Mitochondrial DNA in Mitochondrial DNA in Molecular SystematicsMolecular Systematics

- organelle found in eukaryotic cells- cellular respiration – ATP production

MitochondriaMitochondria

Mitochondria EvolutionMitochondria 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

cyanobacteria

Eukaryotic cell

Perform Symbiotic Relationship

• 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).

mtDNAmtDNA

Comparison of Plant Comparison of Plant mtDNA and cpDNAmtDNA and cpDNA

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

Plant species cpDNA 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 mtDNAPlant mtDNA

Plant mtDNAPlant 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 mtDNAPlant mtDNA

Tricircular structure of the Brassica campesteris mitochondrial genome

Plant mtDNAPlant 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.

Plant mtDNAPlant 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.

Animal mtDNAAnimal mtDNA

• Animal mtDNAs are relatively smaller than the plant mtDNAs.

• The genome size is more conserved.

Comparison Genome Size of Animal mtDNAComparison Genome Size of Animal 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

Animal species mtDNA

Human Mitochondrial GenomeHuman Mitochondrial Genome

Human mtDNA composes of a control region (CR), genes encoding 2 rDNAs (12S and 16S), 22 tRNAs (open circles), 13 polypeptides.

Animal mtDNAAnimal 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).

mtDNA in Plant SystematicsmtDNA 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 SystematicsmtDNA 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.