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Mitochondrial DNA in
Molecular Systematics
- organelle found in eukaryotic cells
- cellular respiration – ATP production
Mitochondria Evolution
• Endosymbiotic Theory – Ivan Wallin (1920s)
and Lynn Margulis (1981).
• Proto-Eukaryotic cell incorporated a
protobacterial cell and formed a symbiotic
relationship (a billion years ago).
Primordial eukaryotic cell
Eukaryotic cell
Perform Symbiotic Relationship
• mtDNA is maternally inherited in animals and
• More than 1300 complete mitochondrial
sequences have been generated.
• Most of the mitochondrial complete sequences
are belonged to animals and algae.
• Only a few plant species have their mitochondrial
genome sequenced: Nicotiana tabacum, Oryza
sativa, Triticum aestivum, Zea mays, Sorghum
bicolor, Marchantia polymorpha.
• Plant mtDNA is far more complex than animal
mtDNA – larger size (300-600kb) and variable in
size (up to 2000kb).
Comparison of Plant
mtDNA and cpDNA
Plant species
Nicotiana tabacum
Oryza sativa
Triticum aestivum
Zea mays
Sorghum bicolor
Marchantia polymorpha
Plant mtDNA
• In addition to larger size, plant mtDNA are
characterized by molecular heterogeneity.
• Large duplications are readily created and
lost. Plant mtDNAs contain at least one
large (1-14kb) repeated sequence. There is
no pattern to the sequences (including
genes) that are duplicated in the
mitochondrial genomes of different plants.
Plant mtDNA
• Recombination between repeats creates a
complex, multipartite genome structure. All
of the large repeats found in plant mtDNAs
appear to be engaged in high-frequency
inter- and intra-molecular recombination.
Plant mtDNA
Tricircular structure of the Brassica campesteris
mitochondrial genome
Plant mtDNA
• mtDNA contains short dispersed (50-1000bp)
repeats scattered throughout the genome.
• mtDNA contains many foreign sequences.
cpDNA sequences of all kinds (labelled as C111), some as large as 12kb in length, are found
integrated in plant mtDNA.
Plant mtDNA
• Plant mtDNAs change very slowly in nucleotide
sequences. Rates of nucleotide substitutions
are 3-4 times lower in plant mtDNA than in
cpDNA, 12 times lower than in plant nuclear
DNA, and 40-100 times lower than in animal
• Plant mtDNAs rearrange very rapidly. No two
eximined species of flowering plants have the
same gene order. Even closely related species
differ by one or a few large inversions, whereas
the genomes of more distantly related species
are virtually randomized with respect to
sequence arrangement.
Animal mtDNA
• Animal mtDNAs are relatively smaller than the
plant mtDNAs.
• The genome size is more conserved.
Comparison Genome Size of Animal mtDNA
Animal species
Aedes aegypti
Alligator sinensis
Apis mellifera
Boa constictor
Elephas maximus
Gallus gallus
Homo sapiens
Octopus ocellatus
Pongo pymaeus
Rana nigromaculata
Human Mitochondrial Genome
Human mtDNA
composes of a
control region (CR),
genes encoding 2
rDNAs (12S and 16S),
22 tRNAs (open
circles), 13
Animal mtDNA
• Non-recombination.
• Contains less non-coding sequences.
• Higher base substitution rate (even higher
than the nuclear DNA regions).
• Gene order/structure is more conserved
mtDNA in Plant Systematics
• Mitochondrial DNA regions commonly used for
plant systematics: coxI, nad2, atpA, cob, coxIII,
18S, 26S etc.
• The high rates of rearrangements and low rates
of point mutations make mtDNA essentially
worthless for the restriction site-based
reconstructions of intrafamilial phylogeny for
which cpDNA is so well suited.
• The occasional losses of mitochondrial genes
and introns may also serve as useful markers
of phylogeny.
• The low rate of mtDNA substitutions suggests
that comparative sequencing efforts will be
most rewarding at higher phylogenetic levels.
mtDNA in Animal Systematics
• RFLP on the whole mitochondrial genome is
common in molecular systematics in
animals. (involves the isolation of mtDNA
from total DNA)
• DNA sequencing is done on variable regions
such as D-loop region (control region),
cytochrome b, cytochrome oxidase I,
cytochrome oxidase III, 16S, 12S etc.