Comparative Genomics

• genes/proteins with similar sequence

• derived from common ancestor

can be classified to orthologs and paralogs

homologs derived thorugh speciation (in different species)

e.g human alpha-globin and chimpanzee alpha-globin

homologs derived through gene duplication

e.g Human alpha-globin and human beta-globin

genes/proteins that perform similar functions, BUT dont share common ancestral gene

due to convergent evolution

e.g wings of birds and wings of insects

bioinformatics technique to identify sequences that are similar to given sequence

first step after genome sequence has determined and genes predicted

—> many complete genomes are sequenced —> compare one genome to another —> determine how many genes they have in common

distantly related species —> often impossible to distinguish orthologs and paralogs

tools: BLAST, FASTA

databases: GenBank, Uniprot, PDB

Basic Local Alignment Search Tool

most commonly-used homology search tool

not align complete sequences, BUT finds subsequences with best possible alignment

• identical: amino acids are same

• positive: amino acids may be different, but similar biochemical properties (size, charge)

matches scored by E-value —> number of matches expected at random when searching database of this size with query of this length

similar to probability (p-value)

E=1 —> 1 match would be expected at random from database

lower the E-value, the greater the confidence that sequences are homologue

faster algorithm based on 11-mers (DNA) or 4-mers (amino acids) to find matches of:

• 95% or greater identity over 25 bases or more (DNA)

• 80% or greater identity over 20 amino acids or more (Proteins)

very quickly map 35-250 base sequences to reference genome

align complete sequences and expect a very close match with the reference sequence

• BWA

• bowtie

• Stampy

• NextGenMap

1. Gene A from species 1 for BLAST search of species 2 genome

   —> best match/hit is gene A’

2. Gene A’ from species 2 for BLAST search of species 1 genome

   —> best match/hit is gene A —> orthologs

BUT: does not guarantee that true orthologs

• Bacteria —> common commensal (lives in relationship with host, without harming) and pathogenic bacteria

• Archaea —> ancient group of mostly extremophiles (live at high temp, …)

• small genom

• little repetetive DNA

• no introns

• medical importance

• Mycobacterium leprae —> causes leprosy

  4000 coding genes, 6 pseudogenes

• Mycobacterium tuberculosis —> causes tuberculosis

  1600 coding genes, 1100 pseudogenes

segments of DNA similar to functional genes, but are non-functional

previously protein-encoding genes with mutations —> lost ability to encode proteins

• insertion of stop codon

• insertion/deletion of bases that causes frameshift in coding regions

lost function of half of its genes

—> longest doubling time of any known bacteria —>

—> cannot be cultured in laboratory (only grows in host cells)

smallest genome known in free-living bacteria (580 Kb)

ancestors had many more genes, that were lost over evolution

• Mycoplasma genitalium (580Kb)

• Ricksettia sp. —> Rocky Mountain Fever (1.2Mb)

• Borrelia burgdorferi —> Lyme disease (1.4Mb)

• many genes involved in energy metabolism:

  —> metabolic intermediates and energy sources taken from host (e.g Buchnera aphidicola)

• many genes required for amino acids and vitamin synthesis

  —> provided by host (e.g Carsonella)

• Selective advantages for smallness

  bacteria with smaller genomes can replicate faster (outcompete others)

  • small changes in DNA content dont affect replication rate

  • many pathogens retain non-functional pseudogene DNA

  • small genomes not more densely packed

• Mutation pressure

  if not selective pressure to maintain gene —> lost due to mutation

  there is bias towards

  • deletions

  • mutations to A or T

—> obligate pathogens and endosymbionts tend to have small genomes and high %AT

• Hyperthermophiles: live at 80-100 C (mostly Archaea, some bacteria

• Thermophiles: live at 50-65 C (mostly Archaea, some bacteria)

• Mesophiles: live under 50 C (mostly bacteria, some Archaea)

tested by searching the COG (Clusters of Orthologous Groups) database

• consider evolutionary relationships

  • some Archaea dont live in high temperatures

  • some bacteria do live in high temperatures

  —> presence of gene should follow temperature, not phylogenetic relationship

—> 1 of 2800 specific to hyperthermophiles

• twists into double-stranded circular DNA

• reverse gyrase

• large protein (>1000)

• 2 protein domains (helicase, topoisomerase)

• What is conserved? - What are common requirements for eukaryotic life?

• What is different? - What makes each species unique?

• D. melanogaster (fly)

• C. elegans (worm)

• S. cerevisiae (yeast)

• Fly, about 50%

• Worm, about 35%

• Yeast, about 37%

• 230/289 (80%) in fly

• 212/289 (73%) in worm

• 120/289 (42%) in yeast

Arabidopsis thaliana - 25.000 genes

• fly - 14.000 genes

• worm - 19.000 genes

• human - 21.000 genes

Arabidopsis has more genes present as paralogs

higher percentage of A. genes are part of multi-gene family

—> gene duplication had huge role in plant genome evolution

Oryza sativa

40.000-50.000 genes

genome size: 430 Mb

• 80-85% of Arabidopsis had homolog in rice

• 50% of rice had homolog in plant

• 30% of genes shared in plant + rice had homolog in yeast, fly or worm

movement of genetic material between organisms in a manner other than traditional reproduction

—> allows for direct transfer of genes between different species

studies suggest yes, BUT

subsequent analyses significantly reduced number (fewer than 40 potential bacterial genes)

hypothesis suggest yes BUT

later studies: these genes are more likely result of independent gene loss in some eukaryotes

35 genes tested in humans by PCR —> confirmed to be real

many of these have orthologs in other vertebrates

these genes were present in common ancestor in eukaryotes

—> lost in yeast, worm, fly, plant, …

require many independent cases of gene loss

when more non-vertebrate eukaryote genomes are searched

—> homologs to these genes can be found

supports independent gene loss in some eukaryotes

tests hypothesis by comparing sequences

if true —> human genes should be more similar to bacterial genes than to other non-vertebrate

below 40, expected to decrease as more eukaryotic genomes are sequenced

1. Contamination - unlikely. 35 genes were tested in PCR —> real, many have orthologs in other vertebrates

2. genes in common ancestor in eukaryotes, lost in yeast, fly, …

   —> requires many independent cases of loss

3. transfer from human to bacteria - 113 found in many diverse bacteria species —> requires many independent gene transfer

4. authors prefer genes directly transferred from bactera to vertebrates (at least 113)

at least 98%

• small scale: well conserved —> same genes found in same order (synteny)

• large scale: many chromosomal re-arrangements

e.g gene blocks from mouse chromosome 16 are spread over 6 different human chromosomes