Funding
This project was funded by the Virginia Agricultural Council (project #677 to JBW, LKB and RF) and National Science Foundation grants (MCB-1817736 to LKB, RF, and DCH; MCB-1817717 to JBW).
Publisher
University Libraries, Virginia TechCorresponding Author Name
David HaakFiles/Folders in Dataset and Description
Raw genome files in .fasta format. Scripts for processing in .zip format.
All bash scripts were run on Virginia Tech’s Advanced Research Computing Clusters.
[lacto_prokka.sh] – bash script used to run Prokka v. 1.14.6 on all 111bee-associated lactobacillaceae genomes that were used in this manuscript. This was done to generate the gff3 files that were used as input files for PIRATE
[lacto_eggNOG.sh] – bash script used to run eggNOG-mapper v.2.0 using eggNOG database v.5.0 on our novel lactobacillaceae strains (LB24, LB25, and LB26) as well as their closest relatives Apilactobcillus kunkeei AR114, Lactobacillus kullabergensis Biut2 and Bombilactobacillus mellis ESL0449 to annotate them.
[lacto_PIRATE.sh] – bash script used to run PIRATE v. 1.0.3 on all 111 bee-associated lactobacillaceae genomes that were used in this manuscript. This was used to identify the core and pangenome of these genomes.
[lacto_RAxML.sh] – bash script used to run RAxML HPC v.8.2.12 to generate a set of 1000 bootstrap replicates of phylogenetic trees. The core genome alignment of the 111 bee-associated lactobacillaceae generated by PIRATE was used as the alignment file.
[lacto_RAxML_consensus.sh] – bash script used to generate a consensus tree from the 1000 bootstrap replicates generated from lacto_RAxML.sh.
[lacto_figure2_final.R] – Script run on R v.4.0.5 and used genoPlotR v.0.8.11. Our isolates, as well as a few of their closest relatives selected from the phylogenetic tree produced from all 111 genomes, were aligned using the default settings of progressive mauve within mauve build v.2.4.0. The resulting backbone file and guide tree generated were used as input files for this script.
[lacto_figure3_final.R] – R script used to generate a stacked bar chart comparing the COG compositions of LB24, LB25, LB26, Apilactobacillus kunkeei AR114, Lactobacillus kullabergensis Biut2 and Bombilactobacillus mellis ESL0449. Script was run on R v. 4.0.5 and uses ggplot2 v. 3.3.5
[lacto_figure4_final.R] – Script run on R v.4.0.5 and used genoPlotR v.0.8.11. Uses the backbone file of mauve alignments of the most similar prophage(s) to those in LB24 and LB25 found in related species. Alignments shown share more than 80% of ANI to at least half of either LB24 or LB25’s prophage ORFs. Isolate LB24 with six Apilactobacillus kunkeei isolates. Isolate LB25 with one other Lactobacillus kullabergensis isolate.
