BIT 295 MRA Genome Announcement Template Narrative - Ensifer - Copy
Lauren Turrentine
Generated April 27, 2022

Ensifer's cool genome

Introduction

For our BIT 295 project we are using Ensifer Bacteria collected by Dr. Jason Whitham and Dr. Amy Grunden at NC State University pokeweed and acid mine drainage. These bacteria were analysed using Nanopore sequencing and this data is used throughout the work. The information gathered by Dr Goller and Dr. Sjogren can be found here: https://docs.google.com/document/d/1xqKYLeBJnFfC5c0DeZtS8vdNo6Oc7u-NgI4FvGJkog4/edit#heading=h.uq3zl9n74m8v

Table of Contents

  1. Background and Experimental Methods
  2. Import and annotation
  3. QC, Assembly, and Annotation
  4. Taxonomic Classification
  5. Metabolic Modeling and Flux Balance Analysis
  6. References
Narrative created by: [Lauren Turrentine and Ankitha Lavu]

Note to Authors

The publication may not be available at the time of the static Narrative creation. This can be added after the fact; please contact engage@kbase.us to update the DOI landing page when this is done.

Background and Experimental Methods

Sample Collection

The sample was collected from an area with acid mine drainage and pokeweed. It was found with 14 other isolates.

Isolation

Each sample was isolated on Trypic Soy Broth dishes.

Genome Sequencing

The Genes were then sequenced using NanoPore sequencing and CLC Cenomics Workbench.

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"
)
Annotate and Distill Assemblies with DRAM
Annotate your assembly with DRAM. Annotations will then be distilled to create an interactive functional summary per assembly.
This app completed without errors in 51m 38s.
Objects
Created Object Name Type Description
Barcode05.fasta_assembly_DRAM Genome Annotated Genome
Ensifer GenomeSet Ensifer genome?
Report
Summary
Here are the results from your DRAM run.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/113838
  • annotations.tsv - DRAM annotations in a tab separate table format
  • genes.fna - Genes as nucleotides predicted by DRAM with brief annotations
  • genes.faa - Genes as amino acids predicted by DRAM with brief annotations
  • genes.gff - GFF file of all DRAM annotations
  • rrnas.tsv - Tab separated table of rRNAs as detected by barrnap
  • trnas.tsv - Tab separated table of tRNAs as detected by tRNAscan-SE
  • genbank.tar.gz - Compressed folder of output genbank files
  • product.tsv - DRAM product in tabular format
  • metabolism_summary.xlsx - DRAM metabolism summary tables
  • genome_stats.tsv - DRAM genome statistics table
Assess Read Quality with FastQC - v0.11.9
A quality control application for high throughput sequence data.
This app is new, and hasn't been started.
No output found.
Barcode05.fasta_assembly
v1 - KBaseGenomeAnnotations.Assembly-5.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/113838
Barcode05.fasta_assembly
v1 - KBaseGenomeAnnotations.Assembly-5.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/113838

QC, Assembly, and Annotation

Author Checklist

We were unable to run the Fast QC after many attempts. The genome was assmebled using RASTtk and Prokka and annotated with both programs. It was found to have between 3 and 4 contigs and 1246 key features. It contains 7,215,895 genes according to Prokka
Annotate Genome/Assembly with RASTtk - v1.073
Annotate or re-annotate genome/assembly using RASTtk (Rapid Annotations using Subsystems Technology toolkit).
This app completed without errors in 26m 39s.
Objects
Created Object Name Type Description
RAST-annotation Genome RAST re-annotated genome
Report
Summary
The RAST algorithm was applied to annotating a genome sequence comprised of 4 contigs containing 7215895 nucleotides. No initial gene calls were provided. Standard gene features were called using: prodigal; glimmer3. A scan was conducted for the following additional feature types: rRNA; tRNA; selenoproteins; pyrrolysoproteins; repeat regions; crispr. The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity. In addition to the remaining original 0 coding features and 0 non-coding features, 8537 new features were called, of which 129 are non-coding. Output genome has the following feature types: Coding gene 8408 Non-coding prophage 5 Non-coding repeat 50 Non-coding rna 74 Overall, the genes have 3519 distinct functions The genes include 3046 genes with a SEED annotation ontology across 1528 distinct SEED functions. The number of distinct functions can exceed the number of genes because some genes have multiple functions.
Links
Annotate Assembly and Re-annotate Genomes with Prokka - v1.14.5
Annotate Assembly and Re-annotate Genomes with Prokka annotation pipeline.
This app completed without errors in 7m 16s.
Objects
Created Object Name Type Description
Prokka-ann Genome Annotated Genome
Summary
Annotated Genome saved to: cgoller:narrative_1649170660833/Prokka-ann Number of genes predicted: 7978 Number of protein coding genes: 7898 Number of genes with non-hypothetical function: 3898 Number of genes with EC-number: 1730 Number of genes with Seed Subsystem Ontology: 0 Average protein length: 255 aa.
Output from Annotate Assembly and Re-annotate Genomes with Prokka - v1.14.5
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/113838

Taxonomic Identification

Ensifer adhaerens

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.

Classify Microbes with GTDB-Tk - v1.7.0
Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB) ver R06-RS202
This app completed without errors in 32m 43s.
Objects
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
Report
Links
Insert Genome Into SpeciesTree - v2.2.0
Add one or more Genomes to a KBase SpeciesTree.
This app completed without errors in 6m 52s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/113838
  • EnsiferTree.newick
  • EnsiferTree-labels.newick
  • EnsiferTree.png
  • EnsiferTree.pdf
Upload File to Staging from Web - v1.0.12
Upload a data file (which may be compressed) from a web URL to your staging area.
This app completed without errors in 2m 27s.
Summary
Uploaded Files: 1 /barcode05.fastq

References


Annotate and Distill Assemblies with DRAM

Annotate Assembly and Re-annotate Genomes with Prokka - v1.14.5

Annotate Genome/Assembly with RASTtk - v1.073

Assess Read Quality with FastQC - v0.11.9

Classify Microbes with GTDB-Tk - v1.7.0

Insert Genome Into SpeciesTree - v2.2.0

Upload File to Staging from Web - v1.0.12

v1 - KBaseGenomeAnnotations.Assembly-5.0

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.

Apps

  1. Annotate and Distill Assemblies with DRAM
    • DRAM source code
    • DRAM documentation
    • DRAM publication
  2. Annotate Assembly and Re-annotate Genomes with Prokka - v1.14.5
    • Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30: 2068 2069. doi:10.1093/bioinformatics/btu153
  3. Annotate Genome/Assembly with RASTtk - v1.073
    • [1] Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics. 2008;9: 75. doi:10.1186/1471-2164-9-75
    • [2] Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2014;42: D206 D214. doi:10.1093/nar/gkt1226
    • [3] Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, et al. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. 2015;5. doi:10.1038/srep08365
    • [4] Kent WJ. BLAT The BLAST-Like Alignment Tool. Genome Res. 2002;12: 656 664. doi:10.1101/gr.229202
    • [5] Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25: 3389-3402. doi:10.1093/nar/25.17.3389
    • [6] Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25: 955 964.
    • [7] Cobucci-Ponzano B, Rossi M, Moracci M. Translational recoding in archaea. Extremophiles. 2012;16: 793 803. doi:10.1007/s00792-012-0482-8
    • [8] Meyer F, Overbeek R, Rodriguez A. FIGfams: yet another set of protein families. Nucleic Acids Res. 2009;37 6643-54. doi:10.1093/nar/gkp698.
    • [9] van Belkum A, Sluijuter M, de Groot R, Verbrugh H, Hermans PW. Novel BOX repeat PCR assay for high-resolution typing of Streptococcus pneumoniae strains. J Clin Microbiol. 1996;34: 1176 1179.
    • [10] Croucher NJ, Vernikos GS, Parkhill J, Bentley SD. Identification, variation and transcription of pneumococcal repeat sequences. BMC Genomics. 2011;12: 120. doi:10.1186/1471-2164-12-120
    • [11] Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11: 119. doi:10.1186/1471-2105-11-119
    • [12] Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007;23: 673 679. doi:10.1093/bioinformatics/btm009
    • [13] Akhter S, Aziz RK, Edwards RA. PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Res. 2012;40: e126. doi:10.1093/nar/gks406
  4. Assess Read Quality with FastQC - v0.11.9
    • FastQC source: Bioinformatics Group at the Babraham Institute, UK.
  5. Classify Microbes with GTDB-Tk - v1.7.0
    • Pierre-Alain Chaumeil, Aaron J Mussig, Philip Hugenholtz, Donovan H Parks, GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database, Bioinformatics, Volume 36, Issue 6, 15 March 2020, Pages 1925 1927. DOI: https://doi.org/10.1093/bioinformatics/btz848
    • Parks, D., Chuvochina, M., Waite, D. et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 36, 996 1004 (2018). DOI: https://doi.org/10.1038/nbt.4229
    • Parks DH, Chuvochina M, Chaumeil PA, Rinke C, Mussig AJ, Hugenholtz P. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat Biotechnol. 2020;10.1038/s41587-020-0501-8. DOI:10.1038/s41587-020-0501-8
    • Rinke C, Chuvochina M, Mussig AJ, Chaumeil PA, Dav n AA, Waite DW, Whitman WB, Parks DH, and Hugenholtz P. A standardized archaeal taxonomy for the Genome Taxonomy Database. Nat Microbiol. 2021 Jul;6(7):946-959. DOI:10.1038/s41564-021-00918-8
    • Matsen FA, Kodner RB, Armbrust EV. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics. 2010;11:538. Published 2010 Oct 30. doi:10.1186/1471-2105-11-538
    • Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9(1):5114. Published 2018 Nov 30. DOI:10.1038/s41467-018-07641-9
    • Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119. Published 2010 Mar 8. DOI:10.1186/1471-2105-11-119
    • Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5(3):e9490. Published 2010 Mar 10. DOI:10.1371/journal.pone.0009490 link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2835736/
    • Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol. 2011;7(10):e1002195. DOI:10.1371/journal.pcbi.1002195
  6. Insert Genome Into SpeciesTree - v2.2.0
    • Price MN, Dehal PS, Arkin AP. FastTree 2 Approximately Maximum-Likelihood Trees for Large Alignments. PLoS One. 2010;5. doi:10.1371/journal.pone.0009490
  7. Upload File to Staging from Web - v1.0.12
    • Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018;36: 566. doi: 10.1038/nbt.4163