Draft Genome Assembly of Rhodobacter Sphaeroides 2.4.1 Substrain H2 from Nanopore Data

Overview

Journal Microbiol Resour Announc

Publisher American Society for Microbiology

Specialty Microbiology

Date 2020 Jul 18

PMID 32675180

Citations 2

Authors

Robert Maximilian Leidenfrost

Nadine Wappler

Robbe Wunschiers

Affiliations

Soon will be listed here.

Abstract

is a purple bacterium with complex genomic architecture. Here, a draft genome is reported for strain 2.4.1 substrain H2, which was generated exclusively from Nanopore sequencing data.

Citing Articles

Jorvik: A membrane-containing phage that will likely found a new family within Vinavirales.

Bardy P, MacDonald C, Pantucek R, Antson A, Fogg P iScience. 2023; 26(11):108104.

PMID: 37867962 PMC: 10589892. DOI: 10.1016/j.isci.2023.108104.

Whole-genome sequence of strain W018, isolated from L. seeds, obtained using nanopore sequencing.

Chebotar V, Gancheva M, Chizhevskaya E, Keleinikova O, Baganova M, Zaplatkin A Microbiol Resour Announc. 2023; 12(10):e0068723.

PMID: 37747250 PMC: 10586160. DOI: 10.1128/MRA.00687-23.

References

VAN NIEL C . THE CULTURE, GENERAL PHYSIOLOGY, MORPHOLOGY, AND CLASSIFICATION OF THE NON-SULFUR PURPLE AND BROWN BACTERIA. Bacteriol Rev. 1944; 8(1):1-118. PMC: 440875. DOI: 10.1128/br.8.1.1-118.1944. View

Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki E, Zaslavsky L . NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 2016; 44(14):6614-24. PMC: 5001611. DOI: 10.1093/nar/gkw569. View

Reyes F, Gavira M, Castillo F, Moreno-Vivian C . Periplasmic nitrate-reducing system of the phototrophic bacterium Rhodobacter sphaeroides DSM 158: transcriptional and mutational analysis of the napKEFDABC gene cluster. Biochem J. 1998; 331 ( Pt 3):897-904. PMC: 1219433. DOI: 10.1042/bj3310897. View

Ribeiro F, Przybylski D, Yin S, Sharpe T, Gnerre S, Abouelleil A . Finished bacterial genomes from shotgun sequence data. Genome Res. 2012; 22(11):2270-7. PMC: 3483556. DOI: 10.1101/gr.141515.112. View

Haft D, DiCuccio M, Badretdin A, Brover V, Chetvernin V, ONeill K . RefSeq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res. 2017; 46(D1):D851-D860. PMC: 5753331. DOI: 10.1093/nar/gkx1068. View

Fornari C, Watkins M, Kaplan S . Plasmid distribution and analyses in Rhodopseudomonas sphaeroides. Plasmid. 1984; 11(1):39-47. DOI: 10.1016/0147-619x(84)90005-2. View

MacCallum I, Przybylski D, Gnerre S, Burton J, Shlyakhter I, Gnirke A . ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads. Genome Biol. 2009; 10(10):R103. PMC: 2784318. DOI: 10.1186/gb-2009-10-10-r103. View

Choudhary M, Zanhua X, Fu Y, Kaplan S . Genome analyses of three strains of Rhodobacter sphaeroides: evidence of rapid evolution of chromosome II. J Bacteriol. 2006; 189(5):1914-21. PMC: 1855717. DOI: 10.1128/JB.01498-06. View

De Coster W, DHert S, Schultz D, Cruts M, Van Broeckhoven C . NanoPack: visualizing and processing long-read sequencing data. Bioinformatics. 2018; 34(15):2666-2669. PMC: 6061794. DOI: 10.1093/bioinformatics/bty149. View

10.

MacKenzie C, Choudhary M, Larimer F, Predki P, Stilwagen S, Armitage J . The home stretch, a first analysis of the nearly completed genome of Rhodobacter sphaeroides 2.4.1. Photosynth Res. 2005; 70(1):19-41. DOI: 10.1023/A:1013831823701. View

11.

Desper R, Gascuel O . Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. J Comput Biol. 2002; 9(5):687-705. DOI: 10.1089/106652702761034136. View

12.

Loman N, Quick J, Simpson J . A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat Methods. 2015; 12(8):733-5. DOI: 10.1038/nmeth.3444. View

13.

Krumsiek J, Arnold R, Rattei T . Gepard: a rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics. 2007; 23(8):1026-8. DOI: 10.1093/bioinformatics/btm039. View

14.

Porter S, Wilkinson D, Byles E, Wadhams G, Taylor S, Saunders N . Genome sequence of Rhodobacter sphaeroides Strain WS8N. J Bacteriol. 2011; 193(15):4027-8. PMC: 3147498. DOI: 10.1128/JB.05257-11. View

15.

Li H . Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018; 34(18):3094-3100. PMC: 6137996. DOI: 10.1093/bioinformatics/bty191. View

16.

Taylor T, Volkening J, DeJesus E, Simmons M, Dimitrov K, Tillman G . Rapid, multiplexed, whole genome and plasmid sequencing of foodborne pathogens using long-read nanopore technology. Sci Rep. 2019; 9(1):16350. PMC: 6841976. DOI: 10.1038/s41598-019-52424-x. View

17.

Darling A, Mau B, Perna N . progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One. 2010; 5(6):e11147. PMC: 2892488. DOI: 10.1371/journal.pone.0011147. View

18.

Krujatz F, Hartel P, Helbig K, Haufe N, Thierfelder S, Bley T . Hydrogen production by Rhodobacter sphaeroides DSM 158 under intense irradiation. Bioresour Technol. 2014; 175:82-90. DOI: 10.1016/j.biortech.2014.10.061. View

19.

Vaser R, Sovic I, Nagarajan N, Sikic M . Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 2017; 27(5):737-746. PMC: 5411768. DOI: 10.1101/gr.214270.116. View

20.

Lim S, Kim S, Cha S, Oh Y, Rhee H, Kim M . Complete genome sequence of Rhodobacter sphaeroides KD131. J Bacteriol. 2008; 191(3):1118-9. PMC: 2632106. DOI: 10.1128/JB.01565-08. View