Download BIO2093_DMS3_phylogeny - COGEME Phytopathogenic Fungi

Phylogeny III
BIO2093 – Molecular Phylogeny 2
Darren Soanes
Using protein sequences to create species
trees
• Advantages
– protein sequences evolve more slowly than DNA
sequences (many DNA mutations are neutral – they do not
change amino acid sequences)
– reversals are less common than in DNA
• Single copy protein encoding genes identified
• Protein sequences joined together to create a
multiple protein sequence for each species
• Sequences aligned
Genetic Code
Protein alignment
Fungal species trees – more proteins = better resolution
oomycete (not fungi)
microsporidia
30 proteins
plant
zygomycete
basidiomycetes
ascomycetes
yeasts
60 proteins
filamentous ascomycetes
Fungal Species Tree (based on 153 concatenated
protein sequences)
Gene trees
• The evolutionary history of genes can be
represented as phylogenetic trees based on
alignment of protein sequences.
• Gene duplication and loss can be inferred
from phylogenetic trees.
• Protein sequences evolve more slowly than
DNA sequences (due to redundancy in genetic
code).
TOR gene duplication events in fungi
TOR: protein kinase,
subunit of a complex
that regulates cell
growth in response to
nutrient availability and
cellular stresses
Gene duplication
• Gene duplication due to unequal crossing over
during meiosis can create gene families.
• Sequence and function of different members
of a gene family can diverge.
Gene duplication
Sequence homology (1)
• Genes are said to be homologous if they share
a common evolutionary ancestor.
• Orthologues are genes in different species
that evolved from a common ancestral gene
by speciation. Normally, orthologues retain
the same function in the course of evolution.
(e.g. myoglobin in mammals).
Sequence homology (2)
• Paralogous genes are related by duplication within a
genome. Paralogues often evolve new functions,
even if these are related to the original one.
• In-paralogues, paralogues that were duplicated after
a speciation and are therefore in the same species
• Out-paralogues, paralogues that were duplicated
before a speciation. Not necessarily in the same
species.
Orthology and paralogy
Paralogues
A, B and C are different species
α and β are different paralogues of
the same gene
Out-paralogues
In-paralogues
Evolution of globin superfamily in human lineage
Whole genome duplication in fungi
Whole genome duplication (WGD)
• Complete duplication of genome, two
copies of every gene.
• Most genes are mutated and lost.
• Two copies of some genes kept for
functional purposes.
• Evidence - conserved order of duplicated
genes across different chromosomal
segments
WGD in Saccharomyces lineage
Kellis et al., Nature 428, 617-624 (8 April 2004)
Glycolysis
Two types of phosphoglycerate mutase (PGM)
•
Both catalyse the same overall reaction:
– 3-phosphoglycerate → 2-phosphoglycerate
•
cofactor-dependent PGM (dPGM) uses 2,3bisphosphoglycerate (2,3BPG) as a co-factor:
•
3PG + P-Enzyme → 2,3BPG + Enzyme → 2PG + P-Enzyme
•
cofactor-independent PGM (iPGM) has two
bound Mn(II) ions at its active site.
•
3PG + Enzyme → PG + P-Enzyme → 2PG + Enzyme
Two types of phosphoglycerate
mutase (PGM)
• dPGM found in yeasts and vertebrates
• iPGM found in filamentous fungi, plants and
some invertebrates
• Both can be found in bacteria.
• No sequence similarity between the two
forms of the enzyme.
Structure of iPGM
Structure of dPGM
Aim
• To look at the distribution of the two forms of
PGM in different classes of fungi.
• To determine the evolutionary history of
genes encoding these two different enzymes
in fungi – duplications and gene loss.
Steps in making a phylogenetic tree
1. Sample sequences from the species you are
interested in (use BLAST to extract sequences from
databases).
2. Align sequences (using programs such as Clustal,
Muscle).
3. Sample conserved region of alignment (GBlocks)
4. Use these regions to create a phylogenetic tree
that shows the evolutionary relationship between
sequences (using programs such as PhyML).
FASTA formatted file
•
•
>YJL052W_Saccharomyces_cerevisiae
MIRIAINGFGRIGRLVLRLALQRKDIEVVAVNDPFISNDYAAYMVKYDSTHGRYKGTVSH
DDKHIIIDGVKIATYQERDPANLPWGSLKIDVAVDSTGVFKELDTAQKHIDAGAKKVVIT
APSSSAPMFVVGVNHTKYTPDKKIVSNASCTTNCLAPLAKVINDAFGIEEGLMTTVHSMT
ATQKTVDGPSHKDWRGGRTASGNIIPSSTGAAKAVGKVLPELQGKLTGMAFRVPTVDVSV
VDLTVKLEKEATYDQIKKAVKAAAEGPMKGVLGYTEDAVVSSDFLGDTHASIFDASAGIQ
LSPKFVKLISWYDNEYGYSARVVDLIEYVAKA*
>YJR009C_Saccharomyces_cerevisiae
MVRVAINGFGRIGRLVMRIALQRKNVEVVALNDPFISNDYSAYMFKYDSTHGRYAGEVSH
DDKHIIVDGHKIATFQERDPANLPWASLNIDIAIDSTGVFKELDTAQKHIDAGAKKVVIT
APSSTAPMFVMGVNEEKYTSDLKIVSNASCTTNCLAPLAKVINDAFGIEEGLMTTVHSMT
ATQKTVDGPSHKDWRGGRTASGNIIPSSTGAAKAVGKVLPELQGKLTGMAFRVPTVDVSV
VDLTVKLNKETTYDEIKKVVKAAAEGKLKGVLGYTEDAVVSSDFLGDSNSSIFDAAAGIQ
LSPKFVKLVSWYDNEYGYSTRVVDLVEHVAKA*
Sequence alignment and sampling
conserved block
in-paralogues
basidiomycetes
2,3-BPG independent
phosphoglycerate
mutases in fungi
filamentous
ascomycetes
chytrid
in-paralogues
zygomycetes
microsporidia
2,3-BPG dependent
phosphoglycerate
mutases in yeasts
in-paralogues
duplication
out-paralogues
TOR gene duplication events in fungi
TOR: protein kinase,
subunit of a complex
that regulate cell growth
in response to nutrient
availability and cellular
stresses
Summary
• Amino acid sequences evolve more slowly
than DNA sequences.
• Concatenated protein sequences can be used
to make species trees.
• Protein sequences can be used to create a
phylogenetic history of a gene, including
duplication and loss.