The Archaeology of the Genome • Haemophilus influenzae, a small Gram-negative b acterium. In July 1995 when the entire 1830 137 DNA base pairs of its genome was publis hed － the first of a free-living organism. A new era in biological science had begun. • The 3.3 billion bases that make up the geno me of Homo sapiens. • Gene sequences are now recognized as an inv aluable document of the history of life on earth. Yeast: Saccharomyces cerevisiae Archaea: Methanococcus jannaschii
Transcript
The Archaeology of the Genome
• Haemophilus influenzae, a small Gram-negative bacterium. In July 1995 when the entire 1830137 DNA base pairs of its genome was published－ the first of a free-living organism. A new era in biological science had begun.
• The 3.3 billion bases that make up the genome of Homo sapiens.
• Gene sequences are now recognized as an invaluable document of the history of life on earth.
• 1970 when Carl Woese and colleagues, using the highly conserve 16S ribosomal RNA (rRNA) gene, showed that there were in fact two very different groups of prokaryotes-the Eubacteria like Haemophilus influenzae, now simply referred to as the Bacteria, and the Archaebacteria whose members include Methanococcus jannaschii, now known as the Archaea.
• Lives on deep-sea hydrothermal chimneys, at pressures of 200 atmospheres and temperatures of 85 .℃
• In 1990 the Centers for Disease Control (CDC) in Atlanta received reports of AIDS in a young woman in Florida whose only risk of HIV infection was seemingly that she had previously been treated by a dentist suffering from AIDS.
The HIV genome had therefore stored evolutionary information, in the form of the mutations which had accumulated.
• The commonly held view was that humans were phylogenetically distinct from the great apes, being placed in different taxonomic families, and that this split occurred at least 15 million years ago.
The split between apes and Old World monkeys some 30 nillion years ago.
• The other hypothesis, the “Out of Africa” or replacement hypothesis, argues that all Homo sapiens throughout the world evolved from a second major migration out of Africa that occurredabout 100,000 years ago.– This migration completely
replaced all the regional populations of Homo derived from the firsthominid migrations.
• Using changes in mitochondrial DNA (mtDNA) among human populations as a molecular clock, research have reported a time of genetic divergence of about 100,000 years ago.
• The mtDNA extracted from Neanderthal bones fall completely outside the range of mtDNA for modern Europeans.
• By comparing the Y chromosomes of males from various geographic regions, researchers were able to infer divergence from a common African ancestor less than 100,000 years ago.
• Nucleotide (DNA) sequences have now replaces proteins as the main source of data, particularly since the invention of the polymerase chain reaction (PCR) in the mid-1980s
• It is now apparent that DNA sequences not only contain a record of their phylogenetic relationship and times of divergence, but also the signatures of what evolutionary processes have shaped their history and even the size of past populations.
Trees
• All of life is related by common ancestry.
• Interpreting them eventually becomes second nature.
Trees
• All of life is related by common ancestry.
• Interpreting them eventually becomes second nature.
請別依老賣老Since we come from a common 老祖宗
•Endeavour to reconstruct the characters of each hypothetical ancestor.
If a node has a degree greater than three then that node is a polytomy
Typically polytomies are treated as ‘s
oft’
That multiple lineages would diverge at exactly the same time; however, if lineages diverge rapidly in time
relative to the rate of character evolution.
This format makes it easy to describe a tree in the body of some text without having to draw it.
The most basic tree is the cladogram which simply was shows relative recency
of common ancestry.
In the biomathematical literature cladograms are often called ‘n-tree’.
Additive trees sometimes also called ‘dendrograms’.
Ultrametric (Dendrogram) In which the tips of the trees are all equidistant fr
This is the point at which the two gene lineages coalesce and the time at which this occurs is the coalescence time.
Alleles 1 and 2 are both found in the same species, they are not each other’s closest relative.
Hypothetical example illustrates the problem of lineage sorting. If the alleles present in a lineage prior to that lineage
speciation are not monophyletic then the distribution and relationships of these alleles need not accurately reflect the
phylogeny of the organisms themselves.
基因的分離與支系的分離不一致
Gene tree and species tree
基因的分化與物種種化一致 好玩
Nature 2003, 421:31
Nature 2003, 421:63
• Independent origin of PK gene in large double-strand DNA viruses: horizontal transfer in situ or gene duplication in vivo
Wen-Bin Yeh and Hong-Hwa Chen
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FWPV(NP_039374)MOCV(T30619)MYXV(NP_051734)
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GaHV-2(NP_057771)
HHV-3(WZBE47)
SuHV-1(WZBEN3)
HHV-1(WMBE71)
HHV-2(NP_044482)
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MeHV-1(JQ2350)
GaHV-1(F48552)
SuHV-1(WZBEN3)
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(T42592)HHV-3(WZBE47)
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Consensus tree
Compare trees derived from different sequences, or from the same sequence using
different methods.
Actual evolutionary history may not be particularly tree-like.
Mitochondria and chloroplasts• Non-coding DNA is rare in mitochondria and chlo
roplasts.• Mitochondria originated more than a billion years
ago when a free-living bacterium, the closest living relatives of which are the α-proteobacteria, entered a eukaryotic cell.
• Bacterial endosymbiosis is also thought to be the origin of chloroplasts, with the cyanobacteria (blue-gree algae) as the most likely ancestors.
• Mitochondrial genome (mtDNA) sizes range from only 6kb (kilobases) up to more than 2000kb, with the human version being some 16kb in length. In animals and plants, mitochondria are maternally inherited through the egg cytoplasm.
• mtDNA does not appear to undergo recombination and in mammals evolves about tenfold faster than nuclear DNA, make it an extremely important study tool in molecular population genetics and systematics.
• In many plant and fungal mtDNAs, self-splicing introns.
• The chloroplast genome (cpDNA) is ranging in size from 120 to 220kb.
• Two inverted repeat (IR) regions which separate a large single copy (LSC) region and a small single copy (SSC) region.
• Sometimes because genes have migrated to the nuclear genome and been lost from the chloroplast genome.
• Consists of about 1000 protein-coding genes, about 30 tRNA genes and four rRNA genes.
• Plant chloroplast genes evolve some four- to fivefold more slowly than those the nucleus, but about threefold faster than plant mtDNA genes.
•Multigene families are located in a specific region of a single chromosome and can be repeated many times, whilst others are dispersed throughout the genome.
• Some have acquired mutations, such as those that block the initiation of transcription, prevent correct RNA splicing or introduce premature stop codons, which inactivate them. These dead genes are called pseudogenes.
• These processed pseudogenes have probably been produced by the reverse transcription of the mature mRNA transcript of a gene (which will itself lack introns and promoter sequences.
• Pseudogenes are sometimes found on a different chromosome from their functional ancestor, it is clear that they can be transmitted throughout the genome.
A A
A A
B B
B B
globin family
• This may act as a ‘hot-spot’ for gene conversion because the DNA here forms a structure that increases the rate of recombination.
• In bacteria recombination can also occur between genes from different species. This interspecific recombination (or horizontal gene transfer).
• The large-scale exchange of genes between bacterial species also means that the evolutionary relationships between them cannot always be represented as simple bifurcating trees, and are better described by an interconnecting network.
Genome organization and evolution
• The vast majority of DNA in the genomes of Bacteria and Archaea produces protein (88% in the case of E. coli), yet 97% of the vertebrate genome is composed of non-coding DNA and may therefore have no function.
• Most of the eukaryote genome is made up of DNA sequences that are repeated very many times and many genes are arranged into multigene families.
One of the first indications that genomes are highly flexible entities was the finding that their sizes can very greatly between species. The amount of DNA per haploid genome, called the C-value.
• Only a twofold variation in genome size among mammalian species (the largest known genome is found in the aardvark, the smallest in a Muntjak deer), there is tenfold variation within anuran amphibians (frogs and toads), at least a hundredfold variation between insects, and an enormous 350-fold variation among bony fish.
• Why are genomes so large if most DNA is redundant?
• The number of genes found in different species also varies considerably.
• These differences in gene number cannot explain the huge variation in C-values.
The evolution of multigene families• Gene number can change between species is through
gene duplication.• Unequal crossing-over.• Can take place is through polyploidy. Polyploidy is
much more common in plants. Occurred fairly regularly in amphibians like the toad Xenopus laevis. Other species in the genus Xenopus verying from 20 to 108.
• Gene duplication can occur is through transposition. The transposable elements, which are a major component of eukaryotic genomes.
Polyploidy may also be important in speciation.
The new copy is automatically redundant.• Becoming a pseudogene, or even being deleted from
the genome.• With a slightly altered function.• With new functions can arise. Crystallins, proteins that play a structure role in the
eye lenses of animals. ε-crystallin, found in the eye lenses of some birds an
d crocodiles, is also the enzyme lactate dehydrogenase (LDH).
The protein’s original function was as an enzyme but it was then recruited into a new structural role through changes.
• In vertebrates are those in the Hox family. For invertebrates, like Drosophila.
• The homeotic gene complex (HOM).• Mutations in the HOM/Hox genes can drastically affect the or
ganisation of body parts.• The antennapedia mutation in Drosophila causes leg-like stru
ctures to grow in place of the antennae.• In some of the HOM clusters, genes at the 3’ end control deve
lopment of the anterior body part of the embryo, while those positioned at the 5’ end control the posterior sections.
• Conservation of genes in vertebrates and invertebrates.• Mutations in the eyeless gene of Drosophila and the homolog
ous Pax6 gene of humans both affect the pattern of eye development.
• In the mouse, each of its four clusters is located on a different chromosome and extends for over 100kb.
• There are two clusters of HOM gene in D. melanogaster, Bithorax and Antennapedia, which are found on the same chromosome.
• Amphioxus has a single cluster of at least 10 Hox gene (spanning 270 kb), each of which is homologous to a different Hox gene in vertebrates, so that the origin of the vertebrates coincided with s series of gene duplications.
• The vertebrate Hox genes, the family members are also dispersed over number of chromosomes. Other multigene families however are repeated side by side many times, so that they contain multiple copies of genes with the same function. These are known as tandem arrays.
• Because the host cell required large amounts of the protein they produce.
• The rDNA array which codes for ribosomal RNA (rRNA), part of the ribosome.
• Three types of rRNA: 18S, also known as the small subunit (~1800 bp), 28S, the large subunit (＞ 4000 bp), and 5.8S rRNA (~160 bp).
• Three types of rRNA: 18S, also known as the small subunit (~1800 bp), 28S, the large subunit (＞ 4000 bp), and 5.8S rRNA (~160 bp).
• In bacteria, the equivalent rRNA types are 16S, 23S and 5S.
• An external transcribed spacer (ETS) and two internal transcribed spacers (ITS-1 and ITS-2).
• From a single copy in the protist Tetrahymena to
• 19300 copies in the lizard Amphiuma means.
• About 200 tandemly repeated copies are found on the X and Y chromosomes of D. melanogaster,
• while in humans there are approximately 300 copies on five chromosomes.
• rDNA sequences have been used frequently in molecular systematics because they include both highly conserved (18S) and highly variable sequences (NTS), and so can reconstruct the phylogenetic relationships between both distant and very closely related species.
• Unequal crossing-over and gene conversion, which transfer DNA sequences between genes so that they evolve together.
• Concerted evolution and is one of the most important acting on multigene families because it means that mutations can spread to all members, even if they reside on different chromosomes.
• It becomes difficult to discern which genes are really homologous, so that orthologous and paralogous gene can be mixed.
• They are often composed of ‘mosaics’ of sequences, each with a different phylogenetic history, rather than strictly homologous gene.
Noncoding repetitive DNA sequence• Other types of repetitive DNA, do not encode
products used by the cell. • Does not mean they are without interest: by some
of these sequences spread solely for their own benefit, a tendency which has earned them the nickname of selfish DNA.
• ‘ultra-selfish’ because they can interfere with the function of other gene to increase their own copy number.
• Species-specific differences in the type and amount of non-coding repetitive DNA is a major reason why genome sizes differ between species.
Tandemly repeated DNA
• Short sequence motifs tandemly repeated many hundreds or thousands of times; termed satellite DNA, is located mainly in regions of heterochromatin and consists of motifs from 2 bp up to 40 kb in length.
• The α-satellite of primates is based on a 171 bp sequence; for hundreds of kilobases.
• For example, 60% of the genome of Drosophila nasutoides is made up to satellite DNA. Although it is usually assumed to be ‘junk DNA’, it is possible that satellite DNA is involved in the structure and function of centromeres.
• Minisatellites and microsatellites.
• Although less frequently than satellite DNA. These short repetitive motifs are thought to be produced by
mutation
unequal crossing-over
DNA slippage.
Minisatellites, or VNTR loci (‘variable number of tandem tepeats’), are found in the euchromatic regions of vertebrates, fungi and plants. Each repeat unit contains a short G-rich ‘core’ sequence, ranging in size from 11 to 60 bp.
New variants arise on average at a frequency of 1-2% per gamete, per generation (although this can be as high as 15%) whereas most gene loci have a mutation rate 10-5 to 10-6 per generation.
• With a simple pattern of Mendelian inheritance.
• They are extremely powerful molecular markers. More precisely, because of variation in allele size, can be used to distinguish different individuals within a population. This is known as DNA profiling (or DNA fingerprinting).
• DNA profiling has been used with great success in both population biology and forensic science. In behavioural ecology, can be used to determine which male in a population is the father of a set of offspring.
• Microsatellites, or STRs (‘short tandem repeat polymorphisms’), are sequences composed of runs of repeat units 2-5 bp in length; again mostly in regions of euchromatin and in the plant chloroplast genome.
• In the human genome there are perhaps 35000 microsatellite loci, with allele lengths of usually between 2 and 50 repeats per locus.
FI2a 5’-AGGCGAAGCCTTCTCCCCTCT-3’
FI2b 5’-ACCCCCTCCTCGCACTCCCCT-3’STR
FI5a 5’-CTGGGCACGATCTGGCTTATT-3’
FI5b 5’-GCATGGGTAAAGGTTTTGATGA-3’STR
FI8a 5’-GAGGGTCTCAAAATTGGCATGTC-3’
FI8b 5’-GTAAGGTTTCTATGGTTGGACA-3’STR
FI9a 5’-CAATACCCCCTCCTCGCACT-3’
FI9b 5’-CCCACGATGGTCCGCGTAC-3’STR
FI10a 5’-TGGCGGCAACCAAAGTGGGT-3’
FI10b 5’-TGGGCTGTCCATGTGCTGGCGT-3’STR
FI11a 5’-ACGCCAGCACATGGACAGCCCA-3’
FI11b 5’-CCTTTCGGGCTTTGTTAGCA-3’STR
FI12a 5’-CCACAGAGTCTTAACATACACA-3’
FI12b 5’-GTGTTTGTTTCTCTGAAGCCT-3’STR
FI14a 5’-CATCACCCAAAGTGAAAGCCA-3’
FI14b 5’-CCTGGCTACCAATCTCATCA-3’STR
• High mutation rates, between 10-2 and 10-5 per gamete, per generation.
• Such high levels of genetic diversity coupled with neutral evolution, codominance and simple Mendelian inheritance mean that they are also an ideal, and currently extremely popular, set of molecular markers.
• Most endangered species of canid, the Ethiopian wolf.
• Microsatellites have also been use in forensic cases.
Male
Female
M F 子代
Male
Female
M F 子代有 2 種可能性
• Microsatellites may also be of medical importance as a number of human genetic diseases, such as fragile X syndrome, Huntingdon’s disease, myotonic dystrophy and spino-bulbo-muscilar dystrophy are associated with a dramatic increase in the copy number of trinucleotide microsatellite repeats.
• Fragile X syndrome, appears to be caused by expansion of a GGG repeat in exon 1 of the FMR1 gene. Normal alleles contain between 6 and 50 repeat units whereas clinically affected individuals have more than 200 repeats, and frequently more than 1000.
The Wanted
DNA Exclusions孩子的老爸是誰
• The transposable elements (TEs)－ increase their copy number by jumping around the genome making additional copies of themselves as they do so. If one group of DNA sequences deserve the title of ‘selfish’, it is these.
• More than 50%of the maize genome is made up of transposable elements and a similar figure may yet be uncovered in humans
• 10-20% of the genome of Drosophila melanogaster is already known to be composed of DNA of this type.
• Transposable elements can be divided into three groups based on their mechanism of transposition. Class I transposable elements, or retroelements, transpose through an intermediate RNA stage (i.e. DNA→RNA→DNA) using the enzyme reverse transcriptase. This process is called retrotransposition.
• In contrast, Class II or DNA elements, transpose directly from DNA to DNA.
• The miniature inverted-repeat transposable elements or MITEs.
Retroposon
• Long Interspersed Nuclear Elements (LINEs) which are a major component of the G-banded regions of mammalian chromosomes.
• 6-8 kb in length and are present in many thousands of copies.
• L1 (Line 1) family have a consensus length of 6 kb (although most are truncated) and are present in a staggering 590000 copies in the human genome, so that they make up almost 17% of all our genomic DNA.
Retroposon
• Short Interspersed Nuclear Elements (SINEs), or Alu-like sequences, which are frequently found in the R-banded regions of mammalian chromosomes.
• Are not considered true retroelements (no RT).• 130 to 300 bp and have copy numbers ranging fro
m 50000to over 1000000 per genome.• Alu sequences are approximately 300 bp in length
and are present in about 1100000 copies in the human genome (almost 12% of four total DNA content).
• Both LINEsand SINEs appear to be originally derived from RNA transcripts: LINEs from RNA polymerase II and SINEs from RNA polymerase III (tRNA) transcripts.
• Also related to retroelements are the endogenous retroviruses.
• These are copies of retroviruses which have integrated as their DNA form (known as the provirus) into the germ-line of eukaryotes and which are now inherited along with the host genomic DNA.
• Class II (DNA) elements also possess terminal repeat sequences, less than 100 bp in length－ and frequently inverted.
• Some 1.6% of the human genome is composed of elements of this kind, the P and hobo elements of Drosophilia, the mariner elements of animals, the Tcl elements of nematodes and the Ac/Ds (‘Activator/Dissociation’) elements of maize.
• Between 0 and 60 copies of this 2907 bp element are found in the genome of D. melanogaster. P elements illustrate two of the most important aspects; Jumping around genomes, sometimes able to move between species and that they can affect the phenotype of their host organism.
• Hybrid dysgenesis－ an increase infertility due to chromosome breakage. However, P elements are only a recent introduction into wild populations of D. melanogaster and flies maintained in laboratory stocks established in the early part of this century do not carry them.
• P elements are not found in the fly species mostly closely related to D. melanogaster－ D. simulans, D. sechellia, D. mauritiana－ but are present in more distantly releated species, such as those from the D. willistoni species group. This means that P elements in D. melanogaster must have been transferred from the D. willistoni group (perhaps by viruses or parasitic mites) after D. melanogaster splitfrom its sibling species about two million years ago.
• Inserted into host gene often inactivate them• Leads to a number of chromosomal rearrangements; Reco
mbination between elements of the same family that occupy different (non-homologous) sites on chromosomes－a process known as ectopic exchange－ will also cause mutations.
• When transposable elements are cut, with sections of indigenous DNA also being removed.
• Studies in Drosophila have shown that transposable elements are very rare in coding regions, yet occur at high frequency in regions of heterochromatin where fewer genes are found and where the rate of meiotic recombination.
• However, despite their deleterious effects, transposable elements may be used to beneficial effect in genetic engineering, where they can act as vectors for carrying genes to new location.
