Transcript Diversity of genomes and the tree of life

Chapter 1
The diversity of genomes and
the tree of life
Living organisms obtain energy in different ways
- Organotrophic
- Phototrophic
- Lithotrophic
- aerobic
- anaerobic
Some Cells Fix Nitrogen and Carbon Dioxide for others
The greatest biochemical diversity is seen among procaryotic cells
The phototrophic bacterium Anabaena cylindrica
A lithotrophic bacterium, Beggiatoa, gets its energy by oxidizing H2S
and can fix carbon even in the dark
The tree of life has three primary branches: Bacteria, Archaea, and Eucaryotes
The three - kingdom classification of
organisms as proposed by Haeckel in
1866
Classification of
organisms into five
kingdoms first
proposed by Whitaker in
1959.
The five kingdoms were:
Animalia, Planta, Fungi,
Protista, and Monera
Since molecular structures and sequences (of bases in DNA/RNA and of
amino acids in proteins) are more revealing of evolutionary relationships
than classical phenotypes (particularly among microorganisms), beginning
in the 1950s, the basis for the definition of taxa shifted from the organismal
to the cellular to the molecular level
Universal phylogenetic tree in rooted form showing the three domains –
Bacteria, Archaea, and Eucarya
Some genes evolve rapidly; others are highly conserved
Most Bacteria and Archaea have 1000 - 4000 genes
Aug 31, 2004
Microbial Genomes – August 30, 2005
Microbial Genomes – complete; August 30, 2005
As of September 5, 2007
Eukaryotic Genomes – August 30, 2005
As of September 5, 2007
As of September 5, 2007
New genes are generated from preexisting genes
Gene duplications give rise to families of related genes within a single cell
Families of evolutionarily related genes in the genome of Bacillus subtilis
47% of the genes in this bacterium have one or more obvious relatives
Paralogous genes and orthologous genes: two types of gene homology based on
different evolutionary pathways
Orthologs -
genes in two separate species that derive from the same
ancestral gene in the last common ancestor of those two species
Paralogs -
related genes that have resulted from a gene duplication event
within a single genome, and are likely to have diverged in their
function
Homologs -
genes that are related by descent in either way
Paralogous genes and orthologous genes: two types of gene homology based on
different evolutionary pathways
Genes can be transferred between
organisms, both in the laboratory
and in nature
Horizontal gene transfers in early evolution
The function of a gene can often be deduced from its sequence
More than 200 gene families are common to all three primary
branches of the tree of life
Mutations reveal the functions of genes
Spotlight on E. coli
We have a more thorough knowledge of the working of E. coli than of any other
living organism, yet we hardly understand everything about this bacterium
The major features of eucaryotic cells
Eucaryotic cells may have originated as predators
Eucaryotic cells evolved from a symbiosis
Eucaryotes have hybrid genomes
Eucaryotic genomes are big