Chloroplast genomes of plants.

Raubeson, Linda A.; Jansen, Robert K.; Henry, R. J.

doi:10.1079/9780851999043.0045

Cited by 268 publications

(194 citation statements)

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“…In Ranunculus (Figure 2), the overall length is 155,129 bp with a LSC of 84,638 bp, a SSC of 18,909 bp, and two IR regions each of 25,791 bp. As is common to chloroplast genomes in general [5,6,9], the nucleotide composition of both of these genomes are biased towards A and T nucleotides, i.e., they are "A+T-rich". Overall the Nuphar genome is 60.9% A+T and Ranunculus 62.1% A+T.…”

Section: Resultsmentioning

confidence: 99%

“…Thus we add to the small number of genomes not representing monocots or crown eudicots, increasing our ability to compare genomes across all angiosperms and determine general characteristics. Most chloroplast genomes in angiosperms (reviewed in: [7-9]) range from 135 to 160 kb and exist, at least in part [10] as single genome circles. In the majority of angiosperm chloroplast genomes two copies of a large inverted repeat (IR) of about 25 kb separate the remainder of the genome into two regions of unique DNA, the large (about 90 kb) and small (about 20 kb) single copy regions (LSC and SSC, respectively).…”

Section: Introductionmentioning

confidence: 99%

“…This is reinforced by the similarity of the tobacco cpDNA to the basal angiosperms, Amborella [12] and Nymphaea [13], and the magnolids, Calycanthus [14] Drimys, Liriodendron , and Piper [6]. In some derived angiosperm lineages, this ancestral condition has been somewhat or highly modified via inversions, gene losses, presence or absence of ORFs and minor ycfs, and changes in IR extent [8,9,15,16]. However, the tobacco-like pattern is widely distributed in crown eudicots, e.g., Panax [17], Eucalyptus [18], and Gossypium [19].…”

Section: Introductionmentioning

confidence: 99%

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Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus

et al. 2007

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Background: The number of completely sequenced plastid genomes available is growing rapidly. This array of sequences presents new opportunities to perform comparative analyses. In comparative studies, it is often useful to compare across wide phylogenetic spans and, within angiosperms, to include representatives from basally diverging lineages such as the genomes reported here: Nuphar advena (from a basal-most lineage) and Ranunculus macranthus (a basal eudicot). We report these two new plastid genome sequences and make comparisons (within angiosperms, seed plants, or all photosynthetic lineages) to evaluate features such as the status of ycf15 and ycf68 as protein coding genes, the distribution of simple sequence repeats (SSRs) and longer dispersed repeats (SDR), and patterns of nucleotide composition.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus

et al. 2007

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“…Aside from the Trebouxiophyceae, chloroplast genomes that experienced complete or almost-complete loss of the IR have been documented for the chlorophyte classes Ulvophyceae [28] and Chlorophyceae [7], for the charophycean lineage leading to the Zygnematales [29,30] and for a number of land plants, including conifers and six tribes of legumes [31,32]. Losses of the IR in conifers and legumes occurred independently and differed in the extent of the IR sequence lost, in the gene content of the IR prior to loss, and in the copy of the IR that was deleted [32]. The site of deletion in pea cpDNA was found to exhibit duplicated gene fragments, but no simple mechanism involving recombination between these repeats could be postulated to account for the IR loss [33].…”

Section: Discussionmentioning

confidence: 99%

The chloroplast genome sequence of the green alga Leptosira terrestris: multiple losses of the inverted repeat and extensive genome rearrangements within the Trebouxiophyceae

et al. 2007

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Background: In the Chlorophyta -the green algal phylum comprising the classes Prasinophyceae, Ulvophyceae, Trebouxiophyceae and Chlorophyceae -the chloroplast genome displays a highly variable architecture. While chlorophycean chloroplast DNAs (cpDNAs) deviate considerably from the ancestral pattern described for the prasinophyte Nephroselmis olivacea, the degree of remodelling sustained by the two ulvophyte cpDNAs completely sequenced to date is intermediate relative to those observed for chlorophycean and trebouxiophyte cpDNAs. Chlorella vulgaris (Chlorellales) is currently the only photosynthetic trebouxiophyte whose complete cpDNA sequence has been reported. To gain insights into the evolutionary trends of the chloroplast genome in the Trebouxiophyceae, we sequenced cpDNA from the filamentous alga Leptosira terrestris (Ctenocladales).

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“…comparative genomics ͉ genome evolution ͉ plastid genome A ngiosperm plastid genomes are generally highly conserved in gene order, gene content, and organization (1). Whereas the rates of nucleotide substitutions are highly variable in protein-coding genes of angiosperm nuclear genomes, rates in plastid genes are generally lower (2).…”

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confidence: 99%

Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions

Guisinger

Kuehl²,

Boore

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

149

171

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Angiosperm plastid genomes are generally conserved in gene content and order with rates of nucleotide substitutions for protein-coding genes lower than for nuclear protein-coding genes. A few groups have experienced genomic change, and extreme changes in gene content and order are found within the flowering plant family Geraniaceae. The complete plastid genome sequence of Pelargonium X hortorum (Geraniaceae) reveals the largest and most rearranged plastid genome identified to date. Highly elevated rates of sequence evolution in Geraniaceae mitochondrial genomes have been reported, but rates in Geraniaceae plastid genomes have not been characterized. Analysis of nucleotide substitution rates for 72 plastid genes for 47 angiosperm taxa, including nine Geraniaceae, show that values of dN are highly accelerated in ribosomal protein and RNA polymerase genes throughout the family. Furthermore, dN/dS is significantly elevated in the same two classes of plastid genes as well as in ATPase genes. A relatively high dN/dS ratio could be interpreted as evidence of two phenomena, namely positive or relaxed selection, neither of which is consistent with our current understanding of plastid genome evolution in photosynthetic plants. These analyses are the first to use protein-coding sequences from complete plastid genomes to characterize rates and patterns of sequence evolution for a broad sampling of photosynthetic angiosperms, and they reveal unprecedented accumulation of nucleotide substitutions in Geraniaceae. To explain these remarkable substitution patterns in the highly rearranged Geraniaceae plastid genomes, we propose a model of aberrant DNA repair coupled with altered gene expression.comparative genomics ͉ genome evolution ͉ plastid genome A ngiosperm plastid genomes are generally highly conserved in gene order, gene content, and organization (1). Whereas the rates of nucleotide substitutions are highly variable in protein-coding genes of angiosperm nuclear genomes, rates in plastid genes are generally lower (2). Rates of nonsynonomous substitutions (dN), those that cause an amino acid change, are substantially lower than rates of synonymous substitutions (dS), those that do not cause an amino acid change. Aside from a recent report describing elevated dN for a single gene in Oenothera and lineages within Caryophyllaceae (3), plastid genes of photosynthetic plants are under strong purifying selection and the rapid accumulation of either dN or dS has not been described.The plastid genomes of nonphotosynthetic plants reveal accelerated rates of nucleotide substitutions in many proteincoding genes; furthermore, these genomes exhibit extensive gene loss and genome rearrangement (4-6). However, analyses involving either few genes or few taxa for photosynthetic angiosperm plastid genomes generally reveal that modest rate variation is locus-and lineage-specific. A few groups of angiosperms have experienced lineage-specific rate variation, including the lineages leading to the grasses (7), pea (2), Gnetum (8), and Welwitschia...

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Chloroplast genomes of plants.

Abstract: This chapter focuses on two aspects of the plant chloroplast genome: (i) its organization and evolution; and (ii) the phylogenetic utility of different approaches to cpDNA characterization.

Cited by 268 publications

References 0 publications

Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus

Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus

The chloroplast genome sequence of the green alga Leptosira terrestris: multiple losses of the inverted repeat and extensive genome rearrangements within the Trebouxiophyceae

Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions

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