Genomes & The Tree of Life Archaea -

Genomes & The Tree of Life  Archaea -

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 Chloroplast DNA in Green Plants 1. Circular, multi-copy (20100/organelle) 2.

~160,000 bp; ~125 genes 3. Most genes of two types: Photosynthesis Genetic functions (mostly translation) Tobacco (Nicotiana tabacum) chloroplast genome rom Kloppstech, Westhof et al.

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 What about genetic complexity? How many genes do organisms have? Organism Genes Mycoplasma Texas wild rice Taxon prokaryote #

517 E. coli prokaryote 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 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) Genomic and species differences contributing to the wide range of nuclear genome sizes There can be great variation in the: 1. Fraction of highly repeated DNA 2. Abundance of "Selfish DNA (transposons, etc.) 3. Frequency and sizes of introns Humans have many & larger introns 4. Genetic redundancy 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. Genetic Redundancy or Duplication yeast No. of genes 6200 No. of gene families 4380 No. of genes from 1820

duplication Drosophila Arabidopsis 13,600 25,000 8065 11,000 5535 14,000 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. What can you do with whole genomes & sequences? 1. Predict much about the functions of a poorly studied or difficult organism - only ~1-5% of bacteria in the environment are culturable

Transport and metabolic pathways of the Lyme disease spirochaete, Borrelia predicted from the genome sequence. Nature 390, 583 What can you do with whole

genomes & sequences? 1. Predict much about the functions of a poorly studied or difficult organism. 2. Can examine genome-wide expression patterns with microarrays (e.g., cancer versus normal cells). 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. Can simultaneously compare 2 different mRNA preparations by using different colored fluorescent nucleotides. Red- induced mRNA Green- decreased mRNA Yellow unchanged mRNA What can you do with whole genome sequences? 1. 2.

3. 4. 5. 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).

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