1- Genomics

• Genomics


  Study of genomes, or ALL the DNA of an organism
• Types of genomics


  • Structural genomics
  • Comparative genomics
  • Functional genomics
• Structural genomics


  • Architecture, genetic mapping, sequencing & assembly
• Comparative genomics


  Multiple genomes allow for comparisons
• Functional genomics


  What do all of the genes do?
• Genome studies are revolutionizing evolutionary biology to a greater extent than DNA sequencing has up to this point
• The Human Genome project was initiated in 1990 and completed 13 years later, but now genomes can be sequenced faster
• Comparative genomics started only 15 years ago for simple genomes, and only 10 years ago for complex eukaryotes
• Every year a new vertebrate genome is sequenced, every week a microbial genome of ca. 2 million bp is sequenced; This rate of sequencing is increasing
• Genomes sequenced by 2009


  • Eukaryotes: ~60
  • Bacteria: ~500
  • Archea: ~40
• Genomes sequenced by 2024

  • Eukaryotes: ~37K
  • Prokaryotes: ~707K
  • Viruses: ~75K
• The Villanova ABI sequencer was used in the Human Genome Project, but more modern sequencers completely automate the process with robots from DNA extraction to PCR to sequencing
• 1 robot can accomplish a day's work for a human in 1 hour
• Two approaches to sequencing genomes


  • The mapping or hierarchical approach: Divide the genome into segments with genetic and physical maps, then home in on the details
  • The whole-genome or shotgun approach: Entire genome broken into random, overlapping segments that are then sequenced
• Genetic map


  Genetic crosses and frequency of crossing over are used with polymorphic genetic markers to map the location of genes on chromosomes
• Humans have 24 genetic maps - 22 autosomal (non sex) chromosomes, the X and Y chromosomes
• Physical map


  More detailed information about genetic markers obtained from genome sequence data
• Restriction enzymes with large restriction sites


  Can be used to develop a physical map of chromosomes, but have low resolution
• Sequence-tagged site


  Unique genetic markers in genome, very helpful for genetic maps
• Clone Contig Map


  Higher resolution than restriction maps, can be used to sequence entire genome. Get a bunch of YAC or BACs with partially overlapping clones that are continuous for genome's chromosome, then sequence the inserts.
• Shotgun approach


  1. Take whole genome

  2. Shear it, put it in 2 kb vectors & 10 kb vectors

  3. Sequence it all (500-1000 bp at a time)

  4. Presto genome
• The shotgun approach is very fast, but limited by computer & repetitive DNA
• Annotating a genome


  1. Open Reading Frames (ORFs): Computer searches for start codons and stop codons to identify areas that are potential genes

  2. Only ORFs with more than 100 codons are likely genes
• Over 35% of genes in ANY organism (including Human) have no deducible function
• The human genome:

  • Genome sequenced in 2003
  • Genes encode noncoding RNA or proteins
  • Approximately 21,000 protein-coding human genes
  • Approximately 22,000 other human genes
  • Repeat sequences are > 50% of genome.
  • Ethnicities have few unique alleles of genes.
  • Greatest amount of genetic variation is in Africa
• The number of human genes is likely to change in the future as additional scrutiny is required for some genes identified in recent studies
• 80,000 years ago there were only 10,000 humans on the planet
• Human genomes vary by at least 9 million base pairs
• There is more genetic diversity within races than between them in most cases
• Caenorhabditis elegans (C. elegans)


  • A hermaphroditic roundworm (1 mm) that lives in soils throughout the world, with a genome of 6 chromosomes sequenced in 1998 and found to have 20,000 genes
  • From egg to adult in 3 days
  • Entire genome (6 chromosomes) sequenced in 1998
  • Genome has 20,000 genes
  • 15% genes code for gene expression
• Genome characteristics

  • GC content varies (e.g. Plasmodium falciparum 20% GC, Thermus thermophilus 70% GC)
  • Gene content and density varies (e.g. Mycoplasma gentialium 480 genes (tiny genome), Homo sapiens ~21,000 genes)
• Methanococcus jannaschii


  An archaea that is a hyperthermophilic methanogen (bacteria that thrives in high temperatures and pressure without oxygen) with genes for energy, cell division and metabolism like bacteria, and genes for DNA replication, transcription & translation like eukaryotes, confirming archaea as a unique branch of life
• Arabidopsis thaliana


  First flowering plant genome sequenced in 2000, a model organism with 25,500 genes (more than humans), including 100 similar to human disease-causing genes
• Bacterial genome trends


  • Mycoplasma has smallest genome at 0.58 Mb
  • Bradyrhizobium soil bacteria has largest at 9.11 Mb
  • On average, about 1 gene per 1-2 kb
  • 85-90% of genomes are coding genes
• Archaea genome trends


  • Used to be considered bacteria- all live in extreme environments
  • Thermoplasma genome is 1.56 Mb
  • Methanosarcina genome is 5.75 Mb
  • About one gene per 1-1.2 Kb
  • 85-90% of genome is coding genes
• Eukaryote genome trends


  • Many examples of partial or whole genome duplications, lots of repetitive DNA
  • Gene density decreases with complexity (e.g. fruit fly 1 per 13 kb, humans 1 per 116 kb)
  • Average mammal genome is 3.1 Gb (Gigabase = billion base pairs), frogs 5.0 Gb, salamanders 34.5 Gb and reach 150Gb
• Fugu


  An unusual vertebrate with a genome size of only 400 Mb, very few introns, and few gene deserts (regions with little genes), with many genes similar to humans so finding a gene in Fugu makes it easier to find in humans
• Bioinformatics


  A marriage between biology with math and computer science, used to find genes, align sequences, predict structure and function, and figure out evolutionary relationships
• GenBank


  A database containing millions of DNA sequences for every organism, used for comparative genomics