1. Genomes & The Tree of Life
Archaea - small circular genome
Prokarya - small to very small (e.g., Mycobacterium) circular genomes
Eukarya - 3 genomes
Mitochondrial – small to micro-sized, linear and circular, prokaryotic origin
Chloroplast – small, circular, prokaryotic origin
Nucleus – large, linear chromosomes; evidence of archaea, prokaryotic and “protoeukaryotic” origins

2. Chloroplast DNA in Green Plants
Circular, multi-copy (20-100/organelle)
~160,000 bp; ~125 genes
Most genes of two types:
Photosynthesis
Genetic functions (mostly translation)

3. Tobacco (Nicotiana tabacum) chloroplast genome
Co-transcribed genes are indicated in the center = polycistronic units or operon-like genes; rps12 is split into two halves that are spliced in trans.
Thick segments outside the circle are differences with rice (Oryza); the light portions are not in the rice IR.
The brackets 1,2,3 are sites of inversions in rice.
From Kloppstech, Westhof et al.

4. Plant nuclear genome sizes are large and widely varied.
x 1000 to get bp
Lilium longiflorum (Easter lily) = 90,000 Mb
Fritillaria assyriaca (butterfly) = 124,900 Mb
Protopterus aethiopicus (lungfish) = 139,000 Mb
10,000-fold variation in angiosperms: Arabidopsis is smallest ~150 MB, Rice is ~440 MB, maize is ~2500 MB, lily is largest at ~90,000 MB (Fig in Buchanan).
Recently, an amphibian has been found to have a genome larger than the lily (Amphioxus?).

5. What about genetic complexity?
How many genes do organisms have?

6. Organism Taxon # Genes
Mycoplasma
prokaryote
517
E. coli
4300
Archaeoglobus
archaeon
2500
Cyanidioschyzon
rhodophyte
4700
Saccharomyces
yeast
6000
Drosophila
insect
13,600
Chlamydomonas
chlorophyte (unicell)
15,500
Arabidopsis
angiosperm, dicot
25,000
Homo sapiens
primate
32,000
Oryza (rice)
angiosperm, monocot
32-39,000
Cyanidioschyzon- smallest eukaryotic genome.
Texas wild rice

7. Mycoplasma : How many genes essential for growth (under lab conditions)?
Using transposon mutagenesis, ~150 of the 517 genes could be knocked out; ~ 300 genes deemed essential (under lab conditions), which included:
~100 of unknown function
Genes for glycolysis & ATP synthesis
ABC transporters
Genes for DNA replication, transcription and translation
Science 286, 2165 (1999)

8. Genomic and species differences contributing to the wide range of nuclear genome sizes
There can be great variation in the:
Fraction of highly repeated DNA
Abundance of "Selfish DNA“ (transposons, etc.)
Frequency and sizes of introns
Humans have many & larger introns
Genetic redundancy
Humans have many large introns; yeast and plants have small introns (yeast also has few introns).

9. Genetic Redundancy
The sizes of many gene families has increased in some organisms more than others
Accounts at least partially for the relatively high genetic complexity of plants.

10. Genetic Redundancy or Duplication
yeast
Drosophila
Arabidopsis
No. of genes
6200
13,600
25,000
No. of gene families
4380
8065
11,000
No. of genes from duplication
1820
5535
14,000
Why more gene duplicates in plants? Need them for survival outdoors?

11. Impact of Horizontal Transfer on Genomes
~ 20% of the E. coli genome was obtained by lateral transfer.
Viral and bacterial pathogens can transfer DNA from host to host.
Some nuclear genes came from organellar genomes (some relatively recently).
Selfish DNAs such as mobile introns and transposons occasionally transfer horizontally.
HT is quite prevalent among unicellullar organisms (germ line and vegetative cell lines the same).

12. What can you do with whole genomes & sequences?
Predict much about the functions of a poorly studied or difficult organism
- only ~1-5% of bacteria in the environment are culturable

13. predicted from the genome sequence.
Transport and metabolic pathways of the Lyme disease spirochaete, Borrelia
predicted from the genome sequence.
Prokarya
Nature 390, 583

14. What can you do with whole genomes & sequences?
Predict much about the functions of a poorly studied or difficult organism.
Can examine genome-wide expression patterns with microarrays (e.g., cancer versus normal cells).

15. Can immobilize 1,000-5,000 DNAs (genes) on one microarray glass slide.
1. Hybridize slide to cDNAs that were obtained by reverse transcription from total mRNAs with a fluorescent nucleotide.
2. Scan slide with a laser and process fluorescent image.
Red dNTP for treatment (hormone), green dNTP for control (no drug).
Can simultaneously compare 2 different mRNA preparations by using different colored fluorescent nucleotides.
Red- induced mRNA
Green- decreased mRNA
Yellow – unchanged mRNA

16. What can you do with whole genome sequences?
Predict much about the functions of a poorly studied or difficult organism.
Can examine genome-wide expression patterns with microarrays (e.g., cancer v. normal cells).
Identify new drug targets.
More rapidly identify genes linked to a trait.
Rapidly identify a gene for an identified protein by mass spectrometry – compare mass spectrum of the protein with the predicted patterns from all of the genes of a sequenced genome (Proteomics).
3. e.g., antibiotic target could be a gene unique to the pathogen.