Book contents
- Frontmatter
- Contents
- List of contributors
- Preface
- Acknowledgments
- Part I Development and morphogenesis
- Part II Genetics and reproduction
- 4 Population genetics
- 5 Antheridiogens
- 6 Structure and evolution of fern plastid genomes
- 7 Evolution of the nuclear genome of ferns and lycophytes
- Part III Ecology
- Part IV Systematics and evolutionary biology
- Index
- References
6 - Structure and evolution of fern plastid genomes
Published online by Cambridge University Press: 11 August 2009
Book contents
- Frontmatter
- Contents
- List of contributors
- Preface
- Acknowledgments
- Part I Development and morphogenesis
- Part II Genetics and reproduction
- 4 Population genetics
- 5 Antheridiogens
- 6 Structure and evolution of fern plastid genomes
- 7 Evolution of the nuclear genome of ferns and lycophytes
- Part III Ecology
- Part IV Systematics and evolutionary biology
- Index
- References
Summary
Introduction
The concept of the genome, as the haploid complement of genes of an organism, is far from recent. The term genome is usually attributed to Hans Winkler in 1920 (Ledergerg and McCray, 2001). However, fine scale maps and understanding of the function of genes in the context of the genome did not begin until the 1970s after DNA sequencing techniques were developed. The term genome (and its corresponding genomics) can mean different things to different people (Ledergerg and McCray, 2001) but here we will focus on structural and evolutionary aspects of genomes in ferns. Although genomics is generally reserved for the main (nuclear) component of an organism, that topic is covered in Chapter 7. Instead we narrow the focus here to the chloroplast (i.e., plastid) genome. This small, well-defined genome is found in all green plants. Among land plants the plastid genome is highly conserved in structure and gene content (Palmer, 1985b). Compared to most nuclear genomes studied, plastid genomes contain a high proportion of DNA that codes for proteins and for RNA (ribosomal and transfer). Much of the non-coding regions (between protein-encoding genes) is transcribed and may well have important regulatory functions.
Because the plastid genome contains a high density of genes of well-studied processes, the genome is an excellent model for investigations into the relationship between genome structure and function. This field represents an ideal starting point leading into the much more complex field of the study of nuclear genomes.
- Type
- Chapter
- Information
- Biology and Evolution of Ferns and Lycophytes , pp. 159 - 174Publisher: Cambridge University PressPrint publication year: 2008
References
(2004). Circular chloroplast chromosomes: the grand illusion. The Plant Cell, 16, 1661–1666.CrossRefGoogle ScholarPubMed
, , , , and (1994). Phylogenetic implications of chloroplast DNA variation in the Cyatheaceae.1. Systematic Botany, 19, 60–72.CrossRefGoogle Scholar
, , and (2004). Chloroplast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomes. BMC Evolutionary Biology, 4, 1–17.CrossRefGoogle ScholarPubMed
, , and (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.CrossRefGoogle ScholarPubMed
, , , and (1996). Ebb and flow of the chloroplast inverted repeat. Molecular and General Genetics, 252, 195–206.CrossRefGoogle ScholarPubMed
and (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.CrossRefGoogle Scholar
and (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.CrossRefGoogle Scholar
and (1992). Gene localization on the chloroplast DNA of the maiden hair fern: Adiantum capillus-veneris. Botanical Magazine (Tokyo), 105, 413–419.CrossRefGoogle Scholar
and (2004). The mitochondrial genome of Phoronis architecta – comparisons demonstrate that phoronids are lophotrochozoan protostomes. Molecular Biology and Evolution, 21, 153–157.CrossRefGoogle ScholarPubMed
, , , , , , , , , , , , , , and (2005). Methods for obtaining and analyzing whole chloroplast genome sequences. Methods in Enzymology, 395, 348–384.CrossRefGoogle ScholarPubMed
, , and (2005). Two chloroplast DNA inversions originated simultaneously during the early evolution of the sunflower family (Asteraceae). Molecular Biology and Evolution, 22, 1783–1792.CrossRefGoogle Scholar
and (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.CrossRefGoogle ScholarPubMed
, , , , and (2003). RNA editing in hornwort chloroplasts makes more than half the genes functional. Nucleic Acids Research, 31, 2417–2423.CrossRefGoogle ScholarPubMed
and (2001). “Ome sweet ”omics – a genealogical treasury of words. The Scientist, 15, 8–9.Google Scholar
(2003). Chloroplast research in the genomic age. Trends in Genetics, 19, 47–56.CrossRefGoogle ScholarPubMed
and (1998). Gene transfer from organelles to the nucleus: how much, what happens, and why? Plant Physiology, 118, 9–17.CrossRefGoogle Scholar
and (1998). The hydrogen hypothesis for the first eukaryote. Nature, 392, 37–41.CrossRefGoogle ScholarPubMed
, , and (1992). Molecular phylogenies of plastid origins and algal evolution. Journal of Molecular Evolution, 35, 385–404.CrossRefGoogle Scholar
, , , , , and (1998). Gene transfer to the nucleus and the evolution of chloroplasts. Nature, 393, 162–165.CrossRefGoogle ScholarPubMed
, , , , , and (2006). Using partial genomic fosmid libraries for sequencing complete organellar genomes. Biotechniques, 41, 69–72.CrossRefGoogle ScholarPubMed
, , , , , , , , , and (2004). Bryophytes are monophyletic and land plants comprise two extant lineages. Molecular Biology and Evolution, 21, 1813–1819.CrossRefGoogle Scholar
, , , , , , , , , , , , and (1986). Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature, 322, 572–574.CrossRefGoogle Scholar
and (1994). Chloroplast DNA systematics: a review of methods and data analysis. American Journal of Botany, 81, 1205–1224.CrossRefGoogle Scholar
(1985a). Comparative organization of chloroplast genomes. Annual Review of Genetics, 19, 325–354.CrossRefGoogle Scholar
Palmer, J. D. (1985b). Evolution of cpDNA and mtDNA in plants and algae. In Molecular and Evolutionary Genetics, ed. . New York: Plenum Press, pp. 131–240.CrossRefGoogle Scholar
(1986). Isolation and structural analysis of chloroplast DNA. Methods in Enzymology, 118, 167–186.CrossRefGoogle Scholar
(1987). Chloroplast DNA evolution and biosystematic uses of chloroplast DNA variation. The American Naturalist, 130, 6–29.CrossRefGoogle Scholar
Palmer, J. D. (1991). Plastid chromosomes: structure and evolution. In Cell Culture and Somatic Genetics of Plant, Vol. 7A, Molecular Biology of Plastids, ed. and . San Diego, CA: Academic Press, pp. 5–53.Google Scholar
and (1986). Conservation of chloroplast genome structure among vascular plants. Current Genetics, 10, 823–833.CrossRefGoogle Scholar
and (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.CrossRefGoogle ScholarPubMed
, , , , , , , and (2000). Proteomics of the chloroplast: systematic identification and targeting analysis of lumenal and peripheral thylakoid proteins. Plant Cell, 12, 319–341.CrossRefGoogle ScholarPubMed
, , , , , and (2004). Phylogeny and evolution of ferns (monilophytes) with a focus on the early leptosporangiate divergences. American Journal of Botany, 91, 1582–1598.CrossRefGoogle ScholarPubMed
and (1992). Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants. Science, 255, 1697–2699.CrossRefGoogle ScholarPubMed
and (1995). Insights into fern evolution from mapping chloroplast genomes. American Fern Journal, 85, 193–204.CrossRefGoogle Scholar
, , , , , , , and (2005). Genome-wide analysis of core cell cycle genes in the unicellular green alga Ostreococcus tauri. Molecular Biology and Evolution, 22, 589–597.CrossRefGoogle ScholarPubMed
, , , , , , , and (2007). The complete plastid genome sequence of Angiopteris evecta (G. Forst.) Hoffm. American Fern Journal, 97, 95–106.CrossRefGoogle Scholar
, , , , , , , , , , , , , , , , , , , , , , and (1986). The complete nucleotide sequence of tobacco chloroplast genome: its gene organization and expression. EMBO Journal, 5, 2043–2049.Google ScholarPubMed
, , , and (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.CrossRefGoogle ScholarPubMed
, , and (1986). Structural evolution and flip-flop recombination of chloroplast DNA in the fern genus Osmunda. Current Genetics, 10, 835–841.CrossRefGoogle Scholar
, , , , , , , , and (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.CrossRefGoogle ScholarPubMed
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. , , and . London: Taylor and Francis, pp. 327–352.CrossRefGoogle Scholar
, , , , and (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.CrossRefGoogle ScholarPubMed
(2000). Proteomics of the chloroplast: experimentation and prediction. Trends in Plant Science, 5, 420–425.CrossRefGoogle Scholar
, , , and (2003). Complete nucleotide sequence of the chloroplast genome from a leptosporangiate fern, Adiantum capillus-veneris L. DNA Research, 10, 59–65.CrossRefGoogle ScholarPubMed
, , and (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.CrossRefGoogle Scholar
, , , , , , , , , and (2005). The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae). Gene, 350, 117–128.CrossRefGoogle Scholar
, , , and (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.CrossRefGoogle ScholarPubMed
, , , , , and (1993). Regulation of chloroplast DNA replication in Chlamydomonas reinhardtii. Botanical Bulletin of Academia Sinica, 34, 115–131.Google Scholar
, , and (2004). Automatic annotation of organellar genomes with DOGMA. Bioinformatics, 20, 3252–3255.CrossRefGoogle ScholarPubMed
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