lecture 15
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Discipline of mapping, sequencing, analyzing, and comparing genomes
Genomics
First genome sequenced
Completed in 1976 RNA virus MS2 3569 bases
First cellular genome
Completed 1995 (J. Caig Venter) Utilized shotgun sequencing Haemophilus influenzae
Determination of the order of basis in a DNA molecule (primary structure)
Sanger method
DNA sequencing/chain termination/Sanger method requirements
Dideoxynucleotide triphosphate Oligonucleotide primer one kind per rxn DNA polymerase and normal deoxynucleotides Highly purified DNA template
Can determine 500-1000 nt sequence/reaction
Sanger method
Genome annotation Allow for predictions of metabolic pathways and transport systems
Comparative analysis
Genome annotation Open reading frames Start codon preceded by…
Shine-Delgarno
Prokaryotic genomes From 0.5 Mbp to >10 Mbp (Megabase pairs) Smallest genomes are those of ____ and ____
Parasites/endosymbionts
Smallest genome of a free-living cell
1354 genes Pelagibacter ubique
Usually 1 ORF per ____ bp
1000
All cells must perform certain tasks
DNA replication, translation, transcription
More of the genome is often dedicated to
Regulatory functions metabolic flexibility
____ genes are related in (primary) sequence due to shared evolutionary ancestry
Homologous
Genes with similarity due to supplication of an ancestral gene; often have related but distinct function
Paralogs
Genes with similarity due to evolution/speciation of their hosts; usually have the same or similiar function in their respective hosts
Orthologs
Horizontal gene transfer Due to various methods of genetic exchange
Transformation, transduction, conjugation
Horizontal gene transfer It can involve transfer of ____ or ____ DNA
Plasmids/chromosomal
What genes are subject to HGT
Genes for drug resistance, pathogenicity, etc Does not usually include genes for core processes such as DNA replication, translation, etc
____% of the hyperthermphilic bacterium Thermooga maritime genome is thought to have come from Archaea by HGT
20
Core genome
Shared by all strains, include necessary (core) functions, typically vertical descent
Dispensable genome
Present in some strains, optional or accessory functions, can include plasmids/prophages/transposons/insertion /sequences/integrons/chromosomal islands/vertical and horizontal descent
Presumed to be of foreign origin; large regions of DNA acquired by HGT
Chromosomal islands
Chromosomal island Base composition and codon usage differ from
Surrounding DNA