View source for Chapter !4 - Comparative Genomics Code : KSI0013

<p style="text-align:center"><span style="font-size:36px">&lt;Index of Chapter 4&gt;</span></p>

<p><span style="color:#0000CD"><strong>Introduction&nbsp;</strong></span></p>

<p>It&#39;s likely that life originated on Earth about 3.5 billion years ago. the first cellular life forms were undoubtedly prokaryotes. Eukaryotes appeared about 2 billion year later. There are enough residual similarities among living things to suggest a common ancestory of us all. The great diversity of living forms is therefore, the result of divergence.</p>

<p>&nbsp;</p>

<p><span style="color:#0000CD"><strong>Unity and diversity of life</strong></span></p>

<p>Binomial /DNA barcoding</p>

<p>Taxonomy based on sequences</p>

<p>- Traditional linnaean biological nomenclature assigns names to species, and classifies apecies according to evolutionary relationships. It&#39;s often difficult todraw boundaries between species, especially for microorganisms.</p>

<p>- Bacteria/ archaea / Eukarya / phylogenetic tree. / horizontal gene transfer ( Please pass the genes)</p>

<p>&nbsp;</p>

<p><span style="color:#0000CD"><strong>Sizes and organization of genomes</strong></span></p>

<p>Genome sizes</p>

<p>Genome sequences/ RNA and protein expression patterns/ The spatial organization of individual macromolecules, their complexes, organelles, entire cells, tissues, and bodies</p>

<p>/ regulatory networs, the internal structure and logic of adaptive control systems.</p>

<p>The term C-value has been used to refer to the amount of DNA in a haploied cell. the letter C refers to the constancy of the amount of DNA per cell in a pspecies.&nbsp;</p>

<p>&nbsp;</p>

<p><span style="color:#0000CD"><strong>Viral genomes</strong></span></p>

<p>Recombinant viruses</p>

<p>BOth HIV- 1 and influenza viruses have become major threats to human health after jumping from animal hosts. Their high mutation rates with severe clinical consequences- reflect the fact that their genomes are RNA</p>

<p>Influenza : a past and current threat</p>

<p>Types of viral genome&nbsp;</p>

<p>- SSDNA&nbsp;</p>

<p>- DSDNA</p>

<p>- SSRNA</p>

<p>- DSRNA</p>

<p>&nbsp;</p>

<p><span style="color:#0000CD"><strong>Genome Organization in prokaryotes</strong></span></p>

<p>Replication and transcription</p>

<p>Gene transfer</p>

<p>- transformation / conjugation / trnasduction&nbsp;</p>

<p>Some but not all prokaryote genomes contain Insertion sequences mobile genetic elements similar to eukaryotic transposons.</p>

<p>Prokaryotes have several mechanisms for sharing genetic material : Transformation by naked DNA conjugation and transfer via viruses.</p>

<p>&nbsp;</p>

<p><span style="color:#0000CD"><strong>Genome Organization in eukaryotes</strong></span></p>

<p>Photosynthetic sea slugs : endosymbiosys of chloroplasts</p>

<p>Mitochondria and chloroplasts carry out their own protein synthesis. Chchloroplasts and plant mitochondria translate their genes according to the standard genetic code, but animal mitochondria use variants.&nbsp;</p>

<p>Traffic between the mitochondrial and nuclear genomes.&nbsp;</p>

<p>&nbsp;</p>

<p>&nbsp;</p>

<p><span style="color:#0000CD"><strong>How genomes differ</strong></span></p>

<p>Variation at the level of individual nucleotides</p>

<p>Duplications</p>

<p>Comparisions at the chromosome level : synteny</p>

<p>What can happen to a gene?</p>

<p>- During evolution&nbsp;</p>

<p>-1 A gene may pass to descendants, accumulating favourable or unavourable mutations or dirifting neutrally.</p>

<p>2. A gene may be lost</p>

<p>3. A gene may be dulicated followed by divergence or by loss of one of the pair</p>

<p>4. A gene may undergo horizontal transfer to an organism of another species.</p>

<p>5. A gene may undergo complex patterns of fusion fission or rearrangemnet perhaps involving regions encoding individual protein domains</p>

<p>Homologues / Paralogues/ orthologues&nbsp;</p>

<p>Neutral evolution&nbsp;</p>

<p>Positive selection&nbsp;</p>

<p>Purifying selection&nbsp;</p>

<p>&nbsp;</p>

<p><span style="color:#0000CD"><strong>What makes us human?</strong></span></p>

<p>Comparative genomics</p>

<p>Combining the approaches : the <em>FOXP2</em> gene</p>

<p>Comparative genomics &nbsp;and study of huan diseases</p>

<p>&nbsp;</p>

<p><span style="color:#0000CD"><strong>Genomes of chimpanzees and humans</strong></span></p>

<p><span style="color:#0000CD"><strong>Genomes of mice and rats</strong></span></p>

<p><span style="color:#0000CD"><strong>Model organisms for study of human diseases</strong></span></p>

<p>The genome of Caenorhabditis elegans</p>

<p>The genome of Drosophilia melanogaster</p>

<p>Homologous genes in humans, worms, and flies</p>

<p><span style="color:#0000CD"><strong>The ENCODE project</strong></span></p>

<p>The modENCODE project</p>

<p>is a systematic development and application of comparative genomics .&nbsp;</p>

<p>It has the ultimate goal of developing methods for comprehensive identification of functional regions of the human genome.&nbsp;</p>

<p>____________________________________________________________________________________________________________________________KSI&nbsp;</p>