Literature DB >> 36129292

Chromosome and Plasmid Sequences of Pantoea sp. Strain SOD02 Isolated from an Urban Freshwater Stream.

Ibrahim Abaherah1, Geraldine Almonte1, Kathryn Donohue1, Daniel Furey1, Kathleen Garvey1, Jacqueline Joyal1, Devyn Luden1, Kathryn Mulvey1, Sean O'Donnell1, Nina Pitre1, Aura Rexach1, Kiley Sheehan1, Laura E Williams1.   

Abstract

After isolating Pantoea sp. strain SOD02 from an urban freshwater stream in Providence, RI, we used PacBio RSII data for de novo assembly and Illumina MiSeq data for polishing. This yielded complete circular sequences for a 4,227,027-bp chromosome with 54.7% GC and a 926,844-bp plasmid with 54.0% GC.

Entities:  

Year:  2022        PMID： 36129292      PMCID： PMC9583809          DOI： 10.1128/mra.00822-22

Source DB:  PubMed          Journal:  Microbiol Resour Announc        ISSN： 2576-098X


  12 in total

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Journal:  Trends Genet       Date:  2000-06       Impact factor: 11.639

2.  Basic local alignment search tool.

Authors:  S F Altschul; W Gish; W Miller; E W Myers; D J Lipman
Journal:  J Mol Biol       Date:  1990-10-05       Impact factor: 5.469

3.  The MaSuRCA genome assembler.

Authors:  Aleksey V Zimin; Guillaume Marçais; Daniela Puiu; Michael Roberts; Steven L Salzberg; James A Yorke
Journal:  Bioinformatics       Date:  2013-08-29       Impact factor: 6.937

4.  Versatile and open software for comparing large genomes.

Authors:  Stefan Kurtz; Adam Phillippy; Arthur L Delcher; Michael Smoot; Martin Shumway; Corina Antonescu; Steven L Salzberg
Journal:  Genome Biol       Date:  2004-01-30       Impact factor: 13.583

5.  Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.

Authors:  Sergey Koren; Brian P Walenz; Konstantin Berlin; Jason R Miller; Nicholas H Bergman; Adam M Phillippy
Journal:  Genome Res       Date:  2017-03-15       Impact factor: 9.043

6.  TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy.

Authors:  Jan P Meier-Kolthoff; Markus Göker
Journal:  Nat Commun       Date:  2019-05-16       Impact factor: 14.919

7.  Variation in genome content and predatory phenotypes between Bdellovibrio sp. NC01 isolated from soil and B. bacteriovorus type strain HD100.

Authors:  Laura E Williams; Nicole Cullen; Joseph A DeGiorgis; Karla J Martinez; Justina Mellone; Molly Oser; Jing Wang; Ying Zhang
Journal:  Microbiology       Date:  2019-10-08       Impact factor: 2.777

8.  Polypolish: Short-read polishing of long-read bacterial genome assemblies.

Authors:  Ryan R Wick; Kathryn E Holt
Journal:  PLoS Comput Biol       Date:  2022-01-24       Impact factor: 4.475

9.  Fast and accurate short read alignment with Burrows-Wheeler transform.

Authors:  Heng Li; Richard Durbin
Journal:  Bioinformatics       Date:  2009-05-18       Impact factor: 6.937

10.  NCBI prokaryotic genome annotation pipeline.

Authors:  Tatiana Tatusova; Michael DiCuccio; Azat Badretdin; Vyacheslav Chetvernin; Eric P Nawrocki; Leonid Zaslavsky; Alexandre Lomsadze; Kim D Pruitt; Mark Borodovsky; James Ostell
Journal:  Nucleic Acids Res       Date:  2016-06-24       Impact factor: 16.971
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