Dataset Information

Sequencing and Annotation of Duggie and Hocus, Two Subcluster B1 Mycobacteriophages.

ABSTRACT: Two mycobacteriophage genomes were newly sequenced and annotated. Duggie and Hocus were discovered, enriched, and isolated from soil using Mycobacterium smegmatis mc2155. The bacteriophages are lytic Siphoviridae and belong to the B1 subcluster. The Hocus and Duggie genomes are highly similar to one another in both nucleotide sequence and gene content.

SUBMITTER: Doyle EL

PROVIDER: S-EPMC7348018 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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Sequencing and Annotation of Duggie and Hocus, Two Subcluster B1 Mycobacteriophages.

Doyle Erin L EL Burke Alexis N AN Coy Samuel J SJ Miller Haley R HR Shatford-Adams Lilly M LM Petersen Reagan M RM Wehrs Kade B KB Bowder Dane M DM

Microbiology resource announcements 20200709 28

Two mycobacteriophage genomes were newly sequenced and annotated. Duggie and Hocus were discovered, enriched, and isolated from soil using <i>Mycobacterium smegmatis</i> mc<sup>2</sup>155. The bacteriophages are lytic Siphoviridae and belong to the B1 subcluster. The Hocus and Duggie genomes are highly similar to one another in both nucleotide sequence and gene content. ...[more]

PMID: 32646900

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Project description:BackgroundAvailability of DNA sequence information is vital for pursuing structural, functional and comparative genomics studies in plastids. Traditionally, the first step in mining the valuable information within a chloroplast genome requires sequencing a chloroplast plasmid library or BAC clones. These activities involve complicated preparatory procedures like chloroplast DNA isolation or identification of the appropriate BAC clones to be sequenced. Rolling circle amplification (RCA) is being used currently to amplify the chloroplast genome from purified chloroplast DNA and the resulting products are sheared and cloned prior to sequencing. Herein we present a universal high-throughput, rapid PCR-based technique to amplify, sequence and assemble plastid genome sequence from diverse species in a short time and at reasonable cost from total plant DNA, using the large inverted repeat region from strawberry and peach as proof of concept. The method exploits the highly conserved coding regions or intergenic regions of plastid genes. Using an informatics approach, chloroplast DNA sequence information from 5 available eudicot plastomes was aligned to identify the most conserved regions. Cognate primer pairs were then designed to generate approximately 1 - 1.2 kb overlapping amplicons from the inverted repeat region in 14 diverse genera.Results100% coverage of the inverted repeat region was obtained from Arabidopsis, tobacco, orange, strawberry, peach, lettuce, tomato and Amaranthus. Over 80% coverage was obtained from distant species, including Ginkgo, loblolly pine and Equisetum. Sequence from the inverted repeat region of strawberry and peach plastome was obtained, annotated and analyzed. Additionally, a polymorphic region identified from gel electrophoresis was sequenced from tomato and Amaranthus. Sequence analysis revealed large deletions in these species relative to tobacco plastome thus exhibiting the utility of this method for structural and comparative genomics studies.ConclusionThis simple, inexpensive method now allows immediate access to plastid sequence, increasing experimental throughput and serving generally as a universal platform for plastid genome characterization. The method applies well to whole genome studies and speeds assessment of variability across species, making it a useful tool in plastid structural genomics.

Dataset Information

Sequencing and Annotation of Duggie and Hocus, Two Subcluster B1 Mycobacteriophages.

Publications

Sequencing and Annotation of Duggie and Hocus, Two Subcluster B1 Mycobacteriophages.

Similar Datasets

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