Data from Kothari et al 2020
John-Marc Chandonia, Aindrila Mukhopadhyay, Elisha WC, Ankita Kothari
Generated November 19, 2020

Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance

Ankita Kothari, Simon Roux, Hanqiao Zhang, Anatori Prieto, John-Marc Chandonia, Sarah Spencer, Xiaoqin Wu, Adam M. Deutschbauer, Adam P. Arkin, Eric J. Alm, Romy Chakraborty, Aindrila Mukhopadhyay

Submitted to mBio

Table of Contents

  1. Background
  2. Data

Background

This work uses some data from a prior study, Kothari et al, 2019, mBio, "Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes." A narrative describing that paper is here: https://narrative.kbase.us/narrative/63111

All raw reads from background wells for the current study are available in this Narrative.

Data

Virus sequences

The 200 viral genome sequences have been imported into this Narrative, as an object called "viral_sequences".

Isolate genomes

The 260 genomes described in this study will be used in several other ENIGMA studies. Therefore, they are included in a separate Narrative, here: https://narrative.kbase.us/narrative/63776

Import FASTA File as Assembly from Staging Area
Import a FASTA file from your staging area into your Narrative as an Assembly data object
This app completed without errors in 2m 9s.
Objects
Created Object Name Type Description
viral_sequences Assembly Imported Assembly
Report
Links
  • report.html - HTML summary report for Imported Assembly
Annotate Assembly and Re-annotate Genomes with Prokka(v1.12)
Annotate Assembly and Re-annotate Genomes with Prokka annotation pipeline.
This app completed without errors in 3m 24s.
Objects
Created Object Name Type Description
viral_sequences_prokka Genome Annotated Genome
Summary
Annotated Genome saved to: jmc:narrative_1605034122360/viral_sequences_prokka Number of genes predicted: 5942 Number of protein coding genes: 5851 Number of genes with non-hypothetical function: 410 Number of genes with EC-number: 136 Number of genes with Seed Subsystem Ontology: 105 Average protein length: 227 aa.
Output from Annotate Assembly and Re-annotate Genomes with Prokka(v1.12)
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/76973
Annotate Genome/Assembly with RASTtk - v1.073
Annotate or re-annotate genome/assembly using RASTtk (Rapid Annotations using Subsystems Technology toolkit).
This app produced errors.
No output found.

Apps

  1. Annotate Assembly and Re-annotate Genomes with Prokka(v1.12)
    • Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30: 2068 2069. doi:10.1093/bioinformatics/btu153
  2. 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
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    • [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
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    • [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.
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    • [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
  3. Import FASTA File as Assembly from Staging Area
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