Evolutionary Genomics of Proteobacteria and the MEGA Program

1
Evolutionary Genomics of ?-Proteobacteria and
the MEGA Program

• Presented by Joel Crawford and Liam Hahn

2
The Evolutionof the Study of Evolution

• A change from working with anatomical and
  behavioral characteristics to metabolic and
  molecular.
• Ultimately genomics.

3
Fields Influenced by Evolutionary Analysis

• Pharmacology
• Epidemiology
• Conservation Biology
• Forensic Science
• Geosciences
• You name it

4
Review of Homologs, Paralogs and Orthologs
This study relied heavily on Orthologous genes to
construct evolutionary phylogenies.
5
Lateral Gene Transfer
6
Why Arent Orthologous Genes Transferred
Laterally?

• Retention of an acquired gene depends on strong
  selection for that new gene.
• If homologous genes already exist within the
  genome, there is no selection pressure to
  maintain the new gene.

7
Small Subunit Ribosomal RNA

• Has highly conserved and highly variable regions,
  all organisms have had it in some form for the
  last 3 billion years of evolution.
• Most commonly used gene for constructing
  phylogenies.
• It is, however, susceptible to LGT and
  recombination.

• Does not provide enough resolution alone to build
  highly accurate phylogenies.

8
From Gene Trees to Organismal Phylogeny in
Prokaryotes The Case of the ?-Proteobacteria
The Paper

• Emmanuelle Lerat1 , Vincent Daubin2 , Nancy A.
  Moran1

9
Reconstructing Genome-Scale Evolutionary Events
Using GenBank Bacterial Genome Sequences

• Why ?-proteobacteria?
• Most extensively studied and sequenced genomes
  with variable relatedness.
• ?-Proteobacteria are ecologically diverse and
  have a long evolutionary heritage (500 million
  years of divergence).
• Most exist as free living organisms, but there
  are pathogenic species and symbionts.

10
Why ?-proteobacteria?

• High levels of LGT
• Structural differences in SSU rRNA
• Goal To build the topology representing the
  history of the reproducing cells that pass genes
  on to the newest generations The Organismal
  Phylogeny

11
The 13 Species Studied

• Chosen because they show various degrees of
  interrelatedness based on SSU rRNA data, and the
  two symbionts were selected because they have
  reduced genomes.
• Escherichia coli K12
• Buchnera aphidicola APS (Aphid symbiont)
• Haemophilus influenzae Rd
• Pasteurella multocida Pm70
• Salmonella typhimurium LT2
• Yersinia pestis CO_92
• Yersinia pestis KIM5 P12
• Vibrio cholerae
• Xanthomonas axonopodis pv. citri 306
• Xanthomonas campestris
• Xylella fastidiosa 9a5c
• Pseudomonas aeruginosa PA01
• Wigglesworthia glossinidia brevipalpis (Tsetse
  fly symbiont)

cholerae
12
Figure 1A
The number of genes per gene family, most
families contain only one gene.
13
Figure 1B
Number of orphan (unique) genes in each genome.
Note the small number in both symbiotic species
(Ba, Wb).
14
Figure 1C
Number of species contained in the homolog
families. Unique genes are considered a family,
and so those species with more unique genes have
more families
275 families had representatives in all 13 species
15
The Selected Gene Families

• A minimal core of genes were selected for wide
  representation and congruent phylogenetic signals
  (the 275 families).
• 205 gene families were found to contain exactly
  one gene per species. These 205 genes represent
  likely orthologs and are good candidates for use
  in inferring phylogeny and the extent of LGT.
• 203 of the 205 fit the final chosen topology.
• All 203 genes are necessary for survival, even in
  the reduced genomes of the symbionts.

16
So 203 of 205 Fit the Final Topology, What About
the Other Two?

• The result of a single LGT event in the history
  of Pseudomonas.

• The genes transferred were BioB (biotin
  synthase), and MviN (a virulence factor).
• To verify the position of Pseudomonas in the
  final topology, GenBank was searched for more
  homologous genes and more trees were calculated,
  each resulting with Pseudomonas in the same
  position.

Pseudomonas
17
Table 1
Number of protein coding genes per species after
removal of insertions and viral sequences.
18
Constructing the Gene Families

• A bank of all annotated protein .
• Used a cutoff for degree of similarity as found
  in the BLASTP bit scores to eliminate
  non-homologous and paralogous sequences.

Figure 6
19
The Symbionts

• Wigglesworthia and Buchnera
• Buchnera was found to be as closely related to E.
  coli as it is to Yersinia pestis utilizing the
  205 orthologous genes, casting doubt on several
  contradictory hypotheses.
• No special genes found to confer predisposition
  to symbiotic activity, eliminating some
  hypotheses on the origins of symbiosis.
• The minimal nature of the genomes of symbionts
  means that they have a much lower chance of
  recombination.
• Sister relationship suggests shared origin of
  symbiosis.

20
Wigglesworthia glossinidia brevipalpis and the
Tsetse Fly

• The Wigglesworthia genome contains over 60 genes
  involved in the synthesis of nutrients that the
  tsetse fly relies on for its fertility.
• Without the bacteria, the tsetse fly is sterile.
• The symbiotic bacteria may also provide essential
  nutrients to the African trypanosomes that cause
  sleeping sickness.

Bacteriome within fly gut
21
Buchnera aphidocola and the Aphid

• 150-250 million year old mutualism and
  coevolution
• Plant phloem juices rich in carbohydrates, low on
  amino acids
• Symbiotic bacteria manufacture the essential
  amino acids within the aphid

Buchnera
-UCONN
22
(No Transcript)
23
Candidate Topologies
24
Figure 3
Topology 5 has the greatest number of alignments.
25
The Chosen Topology (5)
26
Conclusion

• Topology 5 represents the most accurate
  evolutionary history for these 13 proteobacteria.
• Analysis of orthologous genes enables the
  construction of topologies from even the smallest
  and most highly variable of genomes.
• Implications Once we have sequenced many more
  genomes, we can use these methods to build
  accurate phylogenies that take complications such
  as LGT and reduced genome size into account (for
  both bacteria and other organisms).
• A complete and more accurate tree of life, we
  just need the sequences.

27
Sources

• From Gene Trees to Organismal Phylogeny in
  Prokaryotes The Case of the ?-Proteobacteria
  http//www.plosbiology.org/plosonline/?requestget
  -documentdoi10.13712Fjournal.pbio.0000019
• Wigglesworthia wiggles into the world of
  sequenced genomes. Kate Dalke. (2003).http//www.g
  enomene wsnetwork.org/articles/09_02/wiggles.shtml
  
• The Nutritional Symbiosis of Buchnera and Aphids
  http//web.uconn.edu/mcbstaff/graf/BuAp/Baphidrigh
  t.htm
• Birgit Reinert. Genome News Network Inside
  insects, life is unchanged for 50 million years.
  http//www.genomenewsnetwork.org/articl
  es/0702/models.shtml
• Definition of Homolog, Ortholog and Paralog
  http//homepage.usask.c a/ctl271/857/def_homolog.
  shtml