X15901

Wolfe et al. (1992) Shinozaki et al. (1986) Schmitz-Linneweber et al. (2002) Ogihara et al. (2002) Maier et al. (1995) Hiratsuka et al. (1989)

Updated list of completely sequenced chloroplast genomes (for land plants and algae) can be found at http://megasun.bch.umontreal.ca/ogmp/projects/ other/cp_list.html

Fig. 4.1. Gene map of tobacco chloroplast genome (adapted from Wakasugi et al., 1998). The inner circle shows the four major regions of the genome - the two copies of the inverted repeat (IRa and IRb) and the large and small single-copy regions (LSC and SSC). The outer circle represents the tobacco genome with the transcribed regions shown as boxes proportional to gene size. Genes shown on the inside of the circle are transcribed in a clockwise direction, whereas genes on the outside of the circle are transcribed anticlockwise. The IR extent is also shown by the increased width of the circle representing the tobacco genome. Genes with introns are marked with asterisks (*). Arrows between the gene boxes and gene names show those operons known to occur in tobacco cpDNA. Other operons could be present. Genes coding for products that function in protein synthesis are darker grey; genes coding for products that function in photosynthesis are stippled; genes coding for products with various other functions are lighter grey.

Fig. 4.1. Gene map of tobacco chloroplast genome (adapted from Wakasugi et al., 1998). The inner circle shows the four major regions of the genome - the two copies of the inverted repeat (IRa and IRb) and the large and small single-copy regions (LSC and SSC). The outer circle represents the tobacco genome with the transcribed regions shown as boxes proportional to gene size. Genes shown on the inside of the circle are transcribed in a clockwise direction, whereas genes on the outside of the circle are transcribed anticlockwise. The IR extent is also shown by the increased width of the circle representing the tobacco genome. Genes with introns are marked with asterisks (*). Arrows between the gene boxes and gene names show those operons known to occur in tobacco cpDNA. Other operons could be present. Genes coding for products that function in protein synthesis are darker grey; genes coding for products that function in photosynthesis are stippled; genes coding for products with various other functions are lighter grey.

genome has expanded, evolutionary biologists have been able to extend the use of cpDNA in comparative studies. Such studies have contributed to the understanding of mutational processes operating in chloro-plast genomes as well as providing data for phylogenetic purposes. The chloroplast genome has been utilized more than any other plant genome as a marker for investigating plant evolution and diversity due to its many advantages. Because of the genome's small size (generally 120-160 kilobase pairs, kbp) and high copy number (as many as 1000 per cell), it is relatively straightforward to isolate and characterize cpDNA. Plus, the conservative nature of the genome allows for the use of DNA probes from even distantly related species and the design of 'universal' primers. In addition, the genome is a good phylogenetic marker because rates of nucleotide change (while overall being slower than in the nuclear genome) show a range of rates making different parts of the genome appropriate for different levels of comparison, rare changes in gene order can be informative even at deep phylogenetic levels, and the usual pattern of uniparental inheritance and lack of recombination simplify analysis.

The use of cpDNA in phylogenetic studies dates back to the early 1980s when a few plant biologists used the genome to address species relationships in several groups of crop plants by comparing fragment patterns of purified cpDNA digested with restriction enzymes (Palmer and Zamir, 1982; Bowman et al., 1983; Clegg et al., 1984; Hosaka et al., 1984). Later studies compared restriction site changes via filter hybridization at higher taxonomic levels (e.g. Sytsma and Gottlieb, 1986; Jansen and Palmer, 1988). Some studies also mapped gene order and used rearrangements to address evolutionary relationships (e.g. Jansen and Palmer, 1987a; Raubeson and Jansen, 1992a,b). More recently the vast majority of phyloge-netic and systematic studies have employed sequence data for cpDNA-based phylogenetic comparisons. The first sequencing studies (Doebley et al., 1990; Soltis et al., 1990) utilized the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase (rbcL). This has been the most widely sequenced chloroplast gene and the emphasis on this gene culminated in a multi-authored study involving 499 species of seed plants (Chase et al., 1993). Many other individual chloroplast genes and intergenic regions have now been utilized (reviewed in Soltis and Soltis, 1998). Several recent studies have used ten or more protein-coding genes from partially or completely sequenced chloroplast genomes to estimate phylogenetic relationships of plants (e.g. Graham and Olmstead, 2000; Lemieux et al., 2000; Martin et al., 2002).

For the remainder of this chapter, we will focus on two aspects of the plant chloroplast genome: (i) its organization and evolution; and (ii) the phylogenetic utility of different approaches to cpDNA characterization.

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