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Rates and Patterns of Chloroplast DNA Evolution (Chloroplast DNA/Ribulose-L,5-Bisphosphate Carboxylase/Plant Evolution/Evolutionary Rates) MICHAEL T

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Rates and Patterns of Chloroplast DNA Evolution (Chloroplast DNA/Ribulose-L,5-Bisphosphate Carboxylase/Plant Evolution/Evolutionary Rates) MICHAEL T Proc. Nati. Acad. Sci. USA Vol. 91, pp. 6795-6801, July 1994 Colloquium Paper This paper was presented at a colloquium entitled "Tempo and Mode in Evolution" organized by Walter M. Fitch and Francisco J. Ayala, held January 27-29, 1994, by the National Academy of Sciences, in Irvine, CA. Rates and patterns of chloroplast DNA evolution (chloroplast DNA/ribulose-l,5-bisphosphate carboxylase/plant evolution/evolutionary rates) MICHAEL T. CLEGG*, BRANDON S. GAUTt, GERALD H. LEARN, JR.*, AND BRIAN R. MORTON* *Department of Botany and Plant Science, University of California, Riverside, CA 92501; and tDepartment of Statistics, North Carolina State University, Raleigh, NC 27895 ABSTRACT The chloroplast genome (cpDNA) of plants Because the photosynthetic machinery requires many has been a focus of research In plant molecular evolution and more gene functions than are specified on the cpDNA of systematics. Several features of this genome have facilitated plants and algae, it is assumed that many gene functions were molecular evolutionary analyses. First, the genome is smail and transferred to the eukaryotic nuclear genome. The strong constitutes an abundant component of cellular DNA. Second, conservation of cpDNA gene content cited above indicates the chloroplast genome has been extensively characterized at that most transfers of gene function from the chloroplast to the molecular level providing the basic information to support the nuclear genome occurred early following the primordial comparative evolutionary research. And third, rates of nucde- endosymbiotic event. Among land plants, gene content is otide substitution are relatively slow and therefore provide the almost perfectly conserved, although a few recent transfers appropriate window of resolution to study plant phylogeny at of function from the chloroplast to the nuclear genome have deep levels ofevolution. Despite a conservative rate ofevolution been demonstrated (10, 11). and a relatively stable gene content, comparative molecular Conservation of gene content and a relatively slow rate of analyses reveal complex patterns of mutational change. Non- nucleotide substitution in protein-coding genes has made the coding regions of cpDNA diverge through insertion/deletion chloroplast genome an ideal focus for studies of plant evo- changes that are sometimes site dependent. Coding genes lutionary history (reviewed in ref. 12). These efforts have codon bias that to violate culminated in the past year with the publication of a volume exhibit different patterns of appear of papers that presents a detailed molecular phylogeny for the equilibrium assumptions of some evolutionary models. seed plants (13). This effort has involved many laboratories Rates ofmolecular change often vary among plant famile and that have together determined the DNA sequence for more orders in a manner that violates the assumption of a simple than 750 copies (by latest count) of the cpDNA gene rbcL molecular clock. Finally, protein-coding genes exhibit patterns encoding the large subunit of ribulose-1,5-bisphosphate car- of amino acd change that appear to depend on protein boxylase (RuBisCo). The sequence data span the full range of structure, and these patterns may reveal subtle aspects of plant diversity from algae to flowering plants. This very large structure/function relationships. Only comparative studies of collection ofgene sequence data has allowed the reconstruc- molecular sequences have the resolution to reveal this under- tion of plant evolutionary history at a level of detail that is lying complexity. A complete description of the complexity of unprecedented in molecular systematics. molecular change is essential to a full understanding of the Accurate phylogenies are of more than academic interest. mechanisms of evolutionary change and in the formulation of They provide an organizing framework for addressing a host realistic models of mutational processes. of other important questions about biological change. For example, questions about the origins of major morphological The chloroplast genome was almost certainly contributed to adaptions must be placed in a phylogenetic context to recon- the eukaryotic cell through an endosymbiotic association with struct the precise sequence of genetic (and molecular) a cyanobacteria-like prokaryote. Moreover, present evidence changes that give rise to novel structures. The mutational suggests that the association that led to land plants occurred processes that subsume biological change can be revealed in only once in evolution (1). The derivative plastid genome great detail through a phylogenetic analysis. And, questions (cpDNA) is a relictual molecule ofabout 150 kbp that encodes about the frequency and mode of horizontal transfer of roughly 100 genetic functions (reviewed in refs. 2 and 3). This mobile genetic elements can only be addressed in a phylo- genome is the most widely studied plant genome with regard genetic context. One can make a very long list of biological to both molecular organization and evolution. Complete se- problems that are illuminated by phylogenetic analyses. quences of six chloroplast genomes are now available, and Despite their obvious utility, many important questions these represent virtually the full range of plant diversity [an remain about the accuracy of molecular phylogenies. All alga, Euglena (4); a bryophyte, Marchantia (5); a conifer, methods of phylogenetic reconstruction assume a fairly high black pinet; a dicot, tobacco (6); a monocot, rice (7); and a degree of statistical regularity in the underlying mutational parasitic dicot, Epifagus (8)]. With the possible exception of dynamics. Our goal in this article is to analyze the tempo and Euglena and Epifagus, the picture that has emerged is one of mode of cpDNA evolution in greater depth. We will show a relatively stable genome with marked conservation of gene that below the surface impression of conservation there are content and a substantial conservation of structural organiza- a variety of mutational processes that often violate assump- tion. Mapping studies that span land plants and algae confirm the impression of strong conservation in gene content (9). Abbreviations: cpDNA, chloroplast DNA; RuBisCo, ribulose-1,5- bisphosphate carboxylase; indel, insertion/deletion; RFLP, restric- tion fragment length polymorphism. The publication costs of this article were defrayed in part by page charge *Wakasugi, T., Tsudzuki, J., Itoh, S., Nakashima, K., Tsudzuki, T., payment. This article must therefore be hereby marked "advertisement" Shibata, M. & Sugiura, M., 15th International Botanical Congress, in accordance with 18 U.S.C. §1734 solely to indicate this fact. Aug. 28-Sept. 3, 1993, Tokyo, abstr. 7.2.1-6. 6795 Downloaded by guest on September 30, 2021 67% Colloquium Paper: Clegg et al. Proc. Nad. Acad Sci. USA 91 (1994) tions of rate constancy and site independence of mutational 17). Based on flanking sequence data, it has been suggested change. To facilitate an analysis of patterns of cpDNA that recombination between short direct repeats was respon- mutational change, we divide the genome into functional sible for these deletions (17). The four large deletions ob- categories and we then study the pattern of mutational served in the grasses all extend from within, or very close to, change within each functional category. The functional cat- Orpl23 to an area about 400 bases upstream of psaL. The egories are (i) DNA regions that do not code for tRNA, region spanned by the deletions has a low A+T content ribosomal RNA (rRNA), or protein (referred to as "noncod- relative to other chloroplast noncoding sequences (including ing DNA"); (ii) protein-coding genes; and (iii) chloroplast the surrounding noncoding sequences) and may have been a introns. The methodological approach is that of comparative coding sequence inserted by recombination, as was Orpl23, sequence analysis, where complete DNA sequences from prior to the divergence of the grass family (16). The rate of phylogenetically structured samples are analyzed to reveal nucleotide substitution in this noncoding region is roughly the pattern of mutational change in evolution. equal to the rate of synonymous substitution (with the exception of OrpI23) for the neighboring rbcL gene (16), but Evolution of Noncoding DNA Regions a large number of short insertion/deletions (indels) have occurred. In addition to both the high rate of indel mutation The chloroplast genome is highly condensed compared with and the large deletions, an inverted repeat in the noncoding eukaryotic genomes; for example, only 32% of the rice region about 300 bases upstream of the psal gene appears to genome is noncoding. Most of this noncoding DNA is found be labile to complex rearrangement events in the grass family in very short segments separatingfunctional genes. A number (16). of recent studies have revealed complex patterns of muta- A study of the noncoding region upstream of rbcL in the tional change in noncoding regions. The most widely studied grass family revealed similarpatterns ofcomplex change (18). noncoding region of the chloroplast genome is the region Indels were found to occur at a greater frequency than downstream of the rbcL gene in the grass family (Poaceae). nucleotide substitutions, and more complex changes, includ- This noncoding sequence is flanked by the genes rbcL and ing multiple tandem duplication events, were found to be psaf (the gene encoding photosystem I polypeptide I) and is confined to highly labile sites, resulting
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