A wide-ranging examination of plastid (pt)DNA sequence homologies within higher plant nuclear genomes (promiscuous DNA) was undertaken. Digestion with methylation-sensitive restriction enzymes and Southern analysis was used to distinguish plastid and nuclear DNA in order to assess the extent of variability of promiscuous sequences within and between plant species. Some species, such as Gossypium hirsutum (cotton), Nicotiana tabacum (tobacco), and Chenopodium quinoa, showed homogenity of these sequences, while intraspecific sequence variation was observed among different cultivars of Pisum sativum (pea), Hordeum vulgare (barley), and Triticum aestivum (wheat). Hypervariability of plastid sequence homologies was identified in the nuclear genomes of Spinacea oleracea (spinach) and Beta vulgaris (beet), in which individual plants were shown to possess a unique spectrum of nuclear sequences with ptDNA homology. This hypervariability apparently extended to somatic variation in B. vulgaris. No sequences with ptDNA homology were identified by this method in the nuclear genome of Arabidopsis thaliana.
Long tracts of DNA with high sequence homology to chloroplast DNA were isolated from nuclear genomic libraries of Nicotiana tabacum. One lambda EMBL4 clone was characterised in detail and assigned to nuclear DNA. The majority of the 15.5-kb sequence is greater than 99% homologous with its chloroplast DNA counterpart, but a single base deletion causes premature termination of the reading frame of the psaA gene. One region of the clone contains a concentration of deleted regions, and these were used to identify and quantify the sequence in native nuclear DNA by polymerase chain reaction (PCR) methods. An estimated 15 copies of this specific region are present in a 1c tobacco nucleus.
The role of chloroplast (cp) DNA in plastid and chloroplast function is discussed, particularly in relation to the interaction with nuclear DNA. The evolution of the chloroplast genome and the endosymbiont hypothesis are related to our results and those of others which show the occurrence of cpDNA sequences common to the nuclear and chloroplast genome.
Higher plant cells contain three genetic compartments which separately transcribe DNA and translate messenger (m)RNA into polypeptides. Most plant proteins derive from nuclear genes and their mRNAs are translated on ribosomes in the cytoplasm. Many fewer genes are located within mitochondrial (mt) or plastid (including chloroplast (cp)) DNA, and mRNAs from these genomes are translated on separate populations of ribosomes within the particular organelles. The cytoplasmic genomes are much smaller than that of the nucleus and they are present in multiple copies in each organelle. As there are many chloroplasts and mitochondria in each cell, these genomes may contribute a large proportion of total cellular DNA. Chloroplast DNA, in particular, has been extensively used to study plant phylogeny. The reasons why it is useful and some of the possible problems associated with its use in taxonomy are discussed.
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