Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21T)

Abstract

Ktedonobacter racemifer corrig. Cavaletti et al. 2007 is the type species of the genus Ktedonobacter, which in turn is the type genus of the family Ktedonobacteraceae, the type family of the order Ktedonobacterales within the class Ktedonobacteria in the phylum ‘Chloroflexi’. Although K. racemifer shares some morphological features with the actinobacteria, it is of special interest because it was the first cultivated representative of a deep branching unclassified lineage of otherwise uncultivated environmental phylotypes tentatively located within the phylum ‘Chloroflexi’. The aerobic, filamentous, non-motile, spore-forming Gram-positive heterotroph was isolated from soil in Italy. The 13,661,586 bp long non-contiguous finished genome consists of ten contigs and is the first reported genome sequence from a member of the class Ktedonobacteria. With its 11,453 protein-coding and 87 RNA genes, it is the largest prokaryotic genome reported so far. It comprises a large number of over-represented COGs, particularly genes associated with transposons, causing the genetic redundancy within the genome being considerably larger than expected by chance. This work is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

“…1a). For example, Ktedonobacter racemifer 16 , a member of the phylum Chloroflexi, contributed 5,102 genes to GEBA-I-only clusters and singletons (Fig. 2b).…”

Why prokaryotes have pangenomes

“…Though prokaryotic genomes can grow in size to overlap eukaryotic genome sizes 37 , gene loss is obviously just as important as gain and genes that are not relevant for the ecological niche in which an organism finds itself, will soon be lost. Lee and Marx 38 have shown selection-driven genome reduction in Methylobacterium extorquens AM1 experimental populations.…”

Diversity of <i>Ktedonobacteria</i> with Actinomycetes-Like Morphology in Terrestrial Environments

“…The class Ktedonobacteria , the members of which have an actinomycetes-like morphology, was recently proposed (5) and placed in the phylum Chloroflexi (41), which is known to be a deep-branching lineage of the domain Bacteria. This class currently contains only six named species in two orders: in Ktedonobacterales , Ktedonobacter racemifer SOSP1-21 T (isolated from soil under black locust in Italy; [5, 6]), which is the first pure culture in the class, Thermosporothrix hazakensis SK20-1 T (isolated from ripe compost in Japan; [41]), and T. narukonensis F4 T (isolated from fallen leaves deposited on geothermal soil; [43]); and in Thermogemmatisporales , Thermogemmatispora onikobensis ONI-1 T and T. foliorum ONI-5 T (isolated from fallen leaves deposited on geothermal soil; [42]), and T. carboxidivorans PM5 T (isolated from a geothermally heated biofilm; [19]). Other cultivated isolates for which valid names have not yet been proposed include ten isolates (strain SOSP series, from the same source as K. racemifer SOSP1-21 T ; [5]) in Ktedonobacterales ; and four isolates (strains P-352, P-359, T104, and T81 from geothermal soils; [32]) and two isolates (strains BPP55 and PM6 from the same source as T. carboxidivorans PM5 T ; [19]) in Thermogemmatisporales .…”

“…Strains SOSP1-9, from the strain SOSP series, may form sporangia (5). Genome sizes are 13.7 Mbp in K. racemifer SOSP1-21 T (6), 7.3 Mbp in T. hazakensis SK20-1 T (27), and 5.6 Mbp in T. carboxidivorans PM5 T (Integrated Microbial Genomes & Microbiomes database: http://img.jgi.doe.gov/). The genome of K. racemifer SOSP1-21 T encodes 11,453 putative proteins, which is the largest number reported for a prokaryotic genome to date (6).…”