Pacbio sequencing of copper-tolerant Xanthomonas citri reveals presence of a chimeric plasmid structure and provides insights into reassortment and shuffling of transcription activator-like effectors among X. citri strains

BMC Genomics
Alberto M GochezNeha Potnis

Abstract

Xanthomonas citri, a causal agent of citrus canker, has been a well-studied model system due to recent availability of whole genome sequences of multiple strains from different geographical regions. Major limitations in our understanding of the evolution of pathogenicity factors in X. citri strains sequenced by short-read sequencing methods have been tracking plasmid reshuffling among strains due to inability to accurately assign reads to plasmids, and analyzing repeat regions among strains. X. citri harbors major pathogenicity determinants, including variable DNA-binding repeat region containing Transcription Activator-like Effectors (TALEs) on plasmids. The long-read sequencing method, PacBio, has allowed the ability to obtain complete and accurate sequences of TALEs in xanthomonads. We recently sequenced Xanthomonas citri str. Xc-03-1638-1-1, a copper tolerant A group strain isolated from grapefruit in 2003 from Argentina using PacBio RS II chemistry. We analyzed plasmid profiles, copy number and location of TALEs in complete genome sequences of X. citri strains. We utilized the power of long reads obtained by PacBio sequencing to enable assembly of a complete genome sequence of strain Xc-03-1638-1-1, including sequences of ...Continue Reading

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Citations

Apr 21, 2018·The New Phytologist·Nicolas DenancéLaurent D Noël
Apr 12, 2019·Briefings in Bioinformatics·Saman ZeeshanZeeshan Ahmed
Oct 30, 2019·Nature Biotechnology·Ricardo OlivaBing Yang
Apr 30, 2020·Nature Reviews. Microbiology·Sujan TimilsinaJeffrey B Jones
Jul 15, 2020·Science China. Life Sciences·Jiao XueXiuying He
Jun 12, 2018·Frontiers in Microbiology·Paula M M MartinsAlessandra A De Souza
Jan 5, 2020·Applied Microbiology and Biotechnology·Jyutika M RajwadeK M Paknikar
Oct 12, 2018·International Journal of Molecular Sciences·Ana Carolina NazaréLuis Octavio Regasini
Jul 7, 2021·Molecular Plant Pathology·Carlos A Zárate-ChavesBoris Szurek

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Datasets Mentioned

BETA
WP001052942
WP005931726
WP080767064
SRP126789

Methods Mentioned

BETA
electrophoresis
PCR

Software Mentioned

MiSeq
prokka
blasR aligner
Canu
CGView
Blastn
TALE
Quantity One
caller
Mauve

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