Genome Sequence of Ensifer sp., Isolated from pokeweed and acid mine drainage

Introduction

A novel Ensifer species, closely related to Ensifer adhaerens, was collected from pokeweed and acid mine drainage.

The publication by Rosie Maloney, Spencer Leinbach, and Cole Milholen can be found here: https://docs.google.com/document/d/18KPwR29_H5EUOLV4kd-9gq9hCv5dsWLJlIWGek7gv6Y/edit?usp=sharing

Background and Experimental Methods

Microbes found by researchers Dr. Jason Whitham and Dr. Amy Grunden (NC State University Plant and Microbial Biology Department) were being studied. These microbes were isolated from their environmental source, pokeweed and acid mine drainage, by performing serial dilutions. This process allowed the microbes of interest to be separated from soil particles. Glycerol was added to the isolates for stabilization, allowing them to be stored at -80 °C. Samples were then plated on Tryptic Soy Broth (TSB) plates at room temperature by Brenna Bilodeau (an undergraduate working under Dr. Claire Gordy in the NCSU Department of Biological Sciences). First, the mixed culture was plated, and then individual pure cultures were streaked on separate plates. Bilodeau and Dr. Gordy used the isolated microbe cultures and cultured individual microbes by putting them in liquid cultures with TSA and putting them in a shaking incubator at 25°C. These samples were grown with the intention to perform cell lysis (cell death) in order to isolate strands of DNA. After the DNA was collected, it was tested for purity and quantity using a Nanodrop and a Tapestation. The isolated DNA was then run through the NanoPore MinION sequencer to get the whole genomic sequence. Taking the data from the sequencer, Dr. Goller then used the GLC Genomics Workbench to assemble the genomic data. Dr. Carlos Goller is a part of North Carolina State’s Biotechnology program. He prepared the DNA sample of our microbial genus Beijerinckia, and then used the NanoPore MinIon sequencer to sequence its entire genome. In order for this data to be useful, Dr. Goller then had to use CLC Genomic Workbench to assemble the data previously produced. By examining the genome, we will identify potential genes with applicability to the e-waste problem.

Import

Note to authors

Reads or assemblies should be imported through the staging area. See the upload and download guide on the KBase documentation site for details instructions.

from biokbase.narrative.jobs.appmanager import AppManager
AppManager().run_app_bulk(
    [{
        "app_id": "kb_uploadmethods/import_fasta_as_assembly_from_staging",
        "tag": "release",
        "version": "1dbd08a56befada8f204b4d1db5a872796cd45a5",
        "params": [{
            "staging_file_subdir_path": "Barcode05.fasta",
            "assembly_name": "Barcode05.fasta_assembly",
            "type": "draft isolate",
            "min_contig_length": 10000
        }]
    }],
    cell_id="61e87ea3-aab8-4209-86fa-5356051cf780",
    run_id="d9da3558-3ae8-402c-970b-dca0dcfcebc2"
)

QC, Assembly, and Annotation

Author Checklist

Genome GC content and total size.

Note to authors

The recommended app for quality control is FastQC. There are multiple apps for assembly.

There is no "best" assembler, and assembly tools should be evaluated on a case-by-case basis. You are welcome and encouraged to use multiple apps and compare the results.

Annotation can be performed using Prokka or RAST. Again, comparison of multiple tools is encouraged. For downstream steps such as metabolic modeling, however, RAST-annotated genomes perform better with KBase modeling tools.

Taxonomic Identification

Note to Authors

One common way is to use the GTDB-Tk classify app. We recommend adding a phylogenetic tree using the Insert Genome into SpeciesTree app.

Metabolic Modeling and Flux Balance Analysis (optional)

Note to Authors

Metabolic modeling is not listed on the MRA checklist; however, many MRA authors using KBase have included a metaboic model in their Narrative. If you are new to metabolic modeling, we have tutorials and webinars on the docs site and on YouTube.
If you do not use this section, delete this Markdown cell, and remove it from the table of contents at the top of the Narrative.

References

Note to authors

The KBase static Narrative service automatically generates a list of citations for apps used. If you provide any citations for literature or outside tools within the markdown cells, those should be included here.

Created Object Name	Type	Description
Barcode05.fasta_assembly_DRAM	Genome	Annotated Genome
Ensifer	GenomeSet	Ensifer genome?

Created Object Name	Type	Description
Barcode05.fasta_assembly_DRAM	Genome	Taxonomy and taxon_assignment updated with GTDB
Ensifer	GenomeSet	Taxonomy and taxon_assignment updated with GTDB

Genome Sequence of Ensifer sp., Isolated from pokeweed and acid mine drainage

Introduction

Table of Contents

Background and Experimental Methods

Import

Note to authors

QC, Assembly, and Annotation

Author Checklist

Note to authors

Taxonomic Identification

Note to Authors

Metabolic Modeling and Flux Balance Analysis (optional)

Note to Authors

References

Note to authors

Apps