2. Eukaryotic genes are interrupted by large introns. In eukaryotes, repeated sequences characterize great amounts of noncoding DNA. Bacteria have compact genomes rich in genes, having fewer noncoding regions and no introns. Eukaryotic genomes have much more DNA content than bacteria. While eukaryotes have more genes than bacteria, the difference in gene content is not as great as the difference in DNA content: there is much more noncoding DNA in eukaryotes In fact, gene-coding regions comprise only about 2% of the human genome.

4. The first eukaryotic organism to have its entire genome sequenced was yeast, Saccharomyces cerevisiae -1996 Yeast genome contains 5885 protein coding genes: 1. 140 genes specifying ribosomal RNA (rRNA) 2. 40 genes for nuclear RNA molecules 3. over 200 transfer RNA (tRNA) genes Deletion in some genes (18.7%) has a lethal effect while on other genes does not, due to many duplicated genes in the yeast genome Genome sequences of other eukaryotic genomes soon followed: 1. Worm, Caenorbabditis elegans -1998 2. Fruit Fly, Drosophila melanogaster and plant model Arabidosis thaliana - 2000 3. Nearly complete Human Genome sequence-2004

5. Gene density varies among different eukaryotic species – ranging from 1gene/1900 bp in baker’s yeast to 1gene/127 900 bp in humans Species 1,300 4,300 1,900 4,900 9,500 4,500 127,900 1,996 5,317 6,268 20,516 13,792 25,706 22,287 2,497,519 22,820,308 12,057,909 100,291,841 131,000,899 116,566,763 2,851,330’913 Microsporidian Malaria protozoan baker’s yeast roundworm Fruit fly Mouse ear cress Human Protists Encephalitozoon cuniculi Plasmodium falciparum Fungi Saccharomyces cerevisae Nematode Caemorhabditis elegans Insects Drosophila melanogaster Plant Arabidopsis thaliana Vertebrates Homo sapiens Gene Density (bp/gen e) Predicted number of genes Genome Size in nucleotide pairs Common Name Table: Size and Predicted Gene Content of Selected Eukaryotic Genomes

6. Genomes of single-celled eukaryotes eg. yeast have one gene for every 1000-2000 bp Gene density decreases with the increased developmental complexity eg. gene density is the lowest in mammals i.e 1gene for every 115,000 to 129,000 bp Low gene density in the larger eukaryotic genomes, is also due to the considerable amounts of repetitive DNA Yeast contain very little repetitive DNA, although 30% of its genes are duplicated. In multicellular eukaryotes there are lots of repetitive DNA and in most cases, are directly related to genome size Only about 10% of C. elegans contains repetitive DNA whereas in large genomes of mammals there are over 40% of repeat sequences. Most of these repeats are derived from transposable genetic elements (transposons)

7. Transposons are found in genomes of many organisms (bacteria, fungi, protozoa, plants and animals) and are structurally diverse. Transposons are mobile DNA sequences Highly repetitive DNA is more abundant in larger genomes but there is no direct correlation between the amount of highly repetitive DNA and genome size. Much of highly repetitive DNA in most species including humans, is present in the regions of chromosomes that flank the centromeres (centromeric heterochromatin) and in the telomeres This DNA is difficult to sequence, most of the unsequenced DNA in human genome (472million bp) consist of highly repetitive sequences

8. Introns are more prevalent and longer in the large eukaryotic genome. Intergenic regions are also longer in the larger eukaryotic genomes. The number of distinct protein domain encoded by genes does not vary much between genome sizes. Predicted number of proteins domains encoded by A. thaliana, D. melanogaster and human genomes are 1012, 1035, and 1262, respectively Species 4,900 9,500 4,500 127,900 20,516 13,792 25,706 22,287 100,291,841 131,000,899 116,566,763 2,851,330’913 roundworm Fruit fly Mouse ear cress Human Nematode Caemorhabditis elegans Insects Drosophila melanogaster Plant Arabidopsis thaliana Vertebrates Homo sapiens Gene Density (bp/gen e) Predicted number of genes Genome Size in nucleotide pairs Common Name Table: Size of Selected Eukaryotic Genomes

9. Distantly related species have many genes in common, e.g. 18% of Arabidosis and 50% of Drosophila have human homologues The proportion of homologous genes is even greater in closely related species. Furthermore, in closely related species, the entire chromosome often show a similar arrangement of genes

10. Discovered in 1970s Different types of introns Two hypotheses of origin ‘Introns early’  Ancient and gradually being lost from eukaryote genomes ‘Introns late’  evolved relatively recently and gradually accumalating in eukaryote genomes

12. Self splicing

13. ‘introns early’ ‘exon theory of genes’ – Gilbert 1987

15. All genomes originally possessed introns Bacterial genomes do not have GU-AG introns Therefore must have been lost at an early stage How? Without disrupting genes? Not really feasible  introns late hypothesis

16. To begin with, genes had no introns Introns developed in eukaryote genomes and proliferated Group II introns and GU-AG introns similar in terms of splicing Group II moved from organellar genomes to nuclear eukaryote genomes? Or did GU-AG introns evolve from group II introns? – introns early hypothesis

17. Position of introns in homolgous genes from unrelated organisms should be similar since all descended from ancestral gene with introns Initial evidence showed this was true

19. Later evidence (more lineages examined) its was shown that some introns were lost in some positions and gained in others Introns must have moved by recombination events Fits both hypotheses

20. For introns early, introns should split domains of different proteins Again, initial evidence supported this But more globulin genes showed more than 10 introns- therefore no correlation between introns and junctions between domains Domain duplication and shuffling

23. Subsequent gain and loss of introns over time in different lineages

24. Belshaw, R. and Bensasson, D. (2006) The rise and fall of introns. Heredity. 96:204-213.