Genome sets for comparative genomics

Tiffany created a tutorial powerpoint to provide advice on setting up a KBase narrative for Ralstonia phylogenomics including insight into the quality control. It’s a guide for making additional phylogenomics narratives if you want to. Download the tutorial .pptx from this github page. Download button is the ↓ arrow towards the right of the page.

Narrative: RSSC Phylogenomics

The Lowe-Power lab maintains this narrative with all of the publicly available RSSC genomes.

Contributors: Tiffany Lowe-Power, Vienna Elmgreen

Version 2: 600-700 genomes https://narrative.kbase.us/narrative/189849

Version with only the genomes of strains in Lowe-Power lab strain collection: https://narrative.kbase.us/narrative/199187

Original version (don’t use; keep for Legacy) https://narrative.kbase.us/narrative/123807

Useful genome sets:

• RSSC_for_phylogenomics_IncludesBadQualityGenomes.genomeSet
  • Purpose: place new genomes into a phylogenetic tree with all sequenced RSSC. The “Bad Quality” genomes are ones that are non-ideal for functional genomics analyses.
• RSSC_highQuality_v2023-06-24.genomeSet
  • Purpose: Tiffany filtered these genomes based on CheckM completeness and contamination. This genomeSet can be used for functional genomics analysis.

Narrative: Burkholderiales Species Representatives

Tiffany used GTDB to identify genome representatives of approx 300 species in the Burkholderiales order. All genomes were described as complete on GTDB, but it is possible that there are mistakes. The genomes are named according to GTDB taxonomy when the narrative was created in Summer 2023.

https://narrative.kbase.us/narrative/142785

Useful genome set:

• Burkholderiales_speciesReps_HighQuality.genomeSet

Narrative: Other Ralstonia phylogenomics

Tiffany maintains this narrative with all of the publicly available Ralstonia genomes that are not RSSC.

https://narrative.akbase.us/narrative/189428

Narrative: Cupriavidus phylogenomics

Tiffany maintains this narrative with all of the publicly available Cupriavidus genus genomes.

https://narrative.kbase.us/narrative/142720

Narrative: Pandoraea phylogenomics

Tiffany maintains this narrative with all of the publicly available Pandoraea genus genomes.

https://narrative.kbase.us/narrative/142975

Transcriptomics

Quorum sensing transcriptome datasets from multiple sources:

• https://narrative.kbase.us/narrative/153894
  • Includes GMI1000 vs. phcA in tomato from Khokhani et al.
• Perrier phcA transcriptome is in a separative narrative with efpR: https://narrative.kbase.us/narrative/154521

efpR transcriptome from Perrier et al.

• https://narrative.kbase.us/narrative/154521

Phyl. IIB-1 strain UY031 in potato stems and rich media from de Pedro Jove 2020

• https://narrative.kbase.us/narrative/153897

Phyl. I strain RS-SY1 in pepper stems from Du et al 2022.

• https://narrative.kbase.us/narrative/153936

Phyl. IIB-4 strains IBSBF1503 and UW163 in tomato, banana, and melon stems from Ailloud et al. 2016

• https://narrative.kbase.us/narrative/153883

Phyl. IV-BDB strain UGMSS-Db01 in culture. (The in planta transcriptome had almost no bacterial reads)

• https://narrative.kbase.us/narrative/153937