Comparative Genomics

general term for genes/proteins that have similar sequence and are derived from a common ancestral sequence

homologs dervied through speciation

homologs derived through gene duplication

a: homologous

b: paralog

closer: human alpha-globin and chimpanzee alpha-globin

• genes with similar sequence due to convergent evolution

• functional analogs: proteins that have non homologous seq but perform the same molecular function

matching a given sequence to other known genes or proteins in a database

BLAST

finds subsequences with the best possible alignment

identical: AA are the same

positive: AA may be different but have similar biochemcal properties

• by an E value

• E represents number of matches expected at random when searching a database of this size with a query of thie length

• E =1 == 1 match would be expected at random from database

• E=10^-6 = 1 in a milion chance of observing such a match at random

• the lower the evalue the higher the confidence that sequences are homologous ( it is not random that they matcH)

BLAT

• uses faster algorithm based on 11 mers ( =11 bases of DNA) or 4mers (=4 AA)

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

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

BWA, bowtie, Stampy & NextGenMap

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

reciprocal best hits

this approach compares genes in two genomes using two steps:

1. gene A from species 1 is used for a BLAST search of the species 2 genome, the best match is gene A’

2. gene A’ from species 2 is then used for BLAST search of species 1 genome. If the best match is gene A then these are reciprocal best hits and are considered orthologs

-> result can be missleading if there are independetn gene duplication/loss events in the two species

over 44000

a) Bacteria - common commensal and pathogenic bacteria

b) archae - ancient group of mostly extremophiles

• Mycobacterium tuberculosis

  • 3959 coding genes & 6 pseudogenes

• Mycobacterium leprae

  • 1604 coding genes & 1116 pseudogenes

previously protein-encoding genes that have mutations that disrupt their coding sequence (no function anymore)

• lost funcition of about half of its genes

• == reduktive evolution

• only gros in host cells

Mycoplasma with 580 kb

• only genes necessary for survival are left

• rickettsia sp. (1.2 MB)

  • cause rockey mountain and mediterranean spotted fever in humans

• Borrelia burgdorfei (1,4 Mb)

  • causes lyme disease in human

• need other organism to survive

• e.g. aphids, buchnera sp.

• genes involved in energy metabolism

• metabolic intermediates & energy sources

• gene for aa & vitamin syntehesis

buchnera aphidicola

• 10% of its genes are involved in synthesis of essentail amino acids not synthesized by the host( aphids)

• however it has lost the genes needed to synthesize aa that are made by the host

(Blattläuse ernähren sich von Pflanzensaft, der reich an Zucker ist, aber fast keine essenziellen Aminosäuren enthält.

Die Symbiose (Mutualismus): Die Laus bietet Buchnera ein Zuhause in Spezialzellen (Bakteriozyten) und liefert Zucker. Das Bakterium stellt im Gegenzug essenzielle Aminosäuren (z. B. Tryptophan, Leucin) für die Laus her.

Genetische Folge: Buchnera hat durch radikalen Genverlust (nur ca. 600 Gene) seine Eigenständigkeit verloren und funktioniert heute fast wie ein zelluläres Organell. Beide können ohne einander nicht überleben.)

bacterium that is living inside of an organsim

• carsonella (160 kb, 182 genes)

  • live in sap eating insects (low protein diet)

• half of genes are involved in translation & aa metabolism

• 1. selective advantage for smallness

  • bacteria with smaller genomes can replicate faster and outcompetet those with larger genomes that replicate slower

  • no becuase:

    • small changes in DNA contetn do not appear to affect replication rate

    • many pathogens retain non functional pseudogene DNA

    • small genomes are not more densley packed than large

• mutation pressure

  • if there is not slective pressure to maintain a gene it will eventually be lost due to mutation with

    • bias towards deletion

    • bias towards mutation to A or T

-> obligate pathognes & endosymbionts tend to have small genomes and high %AT

• live at 80-100 C mostly Archae some bactera

live at 50-65 C, mostly archae some bacteria

live at under 50 C mostly bacteria, some Archaea

COG (Clusters of orthologous groups) (protein based)

1 protein our of 2791 is specific hyperthermophiles

• reverse gyrase

  • large protein

  • 2 protein domain: helicase & topoisomerase

  • introduces twists into double stranded circular DNA & may help prevent undwinding of DNA at high temperatures

Search Query Database

tool input. database

blastn nucleotide nucleotide

blastp protein protein

blastx translated nucleotide protein

tblastn protein translated nucleotide

tblastx translated nucleotide translated nucleotide