Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads.

De novo microbial genome sequencing reached a turning point with third-generation sequencing (TGS) platforms, and several microbial genomes have been improved by TGS long reads. Bacillus subtilis natto is closely related to the laboratory standard strain B. subtilis Marburg 168, and it has a functio...

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Autores principales:	Mayumi Kamada, Sumitaka Hase, Kengo Sato, Atsushi Toyoda, Asao Fujiyama, Yasubumi Sakakibara
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6b7c8ddc80c94015bb21faad932ba8ca
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spelling	oai:doaj.org-article:6b7c8ddc80c94015bb21faad932ba8ca2021-11-25T05:56:17ZWhole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads.1932-620310.1371/journal.pone.0109999https://doaj.org/article/6b7c8ddc80c94015bb21faad932ba8ca2014-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0109999https://doaj.org/toc/1932-6203De novo microbial genome sequencing reached a turning point with third-generation sequencing (TGS) platforms, and several microbial genomes have been improved by TGS long reads. Bacillus subtilis natto is closely related to the laboratory standard strain B. subtilis Marburg 168, and it has a function in the production of the traditional Japanese fermented food "natto." The B. subtilis natto BEST195 genome was previously sequenced with short reads, but it included some incomplete regions. We resequenced the BEST195 genome using a PacBio RS sequencer, and we successfully obtained a complete genome sequence from one scaffold without any gaps, and we also applied Illumina MiSeq short reads to enhance quality. Compared with the previous BEST195 draft genome and Marburg 168 genome, we found that incomplete regions in the previous genome sequence were attributed to GC-bias and repetitive sequences, and we also identified some novel genes that are found only in the new genome.Mayumi KamadaSumitaka HaseKengo SatoAtsushi ToyodaAsao FujiyamaYasubumi SakakibaraPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 10, p e109999 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Mayumi Kamada Sumitaka Hase Kengo Sato Atsushi Toyoda Asao Fujiyama Yasubumi Sakakibara Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads.
description	De novo microbial genome sequencing reached a turning point with third-generation sequencing (TGS) platforms, and several microbial genomes have been improved by TGS long reads. Bacillus subtilis natto is closely related to the laboratory standard strain B. subtilis Marburg 168, and it has a function in the production of the traditional Japanese fermented food "natto." The B. subtilis natto BEST195 genome was previously sequenced with short reads, but it included some incomplete regions. We resequenced the BEST195 genome using a PacBio RS sequencer, and we successfully obtained a complete genome sequence from one scaffold without any gaps, and we also applied Illumina MiSeq short reads to enhance quality. Compared with the previous BEST195 draft genome and Marburg 168 genome, we found that incomplete regions in the previous genome sequence were attributed to GC-bias and repetitive sequences, and we also identified some novel genes that are found only in the new genome.
format	article
author	Mayumi Kamada Sumitaka Hase Kengo Sato Atsushi Toyoda Asao Fujiyama Yasubumi Sakakibara
author_facet	Mayumi Kamada Sumitaka Hase Kengo Sato Atsushi Toyoda Asao Fujiyama Yasubumi Sakakibara
author_sort	Mayumi Kamada
title	Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads.
title_short	Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads.
title_full	Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads.
title_fullStr	Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads.
title_full_unstemmed	Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads.
title_sort	whole genome complete resequencing of bacillus subtilis natto by combining long reads with high-quality short reads.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/6b7c8ddc80c94015bb21faad932ba8ca
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Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads.

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