/MosAIC_V1

Primary LanguageR

Copy-of-MosAIC-3-1200x737

Overview

MosAIC: Mosquito-Associated Isolate Collection MosAIC (Mosquito-Associated Isolate Collection), a resource consisting of 392 bacterial isolates from mosquitoes. These isolates come with extensive metadata and high-quality draft genome assemblies, publicly available for use by the scientific community. Please see https://kcoonlab.bact.wisc.edu/mosaic/ for more information.

Analysis Overview

Scripts for each analysis are written in R. Each directory contains necessary files and code to recreate each figure of the manuscript. To repeat the analysis, clone the repository, and the run each script. Do not cd into the cloned repository.

Example Create a new project in RStudio. To run the scripts in 01_GenomeQC to recreate Figure 1B in the manuscript.

  • Navigate to the terminal window and git clone https://github.com/MosAIC-Collection/MosAIC_V1.
  • Open open the script checkM_analysis.R from the files panel window.
  • Install required packages.
  • cmd enter from line 1.

Recreate the Manuscript Figures

Once the repository has been cloned (above), recreate each figure as follows:

Fig 1 Origin of bacterial isolates in MosAIC

  • Fig 1 - Script: 04_Sankey_Diagram/Metadata_Snakey_Diagram.R: run code from line 1 to 127

Fig 2 Phylogeny of single species representatives from MosAIC, along with quality-assurance metrics for related genome assemblies

  • Fig 2A - Script: 03_MosAIC_Phylogeny/plot_tree_metadata.R: run code from line 1 to 257
  • Fig 2B - Script: 01_Genome_QC/checkM_analysis.R: run code from line 1 to 60`
  • Fig 2C - Script: 01_Genome_QC/checkM_analysis.R: run code from line 1 to 239
  • Fig 2D - Script: 01_Genome_QC/checkM_analysis.R: run code from line 1 to 136
  • Fig 2E - Script: 01_Genome_QC/checkM_analysis.R: run code from line 1 to 159
  • Fig 2F - Script: 02_GTDB_Drep_Summary/gtdbtk_drep_stat.R: run code from line 1 to 112

Fig 3 Heatmap of the distribution of virulence factors across all MosAIC genomes

  • Fig 3 - Script: 05_Virulence_Factor_Analysis.R: run code from line 1 to 192

Fig 4 Selected genus population structures with improved mosquito representation

  • Fig 4A-C - Script: 06b_EnterobacterPopulationStructure/Enterobacter_Pop_Struc.R: run code from line 1 to 426
  • Fig 4D-F - Script: 06a_SerratiaPopulationStructure/Serratia_Genus_Pop_Structure.R: run code from line 1 to 370
  • Fig 4G-H - Script: 06c_ElizabethkingiaPopulationStructure/ElizabethkingiaPopStruc.R: run code from line 1 to 300

Fig 5 Pangenomes of Enterobacter asburiae, Serratia marcescens, and Elizabethkingia anophelis with highlighted mosquito-associated lineages

  • Fig 5A - Script: 07b_EnterobacterPangenome/EnterobacterPangenomeTree.R: run code from line 1 to 249
  • Fig 5B - Script: 07a_SerratiaPangenome/SerratiaMPangenome.R: run code from line 1 to 210
  • Fig 5C - Script: 07c_ElizabethkingiaPangenome/Elizabethkingia_Anophelis_Pangenome.R: run code from line 1 to 177

Supplementary Figures

  • Fig S1 - Script: 01_Genome_QC/plot_QUAST.R: run code from line 1 to 55
  • Fig S2 - Script: 01_Genome_QC/checkM_analysis.R: run code from line 1 to 184
  • Fig S3 - Script: 02_GTDB_Drep_Summary.R: run code from line 1 to 188
  • Fig S4 - Script: 12_Metadata_Exploration.R: run code from line 1 to 148
  • Fig S5 - Script: 12_Metadata_Exploration.R: run code from line 1 to 255
  • Fig S6 - Script: 05_Virulence_Factor_Analysis.R: run code from line 1 to 340
  • Fig S7 - Script: 06b_EnterobacterPopulationStructure.R: run code from line 1 to 154
  • Fig S8 - Script: 06a_SerratiaPopulationStructure.R: run code from line 1 to 103
  • Fig S9 - Script: 06c_ElizabethkingiaPopulationStructure.R: run code from line 1 to 105
  • Fig S10 - Script: 08_GeneAccumulationCurves.R: run code from line 1 to 42
  • Fig S11-13 - Script: 10_VisPopPUNKClusters.R: run code from line 1 to 67
  • Fig S14 - Script: 11_LineageCoreGeneAnalysis.R: run code from line 1 to 167
  • Fig S15 - Script: 11_LineageCoreGeneAnalysis.R: run code from line 1 to 293

Authors

Citation

Foo A, Brettell LE, Nichols HL, 2022 UW-Madison Capstone in Microbiology Students, Medina Muñoz M, Lysne JA, et al. Establishment and comparative genomics of a high-quality collection of mosquito-associated bacterial isolates - MosAIC (Mosquito-Associated Isolate Collection). 2023 Oct. Available from: http://biorxiv.org/lookup/doi/10.1101/2023.10.04.560816