Elucidation of quantitative structural diversity of remarkable rearrangement regions, shufflons, in IncI2 plasmids

Abstract A multiple DNA inversion system, the shufflon, exists in incompatibility (Inc) I1 and I2 plasmids. The shufflon generates variants of the PilV protein, a minor component of the thin pilus. The shufflon is one of the most difficult regions for de novo genome assembly because of its structura...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Tsuyoshi Sekizuka, Michiko Kawanishi, Mamoru Ohnishi, Ayaka Shima, Kengo Kato, Akifumi Yamashita, Mari Matsui, Satowa Suzuki, Makoto Kuroda
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c20d9e9778be4fe88ea1d4940df5d2ca
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:c20d9e9778be4fe88ea1d4940df5d2ca
record_format	dspace
spelling	oai:doaj.org-article:c20d9e9778be4fe88ea1d4940df5d2ca2021-12-02T11:53:02ZElucidation of quantitative structural diversity of remarkable rearrangement regions, shufflons, in IncI2 plasmids10.1038/s41598-017-01082-y2045-2322https://doaj.org/article/c20d9e9778be4fe88ea1d4940df5d2ca2017-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-01082-yhttps://doaj.org/toc/2045-2322Abstract A multiple DNA inversion system, the shufflon, exists in incompatibility (Inc) I1 and I2 plasmids. The shufflon generates variants of the PilV protein, a minor component of the thin pilus. The shufflon is one of the most difficult regions for de novo genome assembly because of its structural diversity even in an isolated bacterial clone. We determined complete genome sequences, including those of IncI2 plasmids carrying mcr-1, of three Escherichia coli strains using single-molecule, real-time (SMRT) sequencing and Illumina sequencing. The sequences assembled using only SMRT sequencing contained misassembled regions in the shufflon. A hybrid analysis using SMRT and Illumina sequencing resolved the misassembled region and revealed that the three IncI2 plasmids, excluding the shufflon region, were highly conserved. Moreover, the abundance ratio of whole-shufflon structures could be determined by quantitative structural variation analysis of the SMRT data, suggesting that a remarkable heterogeneity of whole-shufflon structural variations exists in IncI2 plasmids. These findings indicate that remarkable rearrangement regions should be validated using both long-read and short-read sequencing data and that the structural variation of PilV in the shufflon might be closely related to phenotypic heterogeneity of plasmid-mediated transconjugation involved in horizontal gene transfer even in bacterial clonal populations.Tsuyoshi SekizukaMichiko KawanishiMamoru OhnishiAyaka ShimaKengo KatoAkifumi YamashitaMari MatsuiSatowa SuzukiMakoto KurodaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-10 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Tsuyoshi Sekizuka Michiko Kawanishi Mamoru Ohnishi Ayaka Shima Kengo Kato Akifumi Yamashita Mari Matsui Satowa Suzuki Makoto Kuroda Elucidation of quantitative structural diversity of remarkable rearrangement regions, shufflons, in IncI2 plasmids
description	Abstract A multiple DNA inversion system, the shufflon, exists in incompatibility (Inc) I1 and I2 plasmids. The shufflon generates variants of the PilV protein, a minor component of the thin pilus. The shufflon is one of the most difficult regions for de novo genome assembly because of its structural diversity even in an isolated bacterial clone. We determined complete genome sequences, including those of IncI2 plasmids carrying mcr-1, of three Escherichia coli strains using single-molecule, real-time (SMRT) sequencing and Illumina sequencing. The sequences assembled using only SMRT sequencing contained misassembled regions in the shufflon. A hybrid analysis using SMRT and Illumina sequencing resolved the misassembled region and revealed that the three IncI2 plasmids, excluding the shufflon region, were highly conserved. Moreover, the abundance ratio of whole-shufflon structures could be determined by quantitative structural variation analysis of the SMRT data, suggesting that a remarkable heterogeneity of whole-shufflon structural variations exists in IncI2 plasmids. These findings indicate that remarkable rearrangement regions should be validated using both long-read and short-read sequencing data and that the structural variation of PilV in the shufflon might be closely related to phenotypic heterogeneity of plasmid-mediated transconjugation involved in horizontal gene transfer even in bacterial clonal populations.
format	article
author	Tsuyoshi Sekizuka Michiko Kawanishi Mamoru Ohnishi Ayaka Shima Kengo Kato Akifumi Yamashita Mari Matsui Satowa Suzuki Makoto Kuroda
author_facet	Tsuyoshi Sekizuka Michiko Kawanishi Mamoru Ohnishi Ayaka Shima Kengo Kato Akifumi Yamashita Mari Matsui Satowa Suzuki Makoto Kuroda
author_sort	Tsuyoshi Sekizuka
title	Elucidation of quantitative structural diversity of remarkable rearrangement regions, shufflons, in IncI2 plasmids
title_short	Elucidation of quantitative structural diversity of remarkable rearrangement regions, shufflons, in IncI2 plasmids
title_full	Elucidation of quantitative structural diversity of remarkable rearrangement regions, shufflons, in IncI2 plasmids
title_fullStr	Elucidation of quantitative structural diversity of remarkable rearrangement regions, shufflons, in IncI2 plasmids
title_full_unstemmed	Elucidation of quantitative structural diversity of remarkable rearrangement regions, shufflons, in IncI2 plasmids
title_sort	elucidation of quantitative structural diversity of remarkable rearrangement regions, shufflons, in inci2 plasmids
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/c20d9e9778be4fe88ea1d4940df5d2ca
work_keys_str_mv	AT tsuyoshisekizuka elucidationofquantitativestructuraldiversityofremarkablerearrangementregionsshufflonsininci2plasmids AT michikokawanishi elucidationofquantitativestructuraldiversityofremarkablerearrangementregionsshufflonsininci2plasmids AT mamoruohnishi elucidationofquantitativestructuraldiversityofremarkablerearrangementregionsshufflonsininci2plasmids AT ayakashima elucidationofquantitativestructuraldiversityofremarkablerearrangementregionsshufflonsininci2plasmids AT kengokato elucidationofquantitativestructuraldiversityofremarkablerearrangementregionsshufflonsininci2plasmids AT akifumiyamashita elucidationofquantitativestructuraldiversityofremarkablerearrangementregionsshufflonsininci2plasmids AT marimatsui elucidationofquantitativestructuraldiversityofremarkablerearrangementregionsshufflonsininci2plasmids AT satowasuzuki elucidationofquantitativestructuraldiversityofremarkablerearrangementregionsshufflonsininci2plasmids AT makotokuroda elucidationofquantitativestructuraldiversityofremarkablerearrangementregionsshufflonsininci2plasmids
_version_	1718394890775166976

Elucidation of quantitative structural diversity of remarkable rearrangement regions, shufflons, in IncI2 plasmids

Ejemplares similares