Genomes and their Evolution. Comparisons of genomes among organisms provide information about the...
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Genomes and their Evolution
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?
New approaches have accelerated the pace of genome sequencing
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
Scientists use bioinformatics to analyze genomes and their functions
Bioinformatics resources are provided by a number of sources
Comparison of sequences of “new” genes with those of known genes in other species may help identify new genes
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
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
By summer of 2007, the sequencing of more than 600 genomes hadbeen completed.
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.
Transposable Elements
• The first evidence for wandering DNA segments– Came from
geneticist Barbara McClintock’s breeding experiments with Indian corn
Nobel Prize 1983
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
The transposable element can alter the expression of a gene at the new location
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
Alu inserts as markers of primate evolution(retrotransposon)
Salem, et al. 2003. PNAS 100:12787-12791
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.
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
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
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
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
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
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
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.
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.
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
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
GHOSTS
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
Fig. 21-3-2Cut the DNAinto overlappingfragments short enoughfor sequencing
1
2
3
Clone the fragmentsin plasmid or phagevectors.
Sequence eachfragment.
Fig. 21-2-1Cytogenetic map
Genes locatedby FISH
Chromosomebands
Three-Stage Approach to Genome Sequencing
Fig. 21-2-2Cytogenetic map
Genes locatedby FISH
Chromosomebands
Linkage mapping1
Geneticmarkers
Fig. 21-2-3Cytogenetic map
Genes locatedby FISH
Chromosomebands
Linkage mapping1
2
Geneticmarkers
Physical mapping
Overlappingfragments
Fig. 21-2-4Cytogenetic map
Genes locatedby FISH
Chromosomebands
Linkage mapping1
2
3
Geneticmarkers
Physical mapping
Overlappingfragments
DNA sequencing
From: National Academy of Science, 2009
Metagenomics
Genetic diversity is explored without isolating intact organisms.