Mitochondrial DNA in Molecular Systematics

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Mitochondrial DNA in Molecular Systematics
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Mitochondria

• organelle found in eukaryotic cells
• cellular respiration ATP production

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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).

cyanobacteria
Eukaryotic cell
Primordial eukaryotic cell
Perform Symbiotic Relationship
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mtDNA

• mtDNA is maternally inherited in animals and
  plants.
• 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).

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Comparison of Plant mtDNA and cpDNA
Plant species cpDNA
mtDNA
Nicotiana tabacum Oryza sativa
Triticum aestivum Zea mays Sorghum
bicolor Marchantia polymorpha
156kb 135kb 135kb 140kb 141kb 121kb
431kb 492kb 453kb 570-680kb 496kb
187kb
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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.

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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.

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Plant mtDNA
Tricircular structure of the Brassica campesteris
mitochondrial genome
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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 C1-11), some
  as large as 12kb in length, are found integrated
  in plant mtDNA.

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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 mtDNA.
• 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.

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Animal mtDNA

• Animal mtDNAs are relatively smaller than the
  plant mtDNAs.
• The genome size is more conserved.

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Comparison Genome Size of Animal mtDNA
Animal species mtDNA
Aedes aegypti Alligator sinensis Apis
mellifera Boa constictor Elephas
maximus Gallus gallus Homo sapiens
Octopus ocellatus Pongo pymaeus Rana
nigromaculata
16.7kb 16.7kb 16.3kb 18.9kb 16.9kb 16.8kb
16.6kb 16kb 16.4kb 17.8kb
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Human Mitochondrial Genome
Human mtDNA composes of a control region (CR),
genes encoding 2 rDNAs (12S and 16S), 22 tRNAs
(open circles), 13 polypeptides.
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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 (stable).

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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.

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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.