Physical mapping of differences in chloroplast DNA of the five wild-type plastomes in Oenothera subsection Euoenothera

Nicotiana chloroplast genome : 8. Localization of genes for subunits of ATP synthase, the cytochrome b-f complex and the 32 kD protein

Using the existing restriction map and probes from wheat and pea ct-DNA, seven protein genes have been localized in the chloroplast genome of N. tabacum. On the clock-like map, the location of each gene is indicated by its time zone: the 15.2 kD polypeptide of the cytochrome b/f complex at 3∶15, cytochrome f at 4∶30, LS of RuBPCase at 4∶50, both β and ɛ subunits of ATP synthase at or near 5∶00, proton-translocating subunit of ATP synthase at 8∶20, α subunit of ATP synthase at 8∶40 and the 32 kD protein at 9∶30. The genome organization of Nicotiana chloroplast DNA is similar to spinach.

Nicotiana chloroplast genome : 6. Deletion and hot spot - a proposed origin of the inverted repeats

A physical map containing six restriction sites of the Nicotiana tabacum chloroplast genome, together with the BamHI maps of N. tabacum, N. otophora and N. knightiana, and the SmaI maps of N. acuminata, N. plumbaginifolia, N. langsdorffii, N. otophora, N. tabacum, N. tomentosiformis and N. knightiana was constructed. In Nicotiana chloroplast genomes, the most frequently observed variations are point mutations. Deletions are also detected. Most of the observed changes are confined to one area of the large single copy region, which is designated as the "hot spot". Based on the evidence obtained from Nicotiana chloroplast genomes, an origin of the inverted repeats in this genus is proposed. We suggest that the inverted repeats represent a vestige of what were once two identical, complete chloroplast genomes joined together in a head-to-head and tail-to-tail fashion, and that deletions generated the current chloroplast genome organization.

Chloroplast DNA evolution and the origin of amphidiploid Brassica species

The origin and evolution of a hybrid species complex in the genus Brassica (cabbage, turnip, mustard, rapeseed oil) has been explored through mutational analysis of the maternally inherited chloroplast genome. A detailed chloroplast DNA phylogeny enables identification of the maternal parent for most of the amphidiploids examined and permits quantitative resolution of the relative time of hybridization as well as the relative divergence of the diploid parents. Contradictory chloroplast and nuclear phylogenies obtained for two accessions of the amphidiploid B. napus (rapeseed oil) lead to the hypothesis that introgressive hybridization has also figured in their recent evolution.

Chloroplast DNA variation between species of Triticum and Aegilops. Location of the variation on the chloroplast genome and its relevance to the inheritance and classification of the cytoplasm

Restriction endonuclease analysis revealed interspecific and intraspecific variation between the chloroplast DNAs and therefore between the cytoplasms of 14 selected species of Triticum and Aegilops. Eleven distinct chloroplast DNA types were detected, the differences between them residing in the varied combination of a relatively few DNA alterations.The variation was simple enough for chloroplast DNA analysis to be used as a basis for the identification and classification of the Triticum and Aegilops cytoplasms. There was good agreement with the classification based on analysis of the phenotypic effects of the cytoplasm when combined with the T. aestivum nucleus in nuclear-cytoplasmic hybrids (Tsunewaki et al. 1976). There was however no correlation between specific chloroplast DNA alterations and any of the phenotypic effects known to be associated with specific cytoplasms.Although the diploid species examined included all those which have been suggested as possible donors of the cytoplasm and the B genome to T. aestivum, none of the chosen accessions belonged to the same cytoplasmic class as T. aestivum itself, except that of the tetraploid T. dicoccoides. Therefore, none of the diploid accessions analysed was the B genome donor. The analyses did however support several other suggestions which have been made concerning wheat ancestry. Scoring the different chloroplast DNA types according to the rarity of their banding patterns indicated that four of the eleven cytoplasms are of relatively recent origin.The DNA alterations most easily detectable by the limited comparison of the eleven Triticum/Aegilops chloroplast DNA types using only 4 endonucleases were insertions and deletions. These ranged between approximately 50 bp and 1,200 bp in size and most of them were clustered in 2 segments of the large single-copy region of the genome. Only two examples of the loss of restriction endonuclease sites through possible point mutations were observed. No variation was detected in the inverted repeat regions. Several of the deletions and insertions map close to known chloroplast protein genes, and there is also an indication that the more variable regions of the chloroplast genome may contain sequences which have allowed DNA recombination and rearrangement to occur.

Chloroplast and mitochondrial DNA variation as indicator of phylogenetic relationships in the genus Coffea L

Chloroplast and mitochondrial DNA from nine species or taxons of coffee-trees were compared as to their phylogenetic relationship by restriction endonuclease fragment analysis. Three types of chloroplast DNA (cp DNA) were detected indicating relationships as follows: (i) C. arabica, C. eugenioides; (ii) C. canephora, C. congensis, "nana" taxon; (iii) C. liberica. The mitochondrial DNA (mt DNA) separated into five types: (i) C. arabica, C. eugenioides, C. congensis; (ii) C. canephora, "nana" taxon; (iii) C. excelsa; (iv) C. liberica; (v) Paracoffea ebracteolata. The divergence in organelle DNAs agrees with the phylogenetic relationship deduced by conventional methods and is presented in some detail. Restriction patterns of the cp and mt DNAs isolated from a clone of C. arabusta have been compared to those of the parents and were found to be inherited from the mother. Cp and mt DNA analyses in the genus Coffea support the hypothesis that C. canephora diverged from C. congensis, whereafter the latter species differentiated into C. eugenioides and C. arabica.