Chapter 1 The 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 H2Sand 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 in1959.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 subtilis47% of the genes in this bacterium have one or more obvious relatives

Paralogous genes and orthologous genes: two types of gene homology based ondifferent evolutionary pathways

Orthologs - genes in two separate species that derive from the sameancestral gene in the last common ancestor of those two species

Paralogs - related genes that have resulted from a gene duplication eventwithin a single genome, and are likely to have diverged in theirfunction

Homologs - genes that are related by descent in either way

Paralogous genes and orthologous genes: two types of gene homology based ondifferent evolutionary pathways

Genes can be transferred betweenorganisms, both in the laboratoryand 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