Nothing in (computational) biology makessense except in the light of evolution

after Theodosius Dobzhansky (1970)

Comparative genomics, genome context and genome annotation

Genome context analysis and genome annotation

Using information other than homologous relationshipsbetween individual gene/proteins for functional prediction(guilt by association)

•phyletic patterns•domain fusion (“Rosetta Stone” proteins)•gene order conservation•co-expression•….

Types of context analysis:

Goals: • Using gene sets from complete genomes, delineate families of orthologs and paralogs - Clusters of Orthologous Groups (of genes) (COGsCOGs) • Using COGs, develop an engine for functional annotation of new genomes

• Apply COGs for analysis of phylogenetic patterns

COG:

- group of homologous proteins such that all proteins from different species are orthologs (all proteins from the same species in a COG are paralogs)

Complete set of proteins from the analyzed genomes

FULL SELF-COMPARISON (BLASTPGP, no cut-off)

Collapse obvious paralogs

Merge triangles with common edges

CONSTRUCTION OF COGs FOR 8 COMPLETE GENOMES

Detect all interspecies Best Hits (BeTs) between individual proteins or groups of paralogs

1

2

3

Detect all triangles of consistent BeTs

4

5

Detect groups with multidomain proteins

and isolate domains

REPEAT STEPS 3-5

6

COGs

A TRIANGLE OF BeTs IS A MINIMAL, ELEMENTARYCOG

A RELATIVELY SIMPLE COG PRODUCED BY MERGING ADJACENT TRIANGLES

A COMPLEX COG WITH MULTIPLE PARALOGS

Current status of the COGs

11 Archaea + 1 unicellular eukaryote + 46 bacteria = 58 complete genomes

149,321 proteins 105,861 proteins in 4075 COGs(71%)

4 animals + 1 plant + 2 fungi + 1 microsporidium = 8 complete genomes

142,498 proteins 74,093 proteins in 4822 COGs (52%)

Prokaryotes

Eukaryotes

COGnitor...

…IN ACTION

The Universal COGs

Search for genomic determinants of hyperthermophily

Search for uniquearchaeo-eukaryoticgenes

A complementary pattern:search for unique bacterial genes

Essential function…but holes in the phyleticpattern

Strict complementary pattern

Relaxed complementary pattern

Relaxed complementary pattern with extra restrictions

Conservation of gene order in bacterial species of the same

genus1

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401

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M. genitaliumvs

M. pneumoniae

Conservation of gene order in closely related bacterial genera

C. trachomatisvs

C. pneumoniae

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1001

1 101 201 301 401 501 601 701 801

Lack of gene order conservation - even in “closely related” bacteria of the same

Proteobacterial subdivision

P. aeruginosavs

E. coli

1101201301401501601701801901

1001110112011301140115011601170118011901200121012201230124012501260127012801290130013101320133013401350136013701380139014001410142014301440145014601470148014901500151015201530154015501

1 101

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ecoli

paer

<0.3

0.3-0.8

0.8-1.3

>1.3

Genome Alignments - MethodProtein sets from completely genomes

BLAST cross-comparison

Pairwise Genome AlignmentLocal alignment algorithmLamarck (gap opening penalty,gap extension penalty); statisticswith Monte Carlo simulations

Table of Hits

Template-Anchored Genome Alignment

Genome Alignments - Statistics

0.0

0.1

0.2

0.3

0.4

0.52 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

>20

cpneu-ctra

mjan-mthe

bsub-ecoli

drad-aero

Distribution of conserved gene string lengths

Genome Alignments - StatisticsPairwise No. No. % in % inalignments: strings genes Gen1 Gen2

all homologsecoli-hinf 138 566 13% 33%ecoli-bsub 89 322 8% 8%ecoli-mjan 10 30 1% 2%

probable orthologsecoli-hinf 105 482 11% 28%ecoli-bsub 34 168 4% 4%ecoli-mjan 12 33 1% 2%

Genome Alignments - Statistics

0

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aero af

ul

mjan

mth

epy

ro

aqua

ebb

urbs

ub cac

cjej

cpne

uct

radr

adec

oli hinf

hpyl

mge

n

mpn

eum

tub

nmen

rpxx

syne

cho

tmar tp

aluu

re

Not in gene strings

In non-conserved gene strings (directons)

In conserved gene strings

Breakdown of genesin the genome

Genome Alignments - StatisticsFraction of the genome in conserved gene strings - from

template-anchored alignments

Minimum Synechocystis sp. 5%

Aquifex aeolicus 10%Archaeoglobus fulgidus 13%Escherichia coli 14%Treponema pallidum 17%

Maximum Thermotoga maritima 23%Mycoplasma genitalium 24%

Context-Based Prediction of Protein Functions

A Novel Translation Factor (COG0536)

L21 L27 GTPase?GTP-bindingtranslation

factor

Context-Based Prediction of Protein Functions

A Novel Translation Factor (COG0012)

TGS domaincontainingGTPase?

Peptidyl-tRNAhydrolase

GTP-bindingtranslation

factor