Iodixanol density gradients as an effective phytoplasma enrichment approach to improve genome sequencing.
16SrII phytoplasma
OptiprepTM
density gradient centrifugation
high-throughput sequencing
host DNA contamination
natural host
phytopathogen
unculturable bacteria
Journal
Frontiers in microbiology
ISSN: 1664-302X
Titre abrégé: Front Microbiol
Pays: Switzerland
ID NLM: 101548977
Informations de publication
Date de publication:
2022
2022
Historique:
received:
06
05
2022
accepted:
29
06
2022
entrez:
29
8
2022
pubmed:
30
8
2022
medline:
30
8
2022
Statut:
epublish
Résumé
Obtaining complete phytoplasma genomes is difficult due to the lack of a culture system for these bacteria. To improve genome assembly, a non-ionic, low- and iso-osmotic iodixanol (Optiprep™) density gradient centrifugation method was developed to enrich for phytoplasma cells and deplete plant host tissues prior to deoxyribonucleic acid (DNA) extraction and high-throughput sequencing (HTS). After density gradient enrichment, potato infected with a '
Identifiants
pubmed: 36033837
doi: 10.3389/fmicb.2022.937648
pmc: PMC9411968
doi:
Types de publication
Journal Article
Langues
eng
Pagination
937648Informations de copyright
Copyright © 2022 Rodrigues Jardim, Tran-Nguyen, Gambley, Rodoni and Constable.
Déclaration de conflit d'intérêts
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Références
Nat Commun. 2018 Nov 30;9(1):5114
pubmed: 30504855
mBio. 2020 Jan 14;11(1):
pubmed: 31937639
Genome Biol Evol. 2018 Jun 1;10(6):1526-1532
pubmed: 29860283
Curr Protoc Bioinformatics. 2020 Jun;70(1):e102
pubmed: 32559359
Int J Syst Evol Microbiol. 2021 Jan;71(1):
pubmed: 33289625
Bioinformatics. 2020 Feb 15;36(4):1303-1304
pubmed: 31553437
Nat Genet. 2004 Jan;36(1):27-9
pubmed: 14661021
Anal Biochem. 1994 Aug 1;220(2):360-6
pubmed: 7978279
Annu Rev Phytopathol. 2011;49:175-95
pubmed: 21838574
Microbiology (Reading). 2000 Apr;146 ( Pt 4):893-902
pubmed: 10784048
Bioinformatics. 2016 Apr 1;32(7):1088-90
pubmed: 26614127
Int J Syst Evol Microbiol. 2022 Apr;72(4):
pubmed: 35471141
Methods Mol Biol. 2013;938:371-9
pubmed: 22987431
Genome Announc. 2014 Sep 18;2(5):
pubmed: 25291766
BMC Genomics. 2013 Aug 02;14:529
pubmed: 23915186
Cell Death Differ. 2022 Feb;29(2):451-464
pubmed: 34511600
BMC Genomics. 2012 Jan 03;13:1
pubmed: 22214261
Clin Chem. 2009 Apr;55(4):611-22
pubmed: 19246619
Mol Plant Microbe Interact. 2004 Nov;17(11):1175-84
pubmed: 15553243
Syst Appl Microbiol. 2013 Dec;36(8):539-48
pubmed: 24034865
BMC Genomics. 2008 Jun 26;9:306
pubmed: 18582369
Appl Environ Microbiol. 2003 Oct;69(10):6268-71
pubmed: 14532090
Methods Mol Biol. 2013;938:381-93
pubmed: 22987432
Bioinformatics. 2018 Sep 1;34(17):i884-i890
pubmed: 30423086
J Biomol Tech. 2007 Apr;18(2):104-12
pubmed: 17496222
Front Microbiol. 2022 Feb 28;13:773608
pubmed: 35300489
Int J Syst Evol Microbiol. 2021 Jan;71(1):
pubmed: 33464199
Front Microbiol. 2019 Jun 12;10:1277
pubmed: 31244801
BMC Genomics. 2018 Sep 19;19(1):689
pubmed: 30231900
Microbiology (Reading). 2008 May;154(Pt 5):1454-1463
pubmed: 18451054
Front Microbiol. 2020 Jul 10;11:1531
pubmed: 32754131
Science. 1987 Oct 9;238(4824):197-200
pubmed: 17800459
Genome Announc. 2018 May 17;6(20):
pubmed: 29773636
J Microbiol Methods. 2016 Sep;128:20-23
pubmed: 27378442
Genome Res. 2017 May;27(5):824-834
pubmed: 28298430
J Bacteriol. 2006 May;188(10):3682-96
pubmed: 16672622
Anal Biochem. 1994 Aug 1;220(2):367-73
pubmed: 7978280
Front Microbiol. 2021 Nov 11;12:766221
pubmed: 34858377
PLoS One. 2013 Apr 23;8(4):e62770
pubmed: 23626855
Nucleic Acids Res. 2004 Jan 02;32(1):11-6
pubmed: 14704338
Int J Syst Evol Microbiol. 2021 Jan;71(1):
pubmed: 33289626
Syst Appl Microbiol. 2019 Mar;42(2):117-127
pubmed: 30455068
Phytopathology. 1999 Sep;89(9):805-10
pubmed: 18944709
Microbiol Resour Announc. 2019 Apr 25;8(17):
pubmed: 31023813
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
pubmed: 9254694
BMC Bioinformatics. 2010 Mar 08;11:119
pubmed: 20211023
PLoS One. 2014 May 05;9(5):e96436
pubmed: 24798075
Methods Mol Biol. 2013;966:359-66
pubmed: 23299746
Genome Announc. 2016 Apr 21;4(2):
pubmed: 27103722
Genome Announc. 2015 Nov 25;3(6):
pubmed: 26607900
J Bacteriol. 2008 Jun;190(11):3979-91
pubmed: 18359806
Genome Biol. 2019 Nov 28;20(1):257
pubmed: 31779668
J Virol Methods. 1998 Mar;71(1):45-50
pubmed: 9628220
Bioinformatics. 2014 Jul 15;30(14):2068-9
pubmed: 24642063
Ann Bot. 2017 Mar 1;119(5):869-884
pubmed: 28069632
Nucleic Acids Res. 2007;35(9):3100-8
pubmed: 17452365