Complete DNA sequences of the plastid genomes of two parasitic flowering plant species, Cuscuta reflexa and Cuscuta gronovii

Funk, Helena T.; Berg, Sabine; Krupinska, Karin; Maier, Uwe G.; Krause, Kirsten

doi:10.1186/1471-2229-7-45

Cited by 181 publications

(242 citation statements)

References 54 publications

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“…The plastid genome contains rpo genes encoding homologs of the cyanobacterial RNAP a (rpoA), b (rpoB), bЈ (rpoC1) and bЉ (rpoC2) subunits. This cyanobacterial-type RNAP is widely conserved in almost all of plant cells, except for achlorophyllous parasitic plant such as C. gronovii (Funk et al, 2007) and E. virginiana (Wolfe et al 1992) The expected molecular masses for the PEP subunits of Arabidopsis are 38 kD (a), 121 kD (b), 79 kD (bЈ), and 156 kD (bЈЈ). These subunits form the core of the plastid-encoded plastid RNA polymerase (PEP).…”

Section: Plastid Rna Polymerasesmentioning

confidence: 99%

Function and evolution of plastid sigma factors

Shiina

Ishizaki

Yagi

et al. 2009

Plant Biotechnology

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Plastids are unique plant organelles that exist in several different forms. Plastids are dynamic and can convert between types by external and developmental signals. The most common plastid type is the chloroplast responsible for photosynthesis in land plants, algae and some protists. All living things depend on energy produced from photosynthesis. Moreover, chloroplasts carry out other essential biochemical processes, including starch, amino acids, fatty acids and pigments synthesis, nitrogen and sulfate assimilation, hormone synthesis and various secondary metabolism. Not only plants but also human life is dependent on these important products from plastids.Plastids are known to have originated from prokaryotic photosynthetic cyanobacteria. Consequently plastids are semi-autonomous and contain their own genetic system. In higher plants, plastids contain a small prokaryotic-type genome which encodes ϳ120 genes. Higher plant plastids contain two types of RNA polymerases, eubacterial-type PEP (plastid-encoded plastid RNA polymerase) and phage-type NEP (nuclearencoded plastid RNA polymerase) (Hess and Börner, 1999). In order to recognize promoters, PEP requires an exchangeable subunit, sigma factor. In bacteria, a variety of sigma factors specifically recognize different promoter sequences. The sigma factor determines which genes are transcribed. Higher plants also encode multiple sigma factor genes (Kanamaru and Tanaka, 2004). Recent molecular and genetic analyses revealed the roles of plastid sigma factors in chloroplast differentiation and environmental responses. In this review, we summarize plastid transcription and its regulation in higher plants, focused on plastid sigma factors. Plastid genomesPlastids have evolved from ancestral photosynthetic cyanobacteria, which were taken into the host cells as endosymbionts. It is believed that chloroplasts are monophyletic, with one primary endosymbiosis. Thus, plastids retain a lot of typical cyanobacterial features such as circular genome of 100-200 kbp and prokaryotictype gene expression system. During plant cell evolution, a large fraction of the original endosymbiont genes has either been lost or transferred to the nucleus. In consequence, the higher plant plastomes contain a limited number of conserved genes. For example, Arabidopsis chloroplast genome encodes only 129 genes, including 47 photosynthesis-related genes, 25 ribosomal genes, four RNA polymerase subunit genes, nine other protein coding genes (total 85 protein genes), 34 tRNA genes and 4 rRNA genes (Sato et al. 1999). On the other hand, chloroplast is believed to contain more than 3,000 proteins. Recent proteome analysis identified 1325 proteins in chloroplasts (Zybailov et al. 2008). More than 90% of them are encoded on nuclear DNA, synthesized in cytosol and transported into chloroplasts. Consequently, chloroplast function is largely dependent on the nuclei via nuclear-encoded proteins. It should be noted that DNA transfer from plastids to the nucleus is Function and evolution of plastid sigma fact...

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Section: Plastid Rna Polymerasesmentioning

confidence: 99%

Function and evolution of plastid sigma factors

Shiina

Ishizaki

Yagi

et al. 2009

Plant Biotechnology

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“…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)(5)(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.…”

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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

170

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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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“…Approximately 110-120 genes are located along the circular genome structure. Although the number of genes is conserved across the plant kingdom, except in some parasitic plants (Funk et al, 2007;McNeal et al, 2007;Wolfe et al, 1992), a wide range of genomic size variations exist (from 72 to 217 kb) due to contraction and expansion of the IR regions. Length variation is the most common mutation encountered in plant cp genomes (Palmer, 1987).…”

Section: Introductionmentioning

confidence: 99%

The Complete Chloroplast DNA Sequence of Eleutherococcus senticosus (Araliaceae); Comparative Evolutionary Analyses with Other Three Asterids

Lee

Sun

et al. 2012

Molecules and Cells

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This study reports the complete chloroplast (cp) DNA sequence of Eleutherococcus senticosus (GenBank: JN 637765), an endangered endemic species. The genome is 156,768 bp in length, and contains a pair of inverted repeat (IR) regions of 25,930 bp each, a large single copy (LSC) region of 86,755 bp and a small single copy (SSC) region of 18,153 bp. The structural organization, gene and intron contents, gene order, AT content, codon usage, and transcription units of the E. senticosus chloroplast genome are similar to that of typical land plant cp DNA. We aligned and analyzed the sequences of 86 coding genes, 19 introns and 113 intergenic spacers (IGS) in three different taxonomic hierarchies; Eleutherococcus vs. Panax, Eleutherococcus vs. Daucus, and Eleutherococcus vs. Nicotiana. The distribution of indels, the number of polymorphic sites and nucleotide diversity indicate that positional constraint is more important than functional constraint for the evolution of cp genome sequences in Asterids. For example, the intron sequences in the LSC region exhibited base substitution rates 5-11-times higher than that of the IR regions, while the intron sequences in the SSC region evolved 7-14-times faster than those in the IR region. Furthermore, the Ka/Ks ratio of the gene coding sequences supports a stronger evolutionary constraint in the IR region than in the LSC or SSC regions. Therefore, our data suggest that selective sweeps by base collection mechanisms more frequently eliminate polymorphisms in the IR region than in other regions. Chloroplast genome regions that have high levels of base substitutions also show higher incidences of indels. Thirty-five simple sequence repeat (SSR) loci were identified in the Eleutherococcus chloroplast genome. Of these, 27 are homopolymers, while six are di-polymers and two are tri-polymers. In addition to the SSR loci, we also identified 18 medium size repeat units ranging from 22 to 79 bp, 11 of which are distributed in the IGS or intron regions. These medium size repeats may contribute to developing a cp genome-specific gene introduction vector because the region may use for specific recombination sites.

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Complete DNA sequences of the plastid genomes of two parasitic flowering plant species, Cuscuta reflexa and Cuscuta gronovii

Cited by 181 publications

References 54 publications

Function and evolution of plastid sigma factors

Function and evolution of plastid sigma factors

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

The Complete Chloroplast DNA Sequence of Eleutherococcus senticosus (Araliaceae); Comparative Evolutionary Analyses with Other Three Asterids

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