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 • 405 Complete microbial genomes • Fungi 9 complete 27 others various stages • 312 in progress 20 Eukaryote genomes • 10 vertebrates • 9 plants semi done or major amounts • 1027 organelles • Statistics

3. Mitochondrial genomes (2006) • 893 mt genomes completed

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

6. Snake mtDNA

7. 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

11. 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

12. Plastids

13. 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

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

17. 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

21. Chloroplast evolution

23. Genomes • The whole genomes of over 1000 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.

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

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

26. 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

27. 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

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

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

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

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

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

34. Arabidopsis genes

36. Whole genome duplication