Hybrid de novo Genome Assembly of Erwinia sp. E602 and Bioinformatic Analysis Characterized a New Plasmid-Borne lac Operon Under Positive Selection

Our previous study identified a new β-galactosidase in Erwinia sp. E602. To further understand the lactose metabolism in this strain, de novo genome assembly was conducted by using a strategy combining Illumina and PacBio sequencing technology. The whole genome of Erwinia sp. E602 includes a 4.8 Mb...

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Autores principales:	Yu Xia, Zhi-Yuan Wei, Rui He, Jia-Huan Li, Zhi-Xin Wang, Jun-Da Huo, Jian-Huan Chen
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	Erwinia hybrid sequencing genome assembly lac operon bioinformatic analysis Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/7c8bb7e6774d45849b0ba41ccf8b3d99
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spelling	oai:doaj.org-article:7c8bb7e6774d45849b0ba41ccf8b3d992021-11-11T10:10:06ZHybrid de novo Genome Assembly of Erwinia sp. E602 and Bioinformatic Analysis Characterized a New Plasmid-Borne lac Operon Under Positive Selection1664-302X10.3389/fmicb.2021.783195https://doaj.org/article/7c8bb7e6774d45849b0ba41ccf8b3d992021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fmicb.2021.783195/fullhttps://doaj.org/toc/1664-302XOur previous study identified a new β-galactosidase in Erwinia sp. E602. To further understand the lactose metabolism in this strain, de novo genome assembly was conducted by using a strategy combining Illumina and PacBio sequencing technology. The whole genome of Erwinia sp. E602 includes a 4.8 Mb chromosome and a 326 kb large plasmid. A total of 4,739 genes, including 4,543 protein-coding genes, 25 rRNAs, 82 tRNAs and 7 other ncRNAs genes were annotated. The plasmid was the largest one characterized in genus Erwinia by far, and it contained a number of genes and pathways responsible for lactose metabolism and regulation. Moreover, a new plasmid-borne lac operon that lacked a typical β-galactoside transacetylase (lacA) gene was identified in the strain. Phylogenetic analysis showed that the genes lacY and lacZ in the operon were under positive selection, indicating the adaptation of lactose metabolism to the environment in Erwinia sp. E602. Our current study demonstrated that the hybrid de novo genome assembly using Illumina and PacBio sequencing technologies, as well as the metabolic pathway analysis, provided a useful strategy for better understanding of the evolution of undiscovered microbial species or strains.Yu XiaYu XiaYu XiaZhi-Yuan WeiRui HeRui HeRui HeJia-Huan LiZhi-Xin WangJun-Da HuoJian-Huan ChenFrontiers Media S.A.articleErwiniahybrid sequencinggenome assemblylac operonbioinformatic analysisMicrobiologyQR1-502ENFrontiers in Microbiology, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Erwinia hybrid sequencing genome assembly lac operon bioinformatic analysis Microbiology QR1-502
spellingShingle	Erwinia hybrid sequencing genome assembly lac operon bioinformatic analysis Microbiology QR1-502 Yu Xia Yu Xia Yu Xia Zhi-Yuan Wei Rui He Rui He Rui He Jia-Huan Li Zhi-Xin Wang Jun-Da Huo Jian-Huan Chen Hybrid de novo Genome Assembly of Erwinia sp. E602 and Bioinformatic Analysis Characterized a New Plasmid-Borne lac Operon Under Positive Selection
description	Our previous study identified a new β-galactosidase in Erwinia sp. E602. To further understand the lactose metabolism in this strain, de novo genome assembly was conducted by using a strategy combining Illumina and PacBio sequencing technology. The whole genome of Erwinia sp. E602 includes a 4.8 Mb chromosome and a 326 kb large plasmid. A total of 4,739 genes, including 4,543 protein-coding genes, 25 rRNAs, 82 tRNAs and 7 other ncRNAs genes were annotated. The plasmid was the largest one characterized in genus Erwinia by far, and it contained a number of genes and pathways responsible for lactose metabolism and regulation. Moreover, a new plasmid-borne lac operon that lacked a typical β-galactoside transacetylase (lacA) gene was identified in the strain. Phylogenetic analysis showed that the genes lacY and lacZ in the operon were under positive selection, indicating the adaptation of lactose metabolism to the environment in Erwinia sp. E602. Our current study demonstrated that the hybrid de novo genome assembly using Illumina and PacBio sequencing technologies, as well as the metabolic pathway analysis, provided a useful strategy for better understanding of the evolution of undiscovered microbial species or strains.
format	article
author	Yu Xia Yu Xia Yu Xia Zhi-Yuan Wei Rui He Rui He Rui He Jia-Huan Li Zhi-Xin Wang Jun-Da Huo Jian-Huan Chen
author_facet	Yu Xia Yu Xia Yu Xia Zhi-Yuan Wei Rui He Rui He Rui He Jia-Huan Li Zhi-Xin Wang Jun-Da Huo Jian-Huan Chen
author_sort	Yu Xia
title	Hybrid de novo Genome Assembly of Erwinia sp. E602 and Bioinformatic Analysis Characterized a New Plasmid-Borne lac Operon Under Positive Selection
title_short	Hybrid de novo Genome Assembly of Erwinia sp. E602 and Bioinformatic Analysis Characterized a New Plasmid-Borne lac Operon Under Positive Selection
title_full	Hybrid de novo Genome Assembly of Erwinia sp. E602 and Bioinformatic Analysis Characterized a New Plasmid-Borne lac Operon Under Positive Selection
title_fullStr	Hybrid de novo Genome Assembly of Erwinia sp. E602 and Bioinformatic Analysis Characterized a New Plasmid-Borne lac Operon Under Positive Selection
title_full_unstemmed	Hybrid de novo Genome Assembly of Erwinia sp. E602 and Bioinformatic Analysis Characterized a New Plasmid-Borne lac Operon Under Positive Selection
title_sort	hybrid de novo genome assembly of erwinia sp. e602 and bioinformatic analysis characterized a new plasmid-borne lac operon under positive selection
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/7c8bb7e6774d45849b0ba41ccf8b3d99
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Hybrid de novo Genome Assembly of Erwinia sp. E602 and Bioinformatic Analysis Characterized a New Plasmid-Borne lac Operon Under Positive Selection

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