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The evolution of the plastid chromosome in land plants: gene content, gene order, gene function.

Wicke S, Schneeweiss GM, dePamphilis CW, Müller KF, Quandt D - Plant Mol. Biol. (2011)

Bottom Line: These include the organization of plastid genes in operons, the usually uniparental mode of plastid inheritance, the activity of highly effective repair mechanisms as well as the rarity of plastid fusion.Nevertheless, structurally rearranged plastomes can be found in several unrelated lineages (e.g. ferns, Pinaceae, multiple angiosperm families).Patterns of ndh-gene loss and functional analyses indicate that these losses are usually found in plant groups with a certain degree of heterotrophy, might rendering plastid encoded Ndh1 subunits dispensable.

View Article: PubMed Central - PubMed

Affiliation: Department of Biogeography and Botanical Garden, University of Vienna, Rennweg 14, 1030 Vienna, Austria. susann.wicke@uni-muenster.de

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Synteny of land plant plastid chromosomes. The plastid chromosomes are shown in linearized form illustrating relative gene synteny. Genes are depicted by boxes colored according to their relevant functional class (see legend). Genes encoded by the leading strand (+ strand) or by the lagging strand (- strand) are shown above or below the grey chromosome bar, respectively. Lengths of boxes do not reflect lengths of genes, but are artificially increased to aid legibility (consequently, overlapping genes on ± strand do not indicate overlapping reading frames). Lines from selected genes/gene-regions mentioned above the first chromosome bar roughly indicate genes clusters that have been reorganizated during land plant evolution. Not all regions that underwent genomic relocations prior or during land plant evolution are depicted here. The chromosome bars are colored gray to highlight the positions of the two large Inverted Repeat regions (IRA/IRB) and are connected by gray lines between the different lineages. Gray lines are discontinued once to indicate loss of the large inverted repeat in Pinus. Drawn with GenomePixelizer (Kozik et al. 2002) using genome annotations deposited in public sequence databases. Refer to the text for genome references and original publications.]
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Fig2: Synteny of land plant plastid chromosomes. The plastid chromosomes are shown in linearized form illustrating relative gene synteny. Genes are depicted by boxes colored according to their relevant functional class (see legend). Genes encoded by the leading strand (+ strand) or by the lagging strand (- strand) are shown above or below the grey chromosome bar, respectively. Lengths of boxes do not reflect lengths of genes, but are artificially increased to aid legibility (consequently, overlapping genes on ± strand do not indicate overlapping reading frames). Lines from selected genes/gene-regions mentioned above the first chromosome bar roughly indicate genes clusters that have been reorganizated during land plant evolution. Not all regions that underwent genomic relocations prior or during land plant evolution are depicted here. The chromosome bars are colored gray to highlight the positions of the two large Inverted Repeat regions (IRA/IRB) and are connected by gray lines between the different lineages. Gray lines are discontinued once to indicate loss of the large inverted repeat in Pinus. Drawn with GenomePixelizer (Kozik et al. 2002) using genome annotations deposited in public sequence databases. Refer to the text for genome references and original publications.]

Mentions: The size of photosynthetic land plant plastid chromosomes ranges from 120 kb to 160 kb. The plastome in photosynthetic plants comprises 70 (gymnosperms) to 88 (liverworts) protein coding genes and 33 (most eudicots) to 35 (liverworts) structural RNA genes (Wakasugi et al. 1994; Ohyama 1996; Bock 2007), totaling 100–120 unique genes (Fig. 1). The vast majority of these genes are arranged in operons (or operon-like structures) and transcribed as polycistronic precursor molecules that are subjected to splicing and nucleolytic cleavage in order to produce mature and translatable mRNAs (Stern et al. 2010). Functional gene classes (translation/transcription, electron transfer, and photosystems) are often arranged in close vicinity to one another (Fig. 2; Cui et al. 2006). Using a parametric bootstrap-approach, Cui et al. (2006) showed that the genomic rearrangements of some chlorophytic algae (e.g. Chlamydomonas) relative to others are not random. Results indicated that the physical clustering of genes belonging to a similar functional class is positively selected. Furthermore, expression analysis indicated that some of these newly formed cluster are co-transcribed which led the authors to speculate that these could represent new regulons (Cui et al. 2006).Fig. 2


The evolution of the plastid chromosome in land plants: gene content, gene order, gene function.

Wicke S, Schneeweiss GM, dePamphilis CW, Müller KF, Quandt D - Plant Mol. Biol. (2011)

Synteny of land plant plastid chromosomes. The plastid chromosomes are shown in linearized form illustrating relative gene synteny. Genes are depicted by boxes colored according to their relevant functional class (see legend). Genes encoded by the leading strand (+ strand) or by the lagging strand (- strand) are shown above or below the grey chromosome bar, respectively. Lengths of boxes do not reflect lengths of genes, but are artificially increased to aid legibility (consequently, overlapping genes on ± strand do not indicate overlapping reading frames). Lines from selected genes/gene-regions mentioned above the first chromosome bar roughly indicate genes clusters that have been reorganizated during land plant evolution. Not all regions that underwent genomic relocations prior or during land plant evolution are depicted here. The chromosome bars are colored gray to highlight the positions of the two large Inverted Repeat regions (IRA/IRB) and are connected by gray lines between the different lineages. Gray lines are discontinued once to indicate loss of the large inverted repeat in Pinus. Drawn with GenomePixelizer (Kozik et al. 2002) using genome annotations deposited in public sequence databases. Refer to the text for genome references and original publications.]
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Related In: Results  -  Collection

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Fig2: Synteny of land plant plastid chromosomes. The plastid chromosomes are shown in linearized form illustrating relative gene synteny. Genes are depicted by boxes colored according to their relevant functional class (see legend). Genes encoded by the leading strand (+ strand) or by the lagging strand (- strand) are shown above or below the grey chromosome bar, respectively. Lengths of boxes do not reflect lengths of genes, but are artificially increased to aid legibility (consequently, overlapping genes on ± strand do not indicate overlapping reading frames). Lines from selected genes/gene-regions mentioned above the first chromosome bar roughly indicate genes clusters that have been reorganizated during land plant evolution. Not all regions that underwent genomic relocations prior or during land plant evolution are depicted here. The chromosome bars are colored gray to highlight the positions of the two large Inverted Repeat regions (IRA/IRB) and are connected by gray lines between the different lineages. Gray lines are discontinued once to indicate loss of the large inverted repeat in Pinus. Drawn with GenomePixelizer (Kozik et al. 2002) using genome annotations deposited in public sequence databases. Refer to the text for genome references and original publications.]
Mentions: The size of photosynthetic land plant plastid chromosomes ranges from 120 kb to 160 kb. The plastome in photosynthetic plants comprises 70 (gymnosperms) to 88 (liverworts) protein coding genes and 33 (most eudicots) to 35 (liverworts) structural RNA genes (Wakasugi et al. 1994; Ohyama 1996; Bock 2007), totaling 100–120 unique genes (Fig. 1). The vast majority of these genes are arranged in operons (or operon-like structures) and transcribed as polycistronic precursor molecules that are subjected to splicing and nucleolytic cleavage in order to produce mature and translatable mRNAs (Stern et al. 2010). Functional gene classes (translation/transcription, electron transfer, and photosystems) are often arranged in close vicinity to one another (Fig. 2; Cui et al. 2006). Using a parametric bootstrap-approach, Cui et al. (2006) showed that the genomic rearrangements of some chlorophytic algae (e.g. Chlamydomonas) relative to others are not random. Results indicated that the physical clustering of genes belonging to a similar functional class is positively selected. Furthermore, expression analysis indicated that some of these newly formed cluster are co-transcribed which led the authors to speculate that these could represent new regulons (Cui et al. 2006).Fig. 2

Bottom Line: These include the organization of plastid genes in operons, the usually uniparental mode of plastid inheritance, the activity of highly effective repair mechanisms as well as the rarity of plastid fusion.Nevertheless, structurally rearranged plastomes can be found in several unrelated lineages (e.g. ferns, Pinaceae, multiple angiosperm families).Patterns of ndh-gene loss and functional analyses indicate that these losses are usually found in plant groups with a certain degree of heterotrophy, might rendering plastid encoded Ndh1 subunits dispensable.

View Article: PubMed Central - PubMed

Affiliation: Department of Biogeography and Botanical Garden, University of Vienna, Rennweg 14, 1030 Vienna, Austria. susann.wicke@uni-muenster.de

Show MeSH
Related in: MedlinePlus