Hello! I am Bérénice, the author of following slides.
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Reductive genome evolution
of bacterial genomes
in silico evolution experiments
and comparative genomics analyses
Bérénice Batut
University of Freiburg
Backofen lab meeting
February 2017
Evolution
How most people see evolution?
But it's WRONG!
Facts about evolution
- Same evolution time for all organisms
- No correlation between complexity and genome size
- Reductive genome evolution case
How to explain the actual differences in genome size?
Reductive genome evolution in endosymbionts
Example of Buchnera aphidicola
Genome degeneration syndrom
Adapted from Batut et al, 2014
Muller's ratchet
Adapted from Mira & Moran, 2002
- Small population size with frequent bottlenecks
- No recombination
Smallest genomes in the smallest populations?
Relation between effective population size and genome size
Figure inspired from Kuo et al, 2009
Reductive genome evolution in Prochlorococcus
An counter-intuitive case
Prochlorococcus
Figure adapted from Flombaum et al, 2013
Prochlorococcus
Table adapted from Batut et al, 2014
Changes during Prochlorococcus evolution
Table adapted from Batut et al, 2014
Hypotheses for reductive genome evolution
Figures adapted from Flombaum et al, 2013
Hypotheses for reductive genome evolution
Hypothesis from Rocap et al, 2003, Dufresne et al, 2005, Giovannoni et al, 2005, Kettler et al, 2007, and other
Table adapted from Batut et al, 2014
Hypotheses for reductive genome evolution
Hypothesis from Marais et al, 2008 and Partensky & Garczarek, 2010
Table adapted from Batut et al, 2014
Hypotheses for reductive genome evolution
Hypothesis from Moris et al, 2012
Table adapted from Batut et al, 2014
Reductive genome evolution in Prochlorococcus
- No hypotheses to explain all genome characteristics for Prochlorococcus
- Need for supplementary studies
- Tests of hypotheses using in silico experimental evolution
- Study of genomic characteristics of Prochlorococcus genomes with comparative genomics approach
in silico experimental evolution
in silico experimental evolution?
Adapted from Hindré et al, 2012
aevol
aevol
aevol
aevol
aevol
An organism in aevol
A structured genome with
- A variable number of genes in a random order
- A variable quantity of non coding sequences
- A variable number of operons
- ...
~ A structure of a bacterial genome
Using aevol to test evolution scenarios
Adapted from Batut et al, 2013
And to test reductive genome evolution?
Comparative genomics analyses of Prochlorococcus
Genome architecture evolution study
using phylogenetic contrasts
Intergenic median distance
and non coding bases proportion
Genome architecture evolution
Reconstruction of the gene losses and gains
Tree with gene losses and gains built with Count on 3,778 gene families
Reconstruction of the gene length evolution
Estimation of insertions and deletions inside 693 gene families using Prank after reconciliation between gene family and species trees using Prunier
Changes in selection?
Changes in selection?
Previous estimations
dN/dS estimated as in Hu & Blanchard, 2009, Yu et al, 2012, Sun & Blanchard, 2014
Changes in selection?
With correction of GC content
dN/dS estimated using Bio++ and a specific model
Analyses of Prochlorococcus
reductive genome evolution
Towards an hypothetical evolution story?
Thanks to the combination of both approaches
Hypothetical evolution story?
Thank You!