Both mitochondrion and chloroplast are semi autonomous organelles with DNA. Majority of proteins required for mitochondrion and chloroplast are coded by genes of the nucleus. Only some proteins are coded by the DNA of mitochondrion and chloroplast. That is why; these organelles are called as semi-autonomous organelles.
Difference between mitochondrial DNA and Chloroplast DNA

Mitochondrial DNA
1. Mitochondrial DNA is called as mt DNA which is double stranded, circular and not covered by a membrane.
2. Size varies between species
· Human mt DNA 16 Kb (16569 bp)
· Plant cell mt DNA 200 kb-2500kb
3. Typically dozens of copies of DNA in each mitochondria
4. Animal mitochondrial genome contains 37 genes that encode 13 proteins, 22 tRNAs, and 2 rRNAs
The 13 mitochondrial genes codes for protein subunits of the enzyme complexes of the oxidative phosphorylation system, which helps mitochondria to act as the powerhouses of our cells.
5. Genes are transcribed in a polycistronic manner- a large mRNA molecule with instruction to make many proteins simultaneously
6. AT (adenine-thymine) rich (65% approx) and lack introns.
· Kinetoplast: In Trypanosomes, each mitochondria contains 1000 of copies of mt DNA arranged into a complex interlinked structure  called Kinetoplast.
Chloroplast DNA
1. Chloroplast DNA is called as ct DNA, cP DNA or plastome
2. Genome size 120-170 kb of DNA
3. Exist in multiple copies
    Each chloroplast with several nucleoid regions containing 8-10 rings of DNA molecules
    The number of DNA copies in mature chloroplast is 15-20.
4. Chloroplast genome include ~100 genes, 46-90 protein coding genes,
    Code for 4 ribosomal RNAs, 21 ribosomal proteins, 4 RNA polymerase subunits and over 30 tRNA genes
    Highly conserved throughput plant species
5.  Majority of genes are transcribed as polycistronic operons
6. Generally, AT rich and lack introns
Similarities between mitochondrial and chloroplast genome
· Both mt DNA and cp DNA are circular, double stranded and not enveloped by a membrane.
· Both mt DNA and cp DNA are devoid of histone proteins
· Both lack introns
· Both are generally AT rich genomes
See the Difference between Mitochondrial DNA and Nuclear DNA


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