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Chapter 21 Genomes and Their Evolution
Lecture Notes
Overview: Reading the leaves from the tree of life
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The chimpanzee genome was sequenced by 2005, two years after the sequencing of the human genome
was completed
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With the genomes of many species fully sequenced, scientists can study whole sets of genes and their
interactions, an approach called genomics
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Concept 21
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○ Organized by an international, publicly funded consortium of scientists at universities and research
institutes, the project involved 20 large sequencing centers in six countries plus many labs working
on small projects
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Francis Collins
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 The project proceeded through three stages that provided progressively more detailed views of the
human genome: linkage mapping, physical mapping, and DNA sequencing
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 In 1992, molecular biologist J
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○ Powerful computer programs would then assemble the resulting very large number of overlapping
short sequences into a single continuous sequence
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 In April 2003, the human genome sequence was announced jointly by Celera and the public consortium
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o Today, the whole-genome shotgun method is widely used
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○ In these new techniques, many very small fragments (fewer than 100 base pairs) are sequenced at the
same time, and computer software rapidly assembles the complete sequence
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2 Scientists use bioinformatics to analyze genomes and their functions
Centralized resources are available for analyzing genome sequences
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 The NCBI database of sequences is called Genbank
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○ The amount of data in Genbank is estimated to double every 18 months
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 Two research institutions, Rutgers University and the University of California, San Diego, maintain a
worldwide Protein Data Bank, a database of all known three-dimensional protein structures
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 The success in sequencing genomes and studying entire sets of genes has encouraged scientists to
attempt similar systematic study of the full protein sets (proteomes) encoded by genomes, an approach
called proteomics
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3 Genomes vary in size, number of genes, and gene density
Gene densities vary
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 Generally, eukaryotes have larger genomes but lower gene density than prokaryotes
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Concept 21
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This noncoding DNA has been described as “junk DNA
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 Only 1
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○ Gene-related regulatory sequences and introns account for, respectively 5% and 20% of the human
genome
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 Most intergenic DNA is repetitive DNA, sequences present in multiple copies in the genome
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Transposable elements can move from one location to another within the genome
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These stretches are known as transposable genetic elements, or simply transposable
elements
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The first evidence for transposable elements came from American geneticist Barbara McClintock’s
breeding experiments with Indian corn (maize) in the 1940s and 1950s
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○ The elements moved into genes for kernel color, disrupting the genes so that they could no longer
produce color
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Her work was validated many years later,
however, when transposable elements were found in bacteria
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Transposons move within a genome by a “cut-and-paste” mechanism, which removes the element from
the original site or a “copy-and-paste” mechanism, which leaves a copy behind
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○ Retrotransposons always leave a copy at the original site during transposition because they are
initially transcribed into an RNA intermediate
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Gene-related DNA makes up about 25% of the human genome
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○ The rest of the transcribed DNA occurs in multigene families, collections of two or more identical
or very similar genes
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○ One family, located on chromosome 16 in humans, encodes various forms of α-globin; the other, on
chromosome 11, encodes forms of β-globin
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○ In humans, embryonic and fetal forms of hemoglobin have a higher affinity for oxygen than the
adult forms, thus ensuring the efficient transfer of oxygen from mother to fetus
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6 Comparing genome sequences provides clues to evolution and development
Comparisons of genome sequences from different species tell about the evolutionary history of life
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 Comparing the genomes of closely related species provides information about recent evolutionary
events; comparing the genomes of distantly related species sheds light on ancient evolutionary history
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○ Comparisons of the complete genome sequences of bacteria, archaea, and eukaryotes strongly
support the theory that these groups are the fundamental domains of life
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 Biologists in the field of evolutionary developmental biology, or evo-devo, compare the developmental
processes of multicellular organisms
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 Homeotic genes in Drosophila specify the identity of body segments in the fruit fly
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An identical or very similar nucleotide sequence has been discovered in the homeotic genes of many
invertebrates and vertebrates (therefore they are “highly conserved” in evolution
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Homeotic genes in animals were named Hox genes, short for homeobox-containing genes, because
homeotic genes were the first genes found to have this sequence
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In some cases, small changes in the regulatory sequences of particular genes cause changes in gene
expression patterns that can lead to major changes in body form

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