Considerations in designing a laboratory passage experiment.

<p>Considerations in designing a laboratory passage experiment.</p

Some of the pathogenic characteristics explored by laboratory passage models.

<p>Examples of the application of experimental evolution to the study of pathogens include modeling the evolution of drug resistance <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003340#ppat.1003340-Almahmoud1" target="_blank">[18]</a>–<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003340#ppat.1003340-Wong1" target="_blank">[20]</a>, trade-offs between generalist versus specialist adaptations to the host <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003340#ppat.1003340-Ensminger1" target="_blank">[9]</a>, <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003340#ppat.1003340-Deardorff1" target="_blank">[12]</a>, pathogen transmission <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003340#ppat.1003340-Herfst1" target="_blank">[13]</a>, <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003340#ppat.1003340-Imai1" target="_blank">[14]</a>, and biofilm formation <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003340#ppat.1003340-Traverse1" target="_blank">[17]</a>.</p

Lp01 "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-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

JR32-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

Lp02-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

Lp03-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

Phylogeny of the <i>Legionella pneumophila</i> Philadelphia-1 laboratory strains as determined by whole-genome Illumina sequencing.

<p>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 <i>L. pneumophila</i> 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 (Lp01^JK) containing <i>luxN</i> and <i>ftsE</i> mutations, but not <i>lpg0716</i> and <i>lpg0718</i> mutations indicates that <i>luxN</i> and <i>ftsE</i> emerged first within the Lp01 lineage <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064129#pone.0064129-Ensminger1" target="_blank">[7]</a>. Not displayed: a putative gene conversion event that emerged independently in only the Lp01^CR and JR32 strains (AGAT 608,162–608,165 GAAG). (For details of each exact isolate sequenced, see materials and methods: JR32^AE, Lp01^CR, Lp01^JK, Lp02^AE, Lp03^AE).</p

Polymorphisms between the Philadelphia-1 progenitor and the original published sequence.

1<p>Nucleotide positions within the published <i>L. pneumophila</i> Philadelphia-1 genome <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064129#pone.0064129-Chien1" target="_blank">[18]</a> (GenBank accession AE017354.1).</p

Lp03 polymorphisms relative to the Philadelphia-1 progenitor.

1<p>Nucleotide positions within the published <i>L. pneumophila</i> Philadelphia-1 genome <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064129#pone.0064129-Chien1" target="_blank">[18]</a> (GenBank accession AE017354.1).</p