Excellent news this morning! The first paper describing a genome sequenced, assembled and annotated in this course has been accepted for publication:
Ryo Miyazaki, Claire Bertelli, Paola Benaglio, Jonas Canton, Nicoló De Coi, Walid H. Gharib, Bebeka Gjoksi, Alexander Goesmann, Gilbert Greub, Keith Harshman, Burkhard Linke, Josip Mikulic, Linda Mueller, Damien Nicolas, Marc Robinson-Rechavi, Carlo Rivolta, Clémence Roggo, Shantanu Roy, Vladimir Sentchilo, Alexandra Von Siebenthal, Laurent Falquet, and Jan Roelof van der Meer. Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds. Environmental Microbiology
Pseudomonas knackmussii B13 was the first strain to be isolated in 1974 that could degrade chlorinated aromatic hydrocarbons. This discovery was the prologue for subsequent characterization of numerous bacterial metabolic pathways, for genetic and biochemical studies, and which spurred ideas for pollutant bioremediation. In this study we determined the complete genome sequence of B13 using next generation sequencing technologies and optical mapping. Genome annotation indicated that B13 has a variety of metabolic pathways for degrading monoaromatic hydrocarbons including chlorobenzoate, aminophenol, anthranilate, and hydroxyquinol, but not polyaromatic compounds. Comparative genome analysis revealed that B13 is closest to Pseudomonas denitrificans and Pseudomonas aeruginosa. The B13 genome contains at least 8 genomic islands (prophages and integrative conjugative elements – ICE), which were absent in closely related pseudomonads. We confirm that two ICE are identical copies of the 103-kb self-transmissible element ICEclc that carries the genes for chlorocatechol metabolism. Comparison of ICEclc showed it is composed of a variable and a “core” region, which is very conserved among proteobacterial genomes, suggesting a widely distributed family of so far uncharacterized ICE. Resequencing of two spontaneous B13 mutants revealed a number of single nucleotide substitutions, as well as excision of a large 220 kb region and a prophage, which drastically change the host metabolic capacity and survivability.
The names of the master students are in bold in the author list.