Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3)

Abstract

Pedobacter heparinus (Payza and Korn 1956) Steyn et al. 1998 comb. nov. is the type species of the rapidly growing genus Pedobacter within the family Sphingobacteriaceae of the phylum 'Bacteroidetes'. P. heparinus is of interest, because it was the first isolated strain shown to grow with heparin as sole carbon and nitrogen source and because it produces several enzymes involved in the degradation of mucopolysaccharides. All available data about this species are based on a sole strain that was isolated from dry soil. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first report on a complete genome sequence of a member of the genus Pedobacter, and the 5,167,383 bp long single replicon genome with its 4287 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Keywords: Gram-negative; Sphingobacteriaceae; dry soil; flexible rods; heparinase producer; mesophile; strictly aerobic.

Figure 1

Phylogenetic tree of P. heparinus strain HIM 762-3^T and the type strains of the genus Pedobacter, as well as all type strains of the other genera within the family Sphingobacteriaceae, inferred from 1373 aligned characters [12,13] of the 16S rRNA gene under the maximum likelihood criterion [14]. The tree was rooted with the type strains of the other families within the order ‘Sphingobacteriales’. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 1000 bootstrap replicates if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [15] are shown in blue, published genomes in bold.

Figure 2

Scanning electron micrograph of P. heparinus HIM 762-3^T

Figure 3

Graphical circular map of the genome. From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.