its own nuclear genome; by far the largest with ~350x109 base pairs (bp) of DNA;
the genome of its mitochondria (48,000 bp);
the genome of the chloroplast in its endosymbiont (121,000 bp);
the genome of the nucleomorph (551,264 bp).
Most thylakoid proteins encoded by a plant's nuclear genome need two targeting signals for proper localization: An N-terminal chloroplast targeting peptide (shown in yellow in the figure), followed by a thylakoid targeting peptide (shown in blue).
Relative to the nuclear genome, this system has several advantages for a comprehensive sampling across life.
A favorite in plant biology is a paper claiming massive and dynamic movement of sequences from the mitochondrial into the nuclear genome, followed by amplification of these mitochondrial sequences - perhaps in the manner of transposons.
A more recent study, using genetic markers from the nuclear genome, shows that limnetic forms in different lakes are more closely related to each other (and to marine lineages) than to benthic forms in the same lake.
Proving a relationship based on comparison of the mitochondrial genome is much easier than that based on the nuclear genome.
genome All the DNA in a haploid set of chromosomes (nuclear genome), organelle (mitochondrial genome, chloroplast genome) or virus (viral genome, which in some viruses consists of RNA rather than DNA).
Genome The complete DNA sequence of an organism (though it may sometimes be used in the sense of 'mitochondrial genome' or 'nuclear genome').
The chloroplast genome consists of about 100 protein coding genes, 30 tRNAs genes and 4 rRNAs genes. Most chloroplast proteins are coded for by the nuclear genome, synthesised in the cytoplasm and transproted into the organelle.
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close symbiotic relationship one may "steal" genes from the other. The most notable example of this are mitochondria. In most organisms with mitochondria most of the original mitochondrial genes have moved from the mitochondria to the nuclear genome.
See also: Genome, Trans, Organ, DNA, Protein