylogenetic affinities incorrectly if close relatives are absent from the sequence database.