Control region
12S rRNA
16S rRNA
Cytochrome b
ND1
ND6
ND2
ND5
ND4
COI
ND4L
ND3
COII
ATPCOIII ATPase8
ase6
Figure 2.1 Typical gene organization of vertebrate mtDNA. Unlabelled dark bands represent 22
transfer RNAs (tRNAs). Gene abbreviations starting with ND are subunits of NADH dehydrogenase, and
those starting with CO are subunits of cytochrome c
23S rRNA
23S rRNA
16S rRNA
16S rRNA
Chloroplast genome
in a liverwort
(121 024 bp)
Subunits of
RNA polymerase
Rubisco
(large subunit)
Figure 2.2 The genome of the chloroplasts found in the liverwort Marchantia polymorpha contains
121,024 base pairs (Ohyama et al., 1986). These make up an estimated 128 genes, and the
approximate locations of some of these are shown on this figure. The dark lines mark the locations of
12 of the 37 tRNAs
Source Credit:
Ohyama, K., Fukuzawa, H., Kohchi, T., Shirai, H., Sano, T., Sano, S., Umesono, K., Shiki, M., Takeuchi,
Y., Chang, Z., Aota, S., Inokuchi, H. and Ozeki, H. 1986. Chloroplast gene organization deduced from
complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature 322: 572–574.
Pseudo-autosomal
region
p arm
SRY gene
q arm
Pseudo-autosomal
region
Figure 2.3
Mammalian Y-chromosome. The SRY gene (sex-determining region Y) effectively
converts an embryo into a male
1A
2A
3A
4A
1B
2B
3B
4B
150 bases
146 bases
144 bases
142 bases
Microsatellite data
AFLP data
Figure 2.4 A gel showing the genotypes of four individuals based on one microsatellite (codominant) locus (1A-4A), and several AFLP (dominant) loci (1B-4B). According to the microsatellite
locus, individuals 1 and 3 are heterozygous for alleles that are 142 and 146 bases long, whereas
individuals 2 and 4 are homozygous for alleles that are 144 and 150 bases, respectively. Since there
are two of each allele in this sample of eight alleles, the frequency of each microsatellite allele is 0.25.
According to the AFLP marker, which screens multiple loci, all four individuals are genetically distinct,
but we cannot identify homozygotes and heterozygotes, nor can we readily calculate allele frequencies
Allele 2
Resulting gel image
Genotypes
Allele 1
Individual A
1
1
Individual B
2
3
2
3
1
Individual C
1
2
3
1
2
2
3
3
Figure 2.5 Three different RFLP genotypes result from sequence differences that affect the restriction
enzyme recognition sites (designated as /). At this locus, individuals A and B are homozygous for
alleles that have two and three restriction sites, respectively. Individual C is heterozygous, with two
restriction sites at one allele, and three restriction sites at the other allele. The numbers of bands that
would be generated by the RFLP profiles are shown in the resulting gel image
Locus 1
TATATATA
TATATATA
Locus 2
TAATAATAATAATAATAATAATAA
TAATAATAATAATAATAATAA
Locus 3
GCGCGCGCGCGCGC
GCGCGCGCGCGCGCGC
Figure 2.6 Diagrammatic representation showing part of a chromosome across which three
microsatellite loci are distributed (note that sequences are provided for only one strand of DNA from
each chromosome). This particular individual is homozygous at locus 1 because both alleles are (TA)4,
is heterozygous at locus 2 because one allele is (TAA)8 and the other is (TAA)7, and heterozygous at
locus 3 because one allele is (GC)7 and the other allele is (GC)8
TTGTCAAAGAGTTCAGCCGAATA CAATTTATTAAGTGAGCTTAATACAGTT
AGCGACGACAAAGGAAGAAGTACAACAGAGAGAGAGAGAGAGAGAGAGAG
AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA
GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGTGTAAAGATATAGGGAG
ACTAGCTAGAGCCAAGCACTAAGATACAACACGC
Figure 2.7 A DNA sequence that includes a microsatellite region that was isolated from the
freshwater bryozoan Cristatella mucedo (Freeland et al., 1999). The microsatellite, which is (AG)53, is
underlined. The flanking sequence regions in bold show the locations of the primers that were used to
amplify this microsatellite in a PCR reaction
Source Credit:
Freeland, J. R., Jones, C. S., Noble, L. R. and Okamura, B. 1999. Polymorphic microsatellite
lociidentified in the highly clonal freshwater bryozoan Cristatella mucedo. Molecular Ecology 8: 341–
342.
(a)
Individual 1
(b)
1
2
Individual 2
Figure 2.8 A) RAPD priming sites (indicated by black boxes) are distributed throughout the genome,
although here only two partial chromosomes are represented. The sizes of the products (shaded in grey)
that will be amplified during PCR will depend on the locations of these priming sites. B) Diagrammatic
representation of the gel that would follow RAPD PCR of these two individuals. Recall that the rate at
which a band migrates through the gel is inversely proportional to its size
5‘-CTCGTAGACTGCGTACCAATTC
3‘-CATCTGACGCATGGTTAAG
Eco RI primer
GACTGCGTACCAATTC(+n+3n)
5‘-CTCGTAGACTGCGTACCAATTC
3‘-CATCTGACGCATGGTTAAG
(+n+3n)AATGAGTCCTGAGTAGCAG
Mse I primer
TTACTCAGGACTCA-3‘
AATGAGTCCTGAGTAGCAG-5‘
(+n)AATGAGTCCTGAGTAGCAG
Mse I primer
TTACTCAGGACTCA-3‘
AATGAGTCCTGAGTAGCAG-5‘
Mse I adaptor
TTACTCAGGACTCA-3‘
AATGAGTCCTGAGTAGCAG-5‘
T-3‘
AATG-5‘
Figure 2.9 A schematic diagram showing how AFLP genotypes are generated. Digestion with two restriction enzymes produces sticky ends to which linkers can be
ligated. During preamplification, the addition of a single base to the 30 end of each primer will reduce the number of amplified fragments to 1/16 of the number of
fragments that would otherwise be amplified. The addition of three more bases to the 30 primer ends during selective amplification further reduces the chance of a
perfect match between primers and target sequences, and as a result only 1/65,536 of the original set of fragments will be amplified
Selective
amplification
Preamplification
Eco RI adaptor
5‘-CTCGTAGACTGCGTACCAATTC
3‘-CATCTGACGCATGGTTAAG
Adaptor ligation
Eco RI primer
GACTGCGTACCAATTC(+n)
5‘-AATTC
3‘-G
Digest with
Eco RI and Mse I
DNA