genomes and their evolution. comparisons of genomes among organisms provide information about the...
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Genomes and their Evolution
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Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups
What genomic information distinguishes a human from a chimpanzee?
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New approaches have accelerated the pace of genome sequencing
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Cut the DNAinto overlappingfragments short enoughfor sequencing
1
2
3
4
Clone the fragmentsin plasmid or phagevectors.
Sequence eachfragment.
Order thesequences intoone overallsequencewith computer software.
Whole-Genome Shotgun Approach
to Genome
Sequencing- developed by Craig
Venter
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Scientists use bioinformatics to analyze genomes and their functions
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Bioinformatics resources are provided by a number of sources
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Comparison of sequences of “new” genes with those of known genes in other species may help identify new genes
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Most recentcommonancestorof all livingthings
Billions of years ago4 3 2 1 0
Bacteria
Eukarya
Archaea
Chimpanzee
Human
Mouse
010203040506070Millions of years ago
Genome comparisons of closely related species help us understand recent evolutionary events
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Translation andribosomal functions
Nuclear-cytoplasmic
transport
RNA processing
Transcriptionand chromatin-
related functions
Mitochondrialfunctions
Nuclear migrationand proteindegradation
Mitosis
DNA replicationand repair
Cell polarity andmorphogenesis
Protein folding,glycosylation, and
cell wall biosynthesis
Secretionand vesicletransport
Metabolismand amino acid
biosynthesis
Peroxisomalfunctions
Glutamatebiosynthesis
Serine-related
biosynthesis
Amino acidpermease pathway
Vesiclefusion
Understanding Genes and Gene Expression at the
Systems Level
Danny Hillis Ted TalkStart at 8 minutes
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By summer of 2007, the sequencing of more than 600 genomes hadbeen completed.
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Fig. 21-7Exons (regions of genes coding for protein
or giving rise to rRNA or tRNA) (1.5%)
RepetitiveDNA thatincludestransposableelementsand relatedsequences(44%)
Introns andregulatorysequences(24%)
UniquenoncodingDNA (15%)
RepetitiveDNAunrelated totransposableelements (15%)
L1sequences(17%)
Alu elements(10%)
Simple sequenceDNA (3%)
Large-segmentduplications (5–6%)
•Eukaryotic genomes are larger and have more protein-coding genes.•Eukaryotic genomes have more regulatory sequences. Greater complexity requires more regulation. •Much of eukaryotic DNA is noncoding, including introns, gene control sequences, and repeated sequences.
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Transposable Elements
• The first evidence for wandering DNA segments– Came from
geneticist Barbara McClintock’s breeding experiments with Indian corn
Nobel Prize 1983
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TransposonNew copy of transposon
Insertion
Transposonis copied
Mobile transposon
DNA ofgenome
(a) Transposon movement (“copy-and-paste” mechanism)
RetrotransposonNew copy of
retrotransposon
Insertion
Reversetranscriptase
RNA
(b) Retrotransposon movement
Transposons, move by means of a DNA intermediate
Retrotransposons move by means of an RNA intermediate
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The transposable element can alter the expression of a gene at the new location
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How Transposable Elements Contribute to Genome Evolution
• Movement of transposable elements– Occasionally generates new sequence combinations that
are beneficial to the organism
• Some mechanisms– Can alter the functions of genes or their patterns of
expression and regulation
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Alu inserts as markers of primate evolution(retrotransposon)
Salem, et al. 2003. PNAS 100:12787-12791
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Genes and Multigene Families
• Many eukaryotic genes are present in one copy per haploid set of chromosomes
• The rest of the genome occurs in multigene families, collections of identical or very similar genes
• Some multigene families consist of identical DNA sequences, usually clustered tandemly, such as those that code for RNA products.
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Fig. 21-10a
(a) Part of the ribosomal RNA gene family
18S
28S
28S18S 5.8S
5.8S
rRNA
DNA
DNARNA transcripts
Nontranscribedspacer Transcription unit
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Heme
Hemoglobin
-Globin
-Globin
-Globin gene family-Globin gene family
Chromosome 16 Chromosome 11
2 1
2
1
G A
Embryo Embryo FetusFetus
and adult Adult
α-globins and β-globins are examples of multigene families of nonidentical genes
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Figure 21.14
Duplication ofancestral gene
Mutation inboth copies
Transposition todifferent chromosomes
Further duplicationsand mutations
Ancestral globin gene
-Globin gene familyon chromosome 16
-Globin gene familyon chromosome 11
Evo
luti
on
ary
tim
e
2
1
2 1 G A
ICE FISH GENE DUPLICATION EVOLUTIONARY HISTORYCLIP
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Alterations of Chromosome Structure
Humanchromosome 2
Telomeresequences
Centromeresequences
Chimpanzeechromosomes
12Telomere-likesequences
Centromere-likesequences
Humanchromosome 16
13
(a) Human and chimpanzee chromosomes (b) Human and mouse chromosomes
7 8 16 17
Mousechromosomes
Humans have 23 pairs of chromosomes, while chimpanzees have 24 pairsChromosomal rearrangements are thought to contribute to the generation of new species
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Most recentcommonancestorof all livingthings
Billions of years ago4 3 2 1 0
Bacteria
Eukarya
Archaea
Chimpanzee
Human
Mouse
010203040506070Millions of years ago
The accumulation of changes in the genomeprovides a record of evolutionary history
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Comparing Genomes Within a Species
• As a species, humans have only been around about 200,000 years and have low within-species genetic variation
• Variation within humans is due to single nucleotide polymorphisms, inversions, deletions, and duplications
• These variations are useful for studying human evolution and human health
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Other Repetitive DNA, Including Simple Sequence DNA
• Simple sequence DNA contains many copies of tandemly repeated short sequences
This repeat number can vary from person to person, producing variation useful inforensic science.
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STRBase: a short tandem repeat DNA database for the human identity testing community
Christian M. Ruitberg, Dennis J. Reeder and John M. Butler*
Biotechnology Division, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 8311, Gaithersburg, MD 20899-8311, USA
AbstractThe National Institute of Standards and Technology (NIST) has compiled and maintained a Short Tandem Repeat DNA Internet Database (http://www.cstl.nist.gov/biotech/strbase/) since 1997 commonly referred to as STRBase. This database is an information resource for the forensic DNA typing community with details on commonly used short tandem repeat (STR) DNA markers.From: Nucl. Acids Res. (2001) 29 (1): 320-322.
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Comparing Developmental Processes
• Evolutionary developmental biology, or evo-devo, is the study of the evolution of developmental processes in multicellular organisms
• Genomic information shows that minor differences in gene sequence or regulation can result in major differences in form
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Adultfruit fly
Fruit fly embryo(10 hours)
Flychromosome
Mousechromosomes
Mouse embryo(12 days)
Adult mouse
Molecular analysis of the homeotic genes in Drosophila has shown that they all include a sequence called a homeobox
Hox genes
Neil Shubin and Sean CarrollDiscuss homeobox genes
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GHOSTS
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Fig. 21-3-1Cut the DNAinto overlappingfragments short enoughfor sequencing
1
2 Clone the fragmentsin plasmid or phagevectors.
Whole-Genome Shotgun Approach to Genome Sequencing- developed by Craig Venter
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Fig. 21-3-2Cut the DNAinto overlappingfragments short enoughfor sequencing
1
2
3
Clone the fragmentsin plasmid or phagevectors.
Sequence eachfragment.
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Fig. 21-2-1Cytogenetic map
Genes locatedby FISH
Chromosomebands
Three-Stage Approach to Genome Sequencing
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Fig. 21-2-2Cytogenetic map
Genes locatedby FISH
Chromosomebands
Linkage mapping1
Geneticmarkers
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Fig. 21-2-3Cytogenetic map
Genes locatedby FISH
Chromosomebands
Linkage mapping1
2
Geneticmarkers
Physical mapping
Overlappingfragments
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Fig. 21-2-4Cytogenetic map
Genes locatedby FISH
Chromosomebands
Linkage mapping1
2
3
Geneticmarkers
Physical mapping
Overlappingfragments
DNA sequencing
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From: National Academy of Science, 2009
Metagenomics
Genetic diversity is explored without isolating intact organisms.