Genome Evolution

1. Genome Evolution • 1st mt genome published in 1981 • 1st plastid genome published in 1986 • 1st complete free-living organism genome published in 1995

2. Genome Evolution • 197 Complete microbial genomes • Fungi 8 complete 25 others various stages • 13 Eukaryote genomes • 10 vertebrates • 7 plants semi done or major amounts

3. Mitochondrial genomes (2004) • 621 mt genomes completed

4. Mitochondrial DNA (mtDNA) • several to thousands per cell, 5-10 copies mtDNA per mitochondrion • genes for cellular respiration

6. Mitochondrial DNA • in plants, considerable variation in size, structure, gene arrangement; recombination; evolves slowly • animals, highly compact, structure conserved, evolves rapidly • maternal inheritance; no recombination

10. Plastid genomes • A small structure occurring in the cytoplasm of plant cells. The most important are the chloroplasts. Other plastids contain red, orange, and yellow pigments, giving color to petals and fruits, and some contain starch, oil, etc., acting as storage organelles. • 40 finished • http://megasun.bch.umontreal.ca/ogmp/projects/other/cp_list.html

11. Plastids

12. Chloroplast DNA (cpDNA) • circular double-helix; 20-80 copies per chl. • sequences for • gene expression (tRNA, rRNA, etc.) • for photosynthesis (prot.) • no recombination • uniparental inheritance • conservative evolution • nuclear genetic code

14. Tree of Life and the evolution of mitochondria and plastids • http://tolweb.org/tree?group=life

15. T F D-Loop 12s V Cyt b rRNA P 0 E ND6 16s rRNA L ND5 ND1 Vertebrate mtDNA I Q L M S H ND2 ND4 A N C W Y ND4L ND3 R COI S COIII G ATPase6 COII D K ATPase8

19. Chloroplast evolution

21. Genomes • The whole genomes of over 800 organisms can be found in Entrez Genomes. The genomes represent both completely sequenced organisms and those for which sequencing is in progress. All three main domains of life - bacteria, archaea, and eukaryota - are represented, as well as many viruses.

22. Genome miniaturization • Use and disuse philosophy • Genome size following endosymbiosis • Reclinomonas(62 protein encoding genes) • Genome size in parasites • Epiphagus (Beech drop)

23. Genes are just one of many types of DNA sequences • single copy genes • multiple copy genes • noncoding repetitive sequences (often, most of genome!)

24. Haploid DNA values • C values • vary enormously among organisms diatom Navicola = 35 (in millions of bases) diatom Coscinodiscus = 25,000 ciliate Paramecium aurelia = 190 ciliate Paramecium caudatum = 8,600 chicken Gallus = 1,200 tobacco Nicotiana = 3,800 human Homo = 3,600 onion Allium = 18,000 lungfish Protopterus = 140,000 fern Ophioglossum = 160,000

25. The C - value paradox • No correlation between DNA amount and morphological complexity! • DNA denaturation experiments show relatively low amount is single copy • Results indicate that nongenic DNA is the cause of the C –value paradox

26. increase in Genome size • Regional (particular sequence is multiplied) • Gene duplication, unequal crossing over • Global (entire genome or chromosome is duplicated) • Polyploidization

27. Polyploidy • Allopolyploidy: the combination off genetically distinct chromosome sets • Autopolyploidy: multiplication of one basic set of chromosomes

28. Tetraploidy • Genome doubling • Most common • Is found in most organisms

29. Survive only rarely • Prolongation of cell division time • Increase the volume of the nucleous • Increase # of chromosome disjuctions • Genetic imbalance • Interference with sexual differentiation

30. Arabidopsis • 115.4 megabase out of 125 MB • Whole genome duplication, gene loss and lateral transfer from plastid

32. Arabidopsis genes

34. Whole genome duplication