A degenerate primer MOB typing (DPMT) method to classify gamma-proteobacterial plasmids in clinical and environmental settings

Transmissible plasmids are responsible for the spread of genetic determinants, such as antibiotic resistance or virulence traits, causing a large ecological and epidemiological impact. Transmissible plasmids, either conjugative or mobilizable, have in common the presence of a relaxase gene. Relaxases were previously classified in six protein families according to their phylogeny. Degenerate primers hybridizing to coding sequences of conserved amino acid motifs were designed to amplify related relaxase genes from γ-Proteobacterial plasmids. Specificity and sensitivity of a selected set of 19 primer pairs were first tested using a collection of 33 reference relaxases, representing the diversity of γ-Proteobacterial plasmids. The validated set was then applied to the analysis of two plasmid collections obtained from clinical isolates. The relaxase screening method, which we call "Degenerate Primer MOB Typing" or DPMT, detected not only most known Inc/Rep groups, but also a plethora of plasmids not previously assigned to any Inc group or Rep-type

Dense sampling of bird diversity increases power of comparative genomics (vol 587, pg 252, 2020)

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Control region sequences

Alignment of control region sequences (438 bp) used for phylogeographic analysi

Microsatellite data

Microsatellite data used for inference of spatial patterns of diversification in Eurasian coal tits with STRUCTURE, GENELAND and TESS; population data set: 145 individuals (ind) from 14 populations (pop) with local samplings of n>5, allele lengths for thirteen microsatellite loci (columns E-AD); including further data from individuals discarded from the population genetic analysis, small local samplings of n< 5; total number of individuals n= 177