Philosophy

Science is a blast: we aim to have fun. Operating within a supportive research environment our lab provides a place for interdisciplinary thinkers interested in an independent and creative approach to doing science.

Our lab is comprised of scientists and researchers from a variety of disciplines:

  • Evolution
  • Microbiology
  • Genetics
  • Ecology
  • Parasitology
  • Plant-microbe interactions
  • Biochemistry

Research

SBW25 genome

This valuable resource became available to us thanks for a grant from the BBSRC back in 2002. The sequencing, assembly and annotation has taken place at the Sanger Centre and was finished some time ago. The genome paper (which incorporates the genome sequence of strain Pf0-1 and the results of a very large scale (and fully comprehensive) screen for SBW25 genes specifically induced on plant surfaces) was published in Genome Biology 10:R51 in 2009. The NCBI entry can be accessed here and the Artemis files are available here.

In terms of specific research on the genome we (Frederic Bertels) are investigating the myriad of short pallendromic repeats: their evolutionary origins and processes determining patterns of distribution.

Genome re-sequencing

The sequence of our ancestral bacterium (and it really is the sequence of the ancestor that sits in our -80 freezer) has facilitated a great deal of our work. In fact it is hard to remember pre-genome sequence times. In 2006 we sent several lines from our reverse evolution experiments to Nimblegen for re-sequencing using their tiling array strategy. This revealed about 50% of the expected mutations. Recently, with the arrival of a Solexa sequencer at the Allan Wilson Centre we re-re-sequenced some of the earlier lines and one not previously sequenced line. We literally reeled under the delightful weight of the data. Thanks to the efforts of the superbly skilled Frederic Bertels the data has been ripped apart: we've found the missing mutations and indeed the data has given us a great deal more to ponder. Our intention is to complete the sequencing of all 12 reverse evolution lines.

Links to the Solexa output data files (Rainey lab only)

Back to research themes