* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Document
Short interspersed nuclear elements (SINEs) wikipedia , lookup
X-inactivation wikipedia , lookup
Koinophilia wikipedia , lookup
Vectors in gene therapy wikipedia , lookup
Epigenetics of neurodegenerative diseases wikipedia , lookup
Human genetic variation wikipedia , lookup
Copy-number variation wikipedia , lookup
Mitochondrial DNA wikipedia , lookup
Whole genome sequencing wikipedia , lookup
Polycomb Group Proteins and Cancer wikipedia , lookup
Quantitative trait locus wikipedia , lookup
Essential gene wikipedia , lookup
Gene desert wikipedia , lookup
Segmental Duplication on the Human Y Chromosome wikipedia , lookup
Genetic engineering wikipedia , lookup
Adaptive evolution in the human genome wikipedia , lookup
Therapeutic gene modulation wikipedia , lookup
Nutriepigenomics wikipedia , lookup
Transposable element wikipedia , lookup
Oncogenomics wikipedia , lookup
Biology and consumer behaviour wikipedia , lookup
Gene expression programming wikipedia , lookup
Genomic library wikipedia , lookup
Ridge (biology) wikipedia , lookup
Epigenetics of human development wikipedia , lookup
Human Genome Project wikipedia , lookup
Metagenomics wikipedia , lookup
Genome editing wikipedia , lookup
Human genome wikipedia , lookup
Public health genomics wikipedia , lookup
Non-coding DNA wikipedia , lookup
Genomic imprinting wikipedia , lookup
Gene expression profiling wikipedia , lookup
History of genetic engineering wikipedia , lookup
Artificial gene synthesis wikipedia , lookup
Genome (book) wikipedia , lookup
Designer baby wikipedia , lookup
Site-specific recombinase technology wikipedia , lookup
Pathogenomics wikipedia , lookup
Minimal genome wikipedia , lookup
Helitron (biology) wikipedia , lookup
Genome Evolution Chapter 24 1 Introduction • Genomes contain the raw material for evolution; • Comparing whole genomes enhances – Our ability to understand evolution; – To improve crops; – To identify genetic basis of disease. 2 Comparative Genomics • Making the connection between a specific change in a gene and a modification in a morphological character is difficult; • Genomes carry information on the history of life; • Evolutionary differences accumulate over long periods. 3 Comparative Genomics • Genomes of viruses and bacteria evolve in a matter of days; • Complex eukaryotic species evolve over millions of years; • Example: tiger pufferfish (Fugu rubripes), mouse (Mus musculus), and human genomes. 4 Comparative Genomics 5 6 Comparative Genomics • Comparison between human and pufferfish genomes: – Last shared common ancestor 450 MYA; – 25% human genes no counterparts in Fugu; – Extensive genome rearrangements since mammal lineage and teleost fish diverged; – Human genome is 97% repetitive DNA; – Repetitive DNA less than 1/6th Fugu genome sequence. 7 Comparative Genomics • Human and mouse genomes: – Human: 400 million more nucleotides than the mouse; – 25,000 genes and they share 99%; – Diverged about 75 MYA; – 300 genes unique to either organism (1%); – Rearrangements of chromosomal regions large and small. 8 Comparative Genomics • Human and chimpanzee genomes: – Diverged 35 MYA; – 1.06% of the two genomes have fixed differences in single nucleotides; – 1.5% difference in insertions and deletions; – 53 of human-specific indels lead to loss-of-function changes; – Smaller ratio in nonsynonymous to synonymous changes; – Purifying selection: removal of nonsynonymous genes. 9 Comparative Genomics • Genomes evolve at different rates; • Mouse DNA has mutated twice as fast as human; • Fruit fly and mosquito evolve more rapidly than vertebrates; • Difference in generation time accounts for different rates of genome evolution. 10 Comparative Genomics Comparison of plants with animals and fungi: – 1/3rd genes in Arabidopsis and rice “plant” genes: distinguish plant kingdom from animal kingdom; – Remaining genes similar to genes found in animal and fungal genomes: • Basic intermediary metabolism • Genome replication and repair • RNA transcription & protein synthesis 11 Evolution of Whole Genomes • Polyploidy can result from: – Genome duplication in one species – Hybridization of two different species • Autopolyploids: genome of one species is duplicated through a meiotic error – Four copies of each chromosome • Allopolyploids: result from hybridization and duplication of the genomes of two different species (tobacco) 12 Evolution of Whole Genomes 13 Evolution of Whole Genomes • Plant polyploidy is ubiquitous, with multiple common origins; • Comparison of soybean, forage legume, and garden pea shows a huge difference in genome size; • Some genomes increased, some decreased in size; • Polyploidy induces elimination of duplicated genes. 14 Evolution of Whole Genomes Polyploidy may be followed by the unequal loss of duplicate genes from the combined genomes. 15 Evolution Within Genomes • Aneuploidy: duplication or loss of an individual chromosome; • Plants are able to tolerate aneuploidy better than animals; • Duplication of segments of DNA is one of the greatest sources of novel traits. duplication loss 16 Evolution Within Genomes • Fates of duplicate gene: – Losing function through mutation; – Gaining a novel function through mutation; – Having total function partitioned into the two duplicates. 17 Evolution Within Genomes • Gene duplication in humans is most likely to occur in three most gene-rich chromosomes: Growth and development genes; Immune system genes; Cell-surface receptor genes; • 5% of human genome consists of segmental duplications; • Duplicated genes have different patterns of gene expression; • Rates of duplication vary for different groups of organisms. 18 Evolution Within Genomes • Drosophila – 31 new duplicates per genome per million years (0.0023 duplications per gene per million years); – C. elegans 10 times fast rate. • Paralogues: two genes within an organism that have arisen from duplication of a single gene in an ancestor. • Orthologues: conservation of a single gene from a common ancestor. 19 Evolution Within Genomes Genome reorganization • Humans have 1 fewer chromosome than chimpanzees, gorillas, and orangutans; • Fusion of two genes into one gene; chromosome 2 in humans; • Chromosomal rearrangements in mouse ancestors have occurred at twice the rate seen in humans. 20 Evolution Within Genomes Chromosomal rearrangement 21 Evolution Within Genomes Variation in genomes: • Conservation of synteny: the preservation over evolutionary time of arrangements of DNA segments in related species: – Long segments of chromosomes in mice and humans are the same; – Allows researchers to locate a gene in a different species using information about synteny. 22 Evolution Within Genomes Gene inactivation results in pseudogenes: • Loss of gene function: way for genomes to evolve – Olfactory receptor (OR) genes: inactivation best explanation for our reduced sense of smell – Primate genomes: > 1000 copies of OR genes; • Pseudogenes: sequences of DNA that are similar to functional genes but do not function – 70% of human OR genes are inactive pseudogenes – >50% gorilla & chimpanzee OR genes function – >95% New World monkey OR genes work well 23 Gene Function and Expression Patterns • Inferred by comparing genes in different species; • Why a mouse develops into a mouse and not a human: – Genes are expressed at different times; – In different tissues; – In different amounts; – In different combinations; – Example: cystic fibrosis gene. 24 Gene Pattern and Expression • Diverse life forms emerge from similar toolkits of genes; • To understand functional difference: – Look at time and place of expression; • Small changes in a protein can affect gene function. 25 Genome Size and Gene Number • Genome size has varied over evolutionary time; • Increases or decreases in size do not correlate with number of genes; • Polyploidy in plants does not by itself explain differences in genome size; • A greater amount of DNA is explained by the presence of introns and nonprotein-coding sequences than gene duplicates. 26