First Prelim Thursday February 18 in class Material included - up to today?s lecture A - Mariano go to PLS 233 McConnell - Z go to RRB125 Reviews on Monday 4:30 - 6:00 pm Warren 245 Wednesday 5:00 - 6:30 pm Warren 131 DNA hybridization is a measure of the relatedness between species Tm #1 70 80 90 100 Temperature (░C) 1.4 1.2 1.0 Relative absorbance (260nm) Tm #2 a b c problems Genome sequencing Comparative genomics Study guide p.109:2 Restriction endonucleases see lecture notes Recombinant DNA technology (Ch.9: 1, 2, 3, 4) Read chapter 9.1 and 9.2 for the two lectures to be covered this week The history of genome sequencing $1/base ~1c/base Systematic versus shotgun sequencing Systematic: sequence chromosome from end to end. Align cloned segments to create a physical map before shotgun sequencing individual segments. Shotgun: Shotgun cloning of a library of sequences. Sequence all of them and then align. Segments can be short. Use computer alignment. >$10/base ~1c/10 b 2010 Shotgun approach eliminates the time consuming step of assembling clones in a chromosome before sequencing. In this approach, random segments (600 -750 bp) of a clone (>100 kb) are sequenced and then assembled by computerized identification of overlaps. On the average, each clone has to be sequenced multiple times in order to fill all the gaps. This method was made possible because of the automation of sequencing and the development of sophisticated software. NIH: Systematic approach Celera: Shotgun approach Director of NIH Multi-billionaire (founder of Celera Genomics, Institute of Genomic Res, Craig Venter Inst.) Labor intensive step Requires >10x coverage to sequence 90 % of genome. Possible only if cost of sequencing is low and computer software is sophisticated. Shotgun versus systematic Study Guide p.117 25. How much of the human genome encodes functional proteins? 26. What are the functions of the rest of the DNA? 27. In what ways can you envision information about the sequence of the human genome being used? Study Guide p.117 25. How much of the human genome encodes functional proteins? 26. What are the functions of the rest of the DNA? 27. In what ways can you envision information about the sequence of the human genome being used? 26,000 genes human ?What is true for E. coli is true for the elephant.? Jacque Monod Genome sequence of human and chimpanzee are 98.8% identical. 35 x106bp differences, 5 x106 indels. Organism genome size (Mb) gene # gene density chrom # (haploid) Homo sapiens (human) 2900 ~26,000 1 /100 kb 23 Rattus norvegicus (rat) 2750 ~30,000 1 /100 kb 21 Mus musculus (mouse) 2500 ~30,000 1 /100 kb 20 Drosophila melanogaster (fruit fly) 180 13,600 1 / 9 kb 4 Arabidopsis thaliana (plant) 125 25,500 1 / 4 kb 5 Caenorhabditis elegans (roundworm) 97 19,100 1 / 5 kb 6 Saccharomyces cerevisiae (yeast) 12 6,300 1 / 2 kb 16 Escherichia coli (bacteria) 4.7 3,200 1 / 1.4 kb 1 H. influenzae (bacteria) 1.8 1,700 1 / 1 kb 1 http://www.ornl.gov/sci/techresources/Human_Genome/faq/compgen.shtml Genome size does not correlate with evolutionary status, nor does the number of genes proportionate with genome size. Gene Number and Genome Size of Organisms in Different Evolutionary Lineages Distribution of sequences in the human genome Flowering plants Birds Mammals Reptiles Amphibians Bony fish Cartilaginous fish Echinoderms Crustaceans Insects Mollusks Worms Molds Algae Fungi Gram(+) bacteria Gram(-) bacteria Mycoplasma DNA content of the haploid genome is related to the morphological complexity of lower eukaryotes, but varies extensively among the higher eukaryotes. The range of DNA values within a phylum is indicated by the shaded area. Is DNA content related to morphological complexity? 106 107 108 109 1010 1011 Comparative genomics of Mice and Men 90.2% of the human genome and 93.3% of the mouse genome lie in conserved syntenic segments. The syntenic blocks have been re-arranged by chromosomal events over time. http://www.evolutionpages.com/Mouse%20genome%20home.htm Of ~30,000 genes, only about 300 genes are unique to either organism. Comparative genomics of Mice and Men 99% of mouse genes have homologues in humans and 96% are in the same syntenic location Pseudogenes can be identified by the ratio of synonymous to non-synonymous mutations occurring over millions of years and by the fact they do not generally have a homologous gene in the same syntenic position in the other genome 90.2% of the human genome and 93.3% of the mouse genome lie in conserved syntenic segments. The syntenic blocks have been re-arranged by chromosomal events over time. homologous genes in the same syntenic álocation are called orthologues http://www.evolutionpages.com/Mouse%20genome%20home.htm Of ~30,000 genes, only about 300 genes are unique to either organism. Man Mouse 99% of mouse genes have homologues in humans! Referring to ~1.3% of genome What makes mice and men different? related genes are similar (up to 70-90%) but not identical. Related genes may have different structures and their protein products may have different activities. Examples of human inherited diseases that result from a single nucleotide change. unique genes likely to confer traits unique to each of these organisms A gene can produce more than one protein product through alternative splicing and posttranslational modifications. Duplicated genes may evolve to acquire new functions unique to each organism. A gene can produce more or less protein in different cells at various times in response to developmental or environmental cues, and many proteins can express disparate functions in various biological contexts. More importantly, there is significant divergence in the noncoding sequences of mice and men! The ?Core Proteome? H. influenzae S. cerevisiae C. elegans D. melanogaster Total no. of 1709 6241 18424 13601 predicted genes No. of genes 284 1858 8971 5536 duplicated Total no of 1425 4383 9453 8065 distinct families ?core proteome? Human disease 120 212 230 genes (289) Science 284:2204-2215 (2000) Proteome = whole genome protein content Gene duplication allows the evolution of simple organisms to complex organisms that have acquired new functions unique to their being. The notion that duplicated genes can evolve to perform new functions is supported by the information provided by the complete genome sequences of two eukaryotes, i.e. that of the single-cell fungus, and that of the multicellular round worm. These genomes each encodes about 6,000 and 20,000 genes, respectively. 27% of the fungal genes show matches to the worm genes and 12% of the worm genes show matches to the fungal genes. Based on this information, i) estimate the minimal number of genes that are required for the basic function of a cell, ii) estimate the approximate number of genes that are required for functions unique to fungus. iii) how many genes from the round worm are duplicated genes derived from the progenitor fungal genome? Yeast 6241 genes Worm 18424 genes 27% 1620 genes 12% 2400 genes Comparing yeast and worm genomes (i) 27% of the fungal genome is conserved in round worm, therefore 1620 is the minimal number of genes essential for the basic function of a cell. (ii) 73% of the fungal genome is unique to fungus, so 4380 genes may be responsible for fungal properties and functions. (iii) 2400 worm genes are derived from the progenitor fungal genome but only 1620 of these are found in fungus, so 780 genes of these must be duplicated genes. Answer:
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