About

This site is composed of four sections that contain the intermediate and final results of a bacterial comparative genomics project that utilized 3837 genomes to associate genetic traits with bacterial adaptation to plant lifestyle. The provided data can be utilized to reproduce our results, in addition feel free to further explore the data and results presented here according to your particular interests. Of particular relevance is the Enrichments section in which you will find tables of the orthogroups that based in our analysis are associated with bacterial adaptarion to plants.

You can find a copy of the manuscript associated with the content in this website in:

Manuscript
Supplemental material
Supplemental Tables
 

Sections

IMG|Trees|Metadata
This section contains the IMG data (FAA,COG,KO,TIGRFAM,PFAM) of the 3837 genomes utlized in this study, the metadata associated with those genomes and the phylogenetic trees depicting the genomes relatedness

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OGS:Matrices|Dataframes|FAA
This section contains the pangenome matrices and orthogroup-genome-gene dataframes constructed using the orthogroups output by Orthofinder. Fasta files for each orthogroup are included too.

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OGS:MAFFT|HMM
This section contains alignments and Hidden Markov Model profiles created for all the orthogroups computed across the 9 taxonomic groups. A pipeline to annotate new genomes with the HMM profiles is included too.

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Enrichments
This section contains tables with the bacterial orthogroups that are associated with plant lifestyle according to our methodology. Additionally, files of enriched operons per taxon are included too.

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