R^— R^— Rz— Rz— R-^— R^— R^— Fz— F^— F^— F^— Rz— F^—

F—^ F—^ F—^ F—^ F—^ F—^ F—^ R—^ R—^ R—^ R—^ F—^ R—^

_rp!2 ndhB_rps7_rrn16_rrn5 rp!32_chIL rrn5_rrn16_rps7 ndhB psbA chIB

LSC IR SSC IR LSC Figure 6.4 Primer locations for the current study of plastid genome organization in ferns: (a) Adiantum and (b) Angiopteris.

Figure 6.5 Current understanding of plastid genome inversions (see Figure 6.1) marked on a simplified phylogenetic framework.

gleichenioid clade and its sister. Inversion 2 occurred on the branch leading to the common ancestor of the heterosporous fern clade and its sister group. Note that either parsimonious acquisition of inversion 1 requires that the gleiche-nioid ferns are not sister to the filmy ferns, as is possible with the unresolved tree in Figure 6.2. That sister relationship was recovered in only some of the analyses by Pryer et al. (2004); see Chapter 15.

The gene order data gathered so far suggest that major rearrangement events do occur in intervals, rather than during temporal hot spots. This being the case, rearrangement events, when present, yield another potential phylogenetic marker to be considered. The one caveat we should add is that our inferences are based on the sampling of only one taxon per major lineage. Although this should be sufficient to infer the sequence of events involved in the major, already characterized, inversions, we could be missing other structural changes that are significant, and even phylogenetically informative within specific lineages.

6.5 Conclusions and prospects

Although our overall understanding of fern plastid genome structure and evolution is increasing, we still lack knowledge of the variation within many groups of ferns, where DNA sequence data from a sample of genes is the preferred approach for phylogenetic studies. In general, the plastid genome structure remains evolutionarily conservative (or perhaps there is convergence to a stable structure), yet in certain clades the structure can become destabilized. Thus, within some angiosperm families, the plastid genome structure provides a wealth of phylogenetic data (Cosner et al., 2004; Kim et al., 2005). In ferns, only a few groups have been examined extensively at the structural level, one excellent example being the tree ferns (Conant et al., 1994). With the shift to sequenced based approaches, it is likely that some potentially very useful data may be missed. In addition to the traditional studies of plastid genome structure and evolution, it is likely that future studies will examine other aspects of plastid "genomics," especially investigations into plastid proteins (Peltier et al., 2000; van Wijk, 2000; Leister, 2003) as well as regulation of plastid-encoded genes (Wu et al, 1993; Eberhard et al, 2002; Robbens et al, 2005). With the variety and combination of genomic tools currently available, it is likely that the next decade will open up exciting new avenues of investigation.


Bendich, A. J. (2004). Circular chloroplast chromosomes: the grand illusion. The Plant Cell, 16, 1661-1666.

Conant, D. S., Stein, D. B., Valinski, A. E. C., Sudarsanam, P., and Ahearn, M. E. (1994). Phylogenetic implications of chloroplast DNA variation in the Cyatheaceae.1. Systematic Botany, 19, 60-72.

Cosner, M. A., Raubeson, L. A., and Jansen, R. K. (2004). Chloroplast DNA

rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomes. BMC Evolutionary Biology, 4, 1-17.

Eberhard, S., Drapier, D., and Wollman, F. A. (2002). Searching limiting steps in the expression of chloroplast-encoded proteins: relations between gene copy number, transcription, transcript abundance and translation rate in the chloroplast of Chlamydomonas reinhardtii. Plant Journal, 31, 149-160.

Goulding, S. E., Olmstead, R. G., Morden, C. W., and Wolfe, K. H. (1996). Ebb and flow of the chloroplast inverted repeat. Molecular and General Genetics, 252, 195-206.

Hasebe, M. and Iwatsuki, K. (1990a). Adiantum capillus-veneris chloroplast DNA clone bank: as useful heterologous probes in the systematics of the leptosporangiate ferns. American Fern Journal, 80, 20-25.

Hasebe, M. and Iwatsuki, K. (1990b). Chloroplast DNA from Adiantum capillus-veneris L., a fern species (Adiantaceae) -- clone bank, physical map and unusual gene localization in comparison with angiosperm chloroplast DNA. Current Genetics, 17, 359-364.

Hasebe, M. and Iwatsuki, K. (1992). Gene localization on the chloroplast DNA of the maiden hair fern: Adiantum capillus-veneris. Botanical Magazine (Tokyo), 105, 413-419.

Helfenbein, K. G. and Boore, J. L. (2004). The mitochondrial genome of Phoronis architecta - comparisons demonstrate that phoronids are lophotrochozoan protostomes. Molecular Biology and Evolution, 21, 153-157.

Jansen, R. K., Raubeson, L. A., Boore, J. L., dePamphilis, C. W., Chumley, T. W.,

Haberle, R. C., Wyman, S. K., Alverson, A. J., Peery, R., Herman, S. J., Fourcade, H. M., Kuehl, J. V., McNeal, J. R., Leebens-Mack, J., and Cui, L. (2005). Methods for obtaining and analyzing whole chloroplast genome sequences. Methods in Enzymology, 395, 348-384.

Kim, K.-J., Choi, K.-S., and Jansen, R. K. (2005). Two chloroplast DNA inversions originated simultaneously during the early evolution of the sunflower family (Asteraceae). Molecular Biology and Evolution, 22, 1783-1792.

Kolodner, R. and Tewari, K. K. (1979). Inverted repeats in chloroplast DNA from higher plants. Proceedings of the National Academy of Sciences of the United States of America, 76, 41-45.

Kugita, M., Yamamoto, Y., Fujikawa, T., Matsumoto, T., and Yoshinaga, K. (2003). RNA editing in hornwort chloroplasts makes more than half the genes functional. Nucleic Acids Research, 31, 2417-2423.

Ledergerg, J. and McCray, A. T. (2001). "Ome sweet "omics - a genealogical treasury of words. The Scientist, 15, 8-9.

Leister, D. (2003). Chloroplast research in the genomic age. Trends in Genetics, 19, 47-56.

Martin, W. and Herrmann, R. G. (1998). Gene transfer from organelles to the nucleus: how much, what happens, and why? Plant Physiology, 118, 9-17.

Martin, W. and Miller, M. (1998). The hydrogen hypothesis for the first eukaryote. Nature, 392, 37-41.

Martin, W., Somerville, C. C., and Loiseaux-de Goel, S. (1992). Molecular phylogenies of plastid origins and algal evolution. Journal of Molecular Evolution, 35, 385-404.

Martin, W., Stoebe, B., Goremyken, V., Hansmann, S., Hasegawa, M., and Kowallik, K. V. (1998). Gene transfer to the nucleus and the evolution of chloroplasts. Nature, 393, 162-165.

McNeal, J. R., Leebens-Mack, J. H., Arumuganathan, K., Kuehl, J. V., Boore, J. L., and dePamphilis, C. W. (2006). Using partial genomic fosmid libraries for sequencing complete organellar genomes. Biotechniques, 41, 69-72.

Nishiyama, T., Kugita, M., Sinclair, R. B., Sugita, M., Sugiura, C., Wakasugi, T., Wolf, P. G., Yamada, K., Yoshinaga, K., and Hasebe, M. (2004). Bryophytes are monophyletic and land plants comprise two extant lineages. Molecular Biology and Evolution, 21, 1813-1819.

Ohyama, K., Fukuzawa, H., Kohchi, T., Shirai, H., Sano, T., Sano, S., Umesono, K., Shiki, Y., Takeuchi, M., Chang, Z., Aota, S., Inokuchi, H., and Ozeki, H. (1986).

Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature, 322, 572-574.

Olmstead, R. G. and Palmer, J. D. (1994). Chloroplast DNA systematics: a review of methods and data analysis. American Journal of Botany, 81, 1205-1224.

Palmer, J. D. (1983). Chloroplast DNA exists in two orientations. Nature, 301, 92-93.

Palmer, J. D. (1985a). Comparative organization of chloroplast genomes. Annual Review of Genetics, 19, 325-354.

Palmer, J. D. (1985b). Evolution of cpDNA and mtDNA in plants and algae. In

Molecular and Evolutionary Genetics, ed. R. J. MacIntyre. New York: Plenum Press, pp. 131-240.

Palmer, J. D. (1986). Isolation and structural analysis of chloroplast DNA. Methods in Enzymology, 118, 167-186.

Palmer, J. D. (1987). Chloroplast DNA evolution and biosystematic uses of chloroplast DNA variation. The American Naturalist, 130, 6-29.

Palmer, J. D. (1991). Plastid chromosomes: structure and evolution. In Cell Culture and Somatic Genetics of Plant, Vol. 7A, Molecular Biology ofPlastids, ed. L. Bogorad and I. K. Vasil. San Diego, CA: Academic Press, pp. 5-53.

Palmer, J. D. and Stein, D. B. (1986). Conservation of chloroplast genome structure among vascular plants. Current Genetics, 10, 823-833.

Palmer, J. D. and Thompson, W. F. (1981). Rearrangements in the chloroplast genomes of mung bean and pea. Proceedings of the National Academy of Sciences of the United States of America, 78, 5533-5537.

Peltier, J., Friso, G., Kalume, D., Roepstorff, P., Nilsson, F., Adamska, I., van Wijk, K., and van Wijk, K. (2000). Proteomics of the chloroplast: systematic identification and targeting analysis of lumenal and peripheral thylakoid proteins. Plant Cell, 12, 319-341.

Pryer, K. M., Schuettpelz, E., Wolf, P. G., Schneider, H., Smith, A. R., and Cranfill, R. (2004). Phylogeny and evolution of ferns (monilophytes) with a focus on the early leptosporangiate divergences. American Journal of Botany, 91, 1582-1598.

Raubeson, L. A. and Jansen, R. K. (1992). Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants. Science, 255, 1697-2699.

Raubeson, L. A. and Stein, D. B. (1995). Insights into fern evolution from mapping chloroplast genomes. American Fern Journal, 85, 193-204.

Robbens, S., Khadaroo, B., Camasses, A., Derelle, E., Ferraz, C., Inze, D., Van de Peer, Y., and Moreau, H. (2005). Genome-wide analysis of core cell cycle genes in the unicellular green alga Ostreococcus tauri. Molecular Biology and Evolution, 22, 589-597.

Roper, J. M., Hansen, S. K., Wolf, P. G., Karol, K. G., Mandoli, D. F., Everett, K. D. E., Kuehl, J., and Boore, J. L. (2007). The complete plastid genome sequence of Angiopteris evecta (G. Forst.) Hoffm. American Fern Journal, 97, 95--106.

Shinozaki, K., Ohme, M., Tanaka, M., Wakasugi, T., Hayashida, N., Matsubayashi, T., Zaita, N., Chunwongse, J., Obokata, J., Yamaguchi-Shinozaki, K., Ohto, C., Torazawa, K., Meng, B. Y., Sugita, M., Deno, H., Kamogashira, T., Yamada, K., Kusuda, J., Takaiwa, F., Kato, A., Tohdoh, N., Shimada, H., and Sugiura, M. (1986).

The complete nucleotide sequence of tobacco chloroplast genome: its gene organization and expression. EMBO Journal, 5, 2043-2049.

Small, R. L., Lickey, E. B., Shaw, J., and Hauk, W. D. (2005). Amplification of noncoding chloroplast DNA for phylogenetic studies in lycophytes and monilophytes with a comparative example of relative phylogenetic utility from Ophioglossaceae. Molecular Phylogenetics and Evolution, 36, 509-522.

Stein, D. B., Palmer, J. D., and Thompson, W. F. (1986). Structural evolution and flip-flop recombination of chloroplast DNA in the fern genus Osmunda. Current Genetics, 10, 835-841.

Stein, D. B., Conant, D. S., Ahearn, M. E., Jordan, E. T., Kirch, S. A., Hasebe, M.,

Iwatsuki, K., Tan, M. K., and Thomson, J. A. (1992). Structural rearrangements of the chloroplast genome provide an important phylogenetic link in ferns. Proceedings of the National Academy of Sciences of the United States of America, 89, 1856-1860.

Stoebe, B., Hansmann, S., Goremykin, V., Kowalik, K. V., and Martin, W. (1999). Proteins encoded in sequenced chloroplast genomes: an overview of gene content, phylogenetic information and endosymbiotic gene transfer to the nucleus. In Molecular Systematics and Plant Evolution, ed. P. M. Hollingsworth, R. M. Batesman, and R. J. Gornall. London: Taylor and Francis, pp. 327-352.

Sugiura, C., Kobayashi, Y., Aoki, S., Sugita, C., and Sugita, M. (2003). Complete chloroplast DNA sequence of the moss Physcomitrella patens: evidence for the loss and relocation of rpoA from the chloroplast to the nucleus. Nucleic Acids Research, 31, 5324-5331.

van Wijk, K. J. (2000). Proteomics of the chloroplast: experimentation and prediction. Trends in Plant Science, 5, 420-425.

Wolf, P. G., Rowe, C. A., Sinclair, R. B., and Hasebe, M. (2003). Complete nucleotide sequence of the chloroplast genome from a leptosporangiate fern, Adiantum capillus-veneris L. DNA Research, 10, 59-65.

Wolf, P. G., Rowe, C. A., and Hasebe, M. (2004). High levels of RNA editing in a vascular plant chloroplast genome: analysis of transcripts from the fern Adiantum capillus-veneris. Gene, 339, 89-97.

Wolf, P. G., Karol, K. G., Mandoli, D. F., Kuehl, J., Arumuganathan, K., Ellis, M. W., Mishler, B. D., Kelch, D. G., Olmstead, R. G., and Boore, J. L. (2005). The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae). Gene, 350, 117-128.

Wolfe, K. H., Morden, C. W., Ems, S. C., and Palmer, J. D. (1992). Rapid evolution of the plastid translational apparatus in a nonphotosynthetic plant: loss or accelerated sequence evolution of tRNA and ribosomal protein genes. Journal of Molecular Evolution, 35, 304-317.

Wu, M., Chang, C. H., Yang, J. M., Zhang, Y. L., Nie, Z. Q., and Hsieh, C. H. (1993).

Regulation of chloroplast DNA replication in Chlamydomonas reinhardtii. Botanical Bulletin of Academia Sinica, 34, 115-131.

Wyman, S. K., Boore, J. L., and Jansen, R. K. (2004). Automatic annotation of organellar genomes with DOGMA. Bioinformatics, 20, 3252-3255.

Was this article helpful?

0 0
10 Ways To Fight Off Cancer

10 Ways To Fight Off Cancer

Learning About 10 Ways Fight Off Cancer Can Have Amazing Benefits For Your Life The Best Tips On How To Keep This Killer At Bay Discovering that you or a loved one has cancer can be utterly terrifying. All the same, once you comprehend the causes of cancer and learn how to reverse those causes, you or your loved one may have more than a fighting chance of beating out cancer.

Get My Free Ebook

Post a comment