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21 genomes and their evolution


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21 genomes and their evolution

  1. 1. LECTURE PRESENTATIONSFor CAMPBELL BIOLOGY, NINTH EDITIONJane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson© 2011 Pearson Education, Inc.Lectures byErin BarleyKathleen FitzpatrickGenomes and Their EvolutionChapter 21
  2. 2. Whole-Genome Shotgun Approach toGenome Sequencing• The whole-genome shotgun approach wasdeveloped by J. Craig Venter in 1992• This approach skips genetic and physical mappingand sequences random DNA fragments directly• Powerful computer programs are used to orderfragments into a continuous sequence© 2011 Pearson Education, Inc.
  3. 3. Cut the DNA intooverlapping frag-ments short enoughfor sequencing.1Clone the fragmentsin plasmid or phagevectors.2Sequence eachfragment.3Order thesequences intoone overallsequencewith computersoftware.4Figure 21.3-3
  4. 4. • Both the three-stage process and the whole-genome shotgun approach were used for theHuman Genome Project and for genomesequencing of other organisms• At first many scientists were skeptical about thewhole-genome shotgun approach, but it is nowwidely used as the sequencing method of choice• The development of newer sequencingtechniques has resulted in massive increases inspeed and decreases in cost© 2011 Pearson Education, Inc.
  5. 5. Genome Size• Genomes of most bacteria and archaea rangefrom 1 to 6 million base pairs (Mb); genomes ofeukaryotes are usually larger• Most plants and animals have genomes greaterthan 100 Mb; humans have 3,000 Mb• Within each domain there is no systematicrelationship between genome size and phenotype© 2011 Pearson Education, Inc.
  6. 6. Table 21.1
  7. 7. Gene Density and Noncoding DNA• Humans and other mammals have the lowestgene density, or number of genes, in a givenlength of DNA• Multicellular eukaryotes have many introns withingenes and noncoding DNA between genes© 2011 Pearson Education, Inc.
  8. 8. Multicellular eukaryotes have muchnoncoding DNA and many multigenefamilies• The bulk of most eukaryotic genomes neitherencodes proteins nor functional RNAs• Much evidence indicates that noncoding DNA(previously called “junk DNA” plays important rolesin the cell• For example, genomes of humans, rats, and miceshow high sequence conservation for about 500noncoding regions© 2011 Pearson Education, Inc.
  9. 9. • Sequencing of the human genome reveals that98.5% does not code for proteins, rRNAs, ortRNAs© 2011 Pearson Education, Inc.
  10. 10. • About 25% of the human genome codes forintrons and gene-related regulatory sequences(5%)• Intergenic DNA is noncoding DNA found betweengenes– Pseudogenes are former genes that haveaccumulated mutations and are nonfunctional– Repetitive DNA is present in multiple copies inthe genome© 2011 Pearson Education, Inc.
  11. 11. • About three-fourths of repetitive DNA is made upof transposable elements and sequences relatedto them© 2011 Pearson Education, Inc.
  12. 12. Figure 21.7Exons (1.5%) Introns (5%)Regulatorysequences(∼20%)UniquenoncodingDNA (15%)RepetitiveDNAunrelated totransposableelements(14%)Large-segmentduplications (5−6%)Simple sequenceDNA (3%)Alu elements(10%)L1sequences(17%)RepetitiveDNA thatincludestransposableelementsand relatedsequences(44%)
  13. 13. Transposable Elements and RelatedSequences• The first evidence for mobile DNA segmentscame from geneticist Barbara McClintock’sbreeding experiments with Indian corn• McClintock identified changes in the color of cornkernels that made sense only by postulating thatsome genetic elements move from other genomelocations into the genes for kernel color• These transposable elements move from onesite to another in a cell’s DNA; they are present inboth prokaryotes and eukaryotes© 2011 Pearson Education, Inc.
  14. 14. Figure 21.8
  15. 15. Movement of Transposons andRetrotransposons• Eukaryotic transposable elements are of twotypes– Transposons, which move by means of a DNAintermediate• Can move by a cut and paste mechanism, whichremoves the element from the original site, or by acopy and paste mechanism• Both mechanisms require the enzyme transposase,which is generally encoded by the transposon– Retrotransposons, which move by means of anRNA intermediate© 2011 Pearson Education, Inc.
  16. 16. Figure 21.9TransposonTransposonis copiedDNA ofgenomeMobile transposonInsertionNew copy oftransposon
  17. 17. Figure 21.10RetrotransposonNew copy ofretrotransposonInsertionReversetranscriptaseRNAFormation of asingle-strandedRNA intermediate
  18. 18. Sequences Related to TransposableElements• Multiple copies of transposable elements andrelated sequences are scattered throughout theeukaryotic genome• In primates, a large portion of transposableelement–related DNA consists of a family ofsimilar sequences called Alu elements• Many Alu elements are transcribed into RNAmolecules; however their function, if any, isunknown© 2011 Pearson Education, Inc.
  19. 19. • The human genome also contains manysequences of a type of retrotransposon calledLINE-1 (L1)• L1 sequences have a low rate of transpositionand may help regulate gene expression© 2011 Pearson Education, Inc.
  20. 20. Other Repetitive DNA, Including SimpleSequence DNA• About 15% of the human genome consists ofduplication of long sequences of DNA from onelocation to another• In contrast, simple sequence DNA containsmany copies of tandemly repeated shortsequences© 2011 Pearson Education, Inc.
  21. 21. • A series of repeating units of 2 to 5 nucleotides iscalled a short tandem repeat (STR)• The repeat number for STRs can vary amongsites (within a genome) or individuals• Simple sequence DNA is common incentromeres and telomeres, where it probablyplays structural roles in the chromosome© 2011 Pearson Education, Inc.