DOI: 10.5061/dryad.1k1ns
title: Data from: Phylogenetic reconstruction of the Legionella pneumophila Philadelphia-1 laboratory strains through comparative genomics.

description: Over 20 years ago, two groups independently domesticated Legionella
 pneumophila from a clinical isolate of bacteria collected during the first
 recognized outbreak of Legionnaires’ disease (at the 1976 American
 Legion’s convention in Philadelphia). These two laboratory strains, JR32
 and Lp01, along with their derivatives, have been disseminated to a number
 of laboratories around the world and form the cornerstone of much of the
 research conducted on this important pathogen to date. Nevertheless, no
 exhaustive examination of the genetic distance between these strains and
 their clinical progenitor has been performed thus far. Such information is
 of paramount importance for making sense of several phenotypic differences
 observed between these strains. As environmental replication of L.
 pneumophila is thought to exclusively occur within natural protozoan
 hosts, retrospective analysis of the domestication and axenic culture of
 the Philadelphia-1 progenitor strain by two independent groups also
 provides an excellent opportunity to uncover evidence of adaptation to the
 laboratory environment. To reconstruct the phylogenetic relationships
 between the common laboratory strains of L. pneumophila Philadelphia-1 and
 their clinical ancestor, we performed whole-genome Illumina resequencing
 of the two founders of each laboratory lineage: JR32 and Lp01. As expected
 from earlier, targeted studies, Lp01 and JR32 contain large deletions in
 the lvh and tra regions, respectively. By sequencing additional strains
 derived from Lp01 (Lp02 and Lp03), we retraced the phylogeny of these
 strains relative to their reported ancestor, thereby reconstructing the
 evolutionary dynamics of each laboratory lineage from genomic data.
description: Legionella pneumophila
 Philadelphia-1 clinical genome (GenBank format)GenBank formatted file
 derived from editing NC_002942 (Legionella pneumophila subsp. pneumophila
 str. Philadelphia 1). Corrects several discrepancies between the 1976
 Philadelphia isolate given to the Isberg laboratory by Barry Fields and
 the original sequence.Phila1_updated.gbkLp01 "core" genome (GenBank format)GenBank formatted file derived from editing NC_002942 (Legionella pneumophila subsp. pneumophila str. Philadelphia 1). Lp01 is a common laboratory strain, a streptomycin resistant, restriction-minus derivative of the Philadelphia-1 clinical strain. This "core" sequence reflects the genome of the original Lp01 isolate, calculated based on the phylogeny between contemporary Lp01 strains and Lp02.Lp01_core.gbkLp01-CR genome (GenBank format)GenBank formatted file derived from editing NC_002942 (Legionella pneumophila subsp. pneumophila str. Philadelphia 1). Lp01 is a common laboratory strain. This Lp01-CR sequence reflects the genome of the Lp01 isolate in Chitong Rao's strain collection.Lp01_CR.gbkLp02-AWE genome (GenBank format)GenBank formatted file derived from editing NC_002942 (Legionella pneumophila subsp. pneumophila str. Philadelphia 1). Lp02 is a thymidine auxotroph, derived from Lp01 by trimethoprim selection. This sequence reflects the genome of the original Lp02 isolate in Alexander Ensminger's strain collection.Lp02_AWE.gbkLp03-AWE genome (GenBank format)GenBank formatted file derived from editing NC_002942 (Legionella pneumophila subsp. pneumophila str. Philadelphia 1). Lp03 is a dotA mutant, derived from a thymidine auxotroph, originally thought to be Lp02. This sequence reflects the genome of the Lp03 isolate in Alexander Ensminger's strain collection.Lp03_AWE.gbkJR32-AWE (GenBank format)GenBank formatted file derived from editing NC_002942 (Legionella pneumophila subsp. pneumophila str. Philadelphia 1). JR32 is a common laboratory strain, a streptomycin resistant, restriction-minus derivative of the Philadelphia-1 clinical strain. This sequence reflects the genome of the JR32 isolate in Alexander Ensminger's strain collection.JR32_AWE.gbk