Complete Genome Sequence and Annotation of the <named-content content-type='genus-species'>Paracoccus pantotrophus</named-content> Type Strain DSM 2944

Paracoccus spp. are metabolically versatile alphaproteobacteria able to perform heterotrophic and chemoautotrophic growth. This study describes the whole-genome sequence of the Paracoccus pantotrophus type strain DSM 2944 (ATCC 35512, LMD 82.5, GB17). The genome sequence revealed the presence of a complete phaZ phaC phaP phaR gene cluster related to polyhydroxyalkanoate metabolism. Paracoccus pantotrophus DSM 2944T (formerly designated Thiosphaera pantotropha) was isolated in 1983 from a denitrifying, sulfide-oxidizing effluent treatment plant in Delft, Netherlands. The strain is a nonmotile, facultative anaerobic, nonpathogenic, Gram-negative coccus occurring singly, pairwise, or as short chains in spherical to rod-shaped forms (1–3). P. pantotrophus DSM 2944T belongs to the family Rhodobacteraceae in the phylum Alphaproteobacteria. This strain can grow chemoautotrophically with carbon dioxide and hydrogen or reduced sulfur compounds and is capable of denitrification. Under nitrogen limitation, polyhydroxybutyrate can be produced (1, 4, 5). The versatile metabolic pathways render P. pantotrophus DSM 2944T a promising strain for biotechnological applications. Strain DSM 2944T was obtained from the German Collection of Microorganisms and Cell Cultures (DSMZ, Braunschweig, Germany) and was grown aerobically in lysogeny broth (LB) medium at 30°C to early exponential phase (6). Genomic DNA was extracted with the standard phenol-chloroform method, followed by construction of a 16-kb library. The sequencing of the whole genome of P. pantotrophus DSM 2944T was performed using the PacBio RS II platform (Menlo Park, CA, USA) with a 240-min movie, obtaining 70,835 total reads, an average read length of 10,089 bp, an average reference coverage of 147-fold, and an N50 value of 14,250 bp. The size of the whole genome was found to be 4,409,379 bp, with a G C content of 67.7%. The raw genome sequence data were proofed and assembled with SMRT v6.0. 0 by using one single-molecule real-time (SMRT) cell featuring HGAP v3 (7), resulting in four circularized DNA elements comprising 2,248,278 bp, 1,525,820 bp, 535,332 bp, and 99,949 bp with coverages of 149-fold, 139-fold, 168-fold, and 157-fold, respectively. Circularization was confirmed by fusing overlapping sequences outside open reading frame regions. Pulsed-field gel electrophoresis was performed following the protocol of Winterstein and Ludwig and verified the presence of four DNA fragments in DSM 2944T, which corresponded with Winterstein and Ludwig’s findings of four DNA fragments of similar sizes (8). Furthermore, the two smaller DNA fragments were already described as megaplasmids named pPAN2 (pHG41), with a size of 535,332 bp, and pPAN1 (pHG42), with a size of 99,949 bp. For the plasmid pPAN1, a partial sequence was recovered with a size of 2,005 bp (2%), and for pPAN2, no sequence information was available (9–12). The two larger DNA elements are assumed to be chromosomes, as the presence of up to three chromosomes within the genus of Paracoccus is already known (8). Furthermore, essential and Citation Bockwoldt JA, Zimmermann M, Tiso T, Blank LM. 2020. Complete genome sequence and annotation of the Paracoccus pantotrophus type strain DSM 2944. Microbiol Resour Announc 9:e01290-19. https://doi.org/10.1128/ MRA.01290-19. Editor J. Cameron Thrash, University of Southern California Copyright © 2020 Bockwoldt et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Lars M. Blank, lars.blank@rwth-aachen.de. Received 21 October 2019 Accepted 2 December 2019 Published 2 January 2020 GENOME SEQUENCES