We have sequenced and assembled the genome of Pseudomonas reidholzensis CCOS 865T, which was isolated in 2014 from forest soil. Members of the genus Pseudomonas play important roles in environmental systems and are utilized in many biotechnological processes. The genome of this species may provide an important resource for the discovery of novel enzyme activities

Blom, Jochen

Frasson, David

Pothier, Joël F.

Rezzonico, Fabio

Rutz, Dominik

Sievers, Martin

Smits, Theo H. M.

ZHAW digitalcollection

High-Quality Draft Genome Sequence of Pseudomonasreidholzensis Strain CCOS 865TDominik Rutz,a,b David Frasson,b Martin Sievers,b Jochen Blom,c Fabio Rezzonico,a Joël F. Pothier,a Theo H. M. SmitsaaEnvironmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil,SwitzerlandbMicrobiology and Molecular Biology Research Group, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences (ZHAW), Wädenswil, SwitzerlandcBioinformatics and Systems Biology, Justus-Liebig-Universität, Giessen, GermanyABSTRACT We have sequenced and assembled the genome of Pseudomonas reidhol-zensis CCOS 865T, which was isolated in 2014 from forest soil. Members of the genusPseudomonas play important roles in environmental systems and are utilized inmany biotechnological processes. The genome of this species may provide an im-portant resource for the discovery of novel enzyme activities.Bacteria in the genus Pseudomonas are some of the most ecologically important andgenetically diverse organisms, and Pseudomonas strains can be isolated from avariety of environmental locations and contexts (1). They are involved in degradation,element cycling, and recycling of biogenic and xenobiotic compounds (2). Based on theenzymatic systems involved in the degradation of aromatic compounds originatingfrom lignin biodegradation (3), pseudomonads have been used in catalytic processesfor the biosynthesis of novel ﬁne chemicals (4). Pseudomonas reidholzensis CCOS 865Tis a newly identiﬁed species within the Pseudomonas putida group and was isolated in2014 from forest soil in Switzerland (5). Here, we report the draft genome sequence ofthe potential new biocatalyst Pseudomonas reidholzensis CCOS 865T.Genomic DNA of P. reidholzensis CCOS 865T, grown overnight at 28°C in LB medium,was isolated using the NucleoSpin tissue kit (Macherey-Nagel, Düren, Germany) andfragmented using the Covaris E220 ultrasonicator (average target size, 550 bp). Librarypreparation was performed using the Illumina NeoPrep library system, according to themanufacturer’s instructions. Genome sequencing was performed at the Zurich Univer-sity of Applied Sciences (ZHAW) using 300-bp paired-end reads and a 550-bp insertlibrary on an Illumina MiSeq instrument (5, 6). For the assembly process, a total of1,731,754 reads were generated. The SeqMan NGen software 12.1.0 (DNAStar, Madison,WI) was used with standard settings for automatic assembly (5). After further assembly,the ﬁnal draft genome sequence has a total of 45 contigs, with an N50 value of261,911 bp, a length of 6,163,129 bp, and a GC content of 64.09%. The genomewas annotated in GenDB (7), while EDGAR version 2.3 (8) was used for comparativegenomics against related pseudomonads.We conﬁrmed the species delineation against other species of the P. putidagroup by calculating the genome-to-genome distance (GGDC; version 2.1) values(9) and the average nucleotide identities based on BLAST (ANIb) with JSpeciesWSversion 3.0.20 (10). An average ANIb of 82.92%  0.37% and GGDC of 28.9%  0.8%were obtained with Pseudomonas guariconensis LMG 27394T (GenBank accessionnumber FMYX00000000), Pseudomonas plecoglossicida NBRC 103162T (GenBank acces-sion number BBIV00000000), and Pseudomonas sp. strain GM84 (GenBank accessionnumber AKJC00000000). Based on these results, P. reidholzensis CCOS 865T differs fromother members of the P. putida group at the genome level. The ﬁrst comparativeCitation Rutz D, Frasson D, Sievers M, Blom J,Rezzonico F, Pothier JF, Smits THM. 2019. High-quality draft genome sequence ofPseudomonas reidholzensis strain CCOS 865T.Microbiol Resour Announc 8:e01502-18.https://doi.org/10.1128/MRA.01502-18.Editor Jason E. Stajich, University of California,RiversideCopyright © 2019 Rutz et al. This is an open-access article distributed under the terms ofthe Creative Commons Attribution 4.0International license.Address correspondence to Joël F. Pothier,joel.pothier@zhaw.ch.Received 1 November 2018Accepted 12 December 2018Published 17 January 2019GENOME SEQUENCEScrossmVolume 8 Issue 3 e01502-18 mra.asm.org 1 on January 17, 2019 by guesthttp://mra.asm.org/Downloaded from genome analysis of P. reidholzensis CCOS 865T revealed several gene clusters for thedegradation of aromatic compounds, such as genes for mandelic acid, vanillin, or gallicacid (11–13), which are similar to those found in other Pseudomonas species.Data availability. The draft genome sequence of P. reidholzensis CCOS 865T wasdeposited at DDBJ/EMBL/GenBank under BioProject number PRJEB28254 and theaccession number UNOZ00000000. The version described in this paper is versionUNOZ01000000. Raw sequence reads (Illumina) have been deposited at EMBL underthe accession number ERR2814816.ACKNOWLEDGMENTThis study was supported by the Department of Life Sciences and Facility Manage-ment of the Zurich University of Applied Sciences (ZHAW) in Wädenswil, Switzerland.REFERENCES1. Kiil K, Binnewies TT, Willenbrock H, Hansen SK, Yang L, Jelsbak L, UsseryDW, Friis C. 2008. Comparative genomics of Pseudomonas, p 1–24. InRehm BHA (ed), Pseudomonas: model organism, pathogen, cell factory.Wiley-VCH, Weinheim, Germany.2. Timmis KN. 2002. Pseudomonas putida: a cosmopolitan opportunist parexcellence. Environ Microbiol 4:779–781. https://doi.org/10.1046/j.1462-2920.2002.00365.x.3. Bugg TD, Ahmad M, Hardiman EM, Singh R. 2011. The emerging role forbacteria in lignin degradation and bio-product formation. Curr OpinBiotechnol 22:394–400. https://doi.org/10.1016/j.copbio.2010.10.009.4. Poblete-Castro I, Becker J, Dohnt K, dos Santos VM, Wittmann C. 2012.Industrial biotechnology of Pseudomonas putida and related species. ApplMicrobiol Biotechnol 93:2279–2290. https://doi.org/10.1007/s00253-012-3928-0.5. Frasson D, Opoku M, Picozzi T, Torossi T, Balada S, Smits THM, Hilber U.2017. Pseudomonas wadenswilerensis sp. nov. and Pseudomonas reidhol-zensis sp. nov., two new species within the Pseudomonas putida groupisolated from forest soil. Int J Syst Evol Microbiol 67:2853–2861. https://doi.org/10.1099/ijsem.0.002035.6. Rutz D, Frasson D, Sievers M, Blom J, Rezzonico F, Pothier JF, Smits THM.2018. High-quality draft genome sequence of Pseudomonas wadenswil-erensis CCOS 864T. Microbiol Resour Announc 7:e01059-18. https://doi.org/10.1128/MRA.01059-18.7. Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, KalinowskiJ, Linke B, Rupp O, Giegerich R, Pühler A. 2003. GenDB–an open sourcegenome annotation system for prokaryote genomes. Nucleic Acids Res31:2187–2195. https://doi.org/10.1093/nar/gkg312.8. Blom J, Kreis J, Spänig S, Juhre T, Bertelli C, Ernst C, Goesmann A. 2016.EDGAR 2.0: an enhanced software platform for comparative gene con-tent analyses. Nucleic Acids Res 44:W22–W28. https://doi.org/10.1093/nar/gkw255.9. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. 2013. Genome sequence-based species delimitation with conﬁdence intervals and improved dis-tance functions. BMC Bioinformatics 14:60. https://doi.org/10.1186/1471-2105-14-60.10. Richter M, Rosselló-Móra R, Glöckner FO, Peplies J. 2016. JSpeciesWS: aWeb server for prokaryotic species circumscription based on pairwisegenome comparison. Bioinformatics 32:929–931. https://doi.org/10.1093/bioinformatics/btv681.11. Tsou AY, Ransom SC, Gerlt JA, Buechter DD, Babbitt PC, Kenyon GL.1990. Mandelate pathway of Pseudomonas putida: sequence relation-ships involving mandelate racemase, (S)-mandelate dehydrogenase, andbenzoylformate decarboxylase and expression of benzoylformate decar-boxylase in Escherichia coli. Biochemistry 29:9856–9862. https://doi.org/10.1021/bi00494a015.12. Priefert H, Rabenhorst J, Steinbüchel A. 1997. Molecular characterizationof genes of Pseudomonas sp. strain HR199 involved in bioconversion ofvanillin to protocatechuate. J Bacteriol 179:2595–2607. https://doi.org/10.1128/jb.179.8.2595-2607.1997.13. Nogales J, Canales Á, Jiménez-Barbero J, Serra B, Pingarrón JM, García JL,Díaz E. 2011. Unravelling the gallic acid degradation pathway in bacteria:the gal cluster from Pseudomonas putida: aerobic gallic acid degrada-tion. Mol Microbiol 79:359–374. https://doi.org/10.1111/j.1365-2958.2010.07448.x.Rutz et al.Volume 8 Issue 3 e01502-18 mra.asm.org 2 on January 17, 2019 by guesthttp://mra.asm.org/Downloaded from 

High-quality draft genome sequence of Pseudomonas reidholzensis strain CCOS 865T

https://digitalcollection.zhaw.ch/bitstream/11475/15031/1/65_RutzMicrobiolResourAnnounc2019.pdf

High-quality draft genome sequence of Pseudomonas reidholzensis strain CCOS 865T

Abstract

Similar works

Full text

Available Versions

ZHAW digitalcollection