Figure 1.
Legionella pneumophila Philadelphia-1 laboratory strains.
(A) Presumed phylogeny of the laboratory strains of L. pneumophila Philadelphia-1 based on the parallel experimental methods used to generate each strain. Both the Lp01 and JR32 lineages were derived from a clinical isolate, L. pneumophila Philadelphia-1, collected during the first recognized outbreak of Legionnaires' disease at a 1976 convention of the American Legion in Philadelphia, Pennsylvania. Lp01 was subsequently used to derive a spontaneous thymidine auxotroph Lp02. An avirulent dotA mutant, Lp03, reportedly derived from Lp02, is commonly used in studies as a translocation-deficient, intracellular replication defective control. (B) Out of a total of 700 publications, an estimate of the relative number which reference the Lp01/Lp02 lineage, JR32, or both. (See Materials and Methods).
Table 1.
Polymorphisms between the Philadelphia-1 progenitor and the original published sequence.
Table 2.
JR32 polymorphisms relative to the Philadelphia-1 progenitor.
Table 3.
Lp01 polymorphisms relative to the Philadelphia-1 progenitor.
Figure 2.
Short, GC-rich direct repeats flank each of the large genomic regions lost in the Lp01 and JR32 lineages.
(A) The 45.4 kb lvh region that is deleted in the Lp01/Lp02/Lp03 lineage is flanked by a set of 69% GC, 49 nt direct repeats that likely facilitated intrachromosomal recombination and loss of the lvh region, which includes a type IVA secretion system as well as a restriction endonuclease, lpg1237, and its cognate methytransferase, lpg1236. (B) The 64.2 kb tra region is flanked by a set of 67% GC, 43 nt direct repeats that share no sequence homology with the lvh repeat. The genomic sequence of JR32 is consistent with an intrachromosomal recombination event between these repeats and subsequent loss of the intervening tra region.
Table 4.
Lp02 polymorphisms relative to the Philadelphia-1 progenitor.
Table 5.
Lp03 polymorphisms relative to the Philadelphia-1 progenitor.
Figure 3.
Phylogeny of the Legionella pneumophila Philadelphia-1 laboratory strains as determined by whole-genome Illumina sequencing.
Illumina sequencing was performed on the Philadelphia-1 progenitor and each of its laboratory derivatives, JR32, Lp01, Lp02, and Lp03. Each genome was aligned to the published L. pneumophila Philadelphia-1 sequence (GenBank accession AE017354.1). The identification of single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs) in each laboratory strain was used to determine genetic distances with maximum likelihood between each strain. To explain these relationships, intermediate ancestral strains were proposed, as represented by open circles. A previously sequenced Lp01 derivative (Lp01JK) containing luxN and ftsE mutations, but not lpg0716 and lpg0718 mutations indicates that luxN and ftsE emerged first within the Lp01 lineage [7]. Not displayed: a putative gene conversion event that emerged independently in only the Lp01CR and JR32 strains (AGAT 608,162–608,165 GAAG). (For details of each exact isolate sequenced, see materials and methods: JR32AE, Lp01CR, Lp01JK, Lp02AE, Lp03AE).