Cucumber, melon, pumpkin, and squash: Are rules of editing in flowering plants chloroplast genes so well known indeed?

Guzowska, Magdalena; Fiedorowicz, Ewa; Pląder, Wojciech

doi:10.1016/j.gene.2008.12.017

Cited by 23 publications

(20 citation statements)

References 52 publications

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“…For example, 10 potential RNA editing sites were shared by orchids and Cocos nucifera ; comparisons among Nicotiana tabacum , Arabidopsis thaliana , grasses and orchid RNA editing sites showed low conservation of editing sites (only one common editing sites in rpo B)(Table S5). These cases indicate that the evolutionary conservation of RNA editing is essential for only a few plastid-editing sites [64]–[66].…”

Section: Discussionmentioning

confidence: 99%

Comparative Chloroplast Genomes of Photosynthetic Orchids: Insights into Evolution of the Orchidaceae and Development of Molecular Markers for Phylogenetic Applications

et al. 2014

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The orchid family Orchidaceae is one of the largest angiosperm families, including many species of important economic value. While chloroplast genomes are very informative for systematics and species identification, there is very limited information available on chloroplast genomes in the Orchidaceae. Here, we report the complete chloroplast genomes of the medicinal plant Dendrobium officinale and the ornamental orchid Cypripedium macranthos, demonstrating their gene content and order and potential RNA editing sites. The chloroplast genomes of the above two species and five known photosynthetic orchids showed similarities in structure as well as gene order and content, but differences in the organization of the inverted repeat/small single-copy junction and ndh genes. The organization of the inverted repeat/small single-copy junctions in the chloroplast genomes of these orchids was classified into four types; we propose that inverted repeats flanking the small single-copy region underwent expansion or contraction among Orchidaceae. The AT-rich regions of the ycf1 gene in orchids could be linked to the recombination of inverted repeat/small single-copy junctions. Relative species in orchids displayed similar patterns of variation in ndh gene contents. Furthermore, fifteen highly divergent protein-coding genes were identified, which are useful for phylogenetic analyses in orchids. To test the efficiency of these genes serving as markers in phylogenetic analyses, coding regions of four genes (accD, ccsA, matK, and ycf1) were used as a case study to construct phylogenetic trees in the subfamily Epidendroideae. High support was obtained for placement of previously unlocated subtribes Collabiinae and Dendrobiinae in the subfamily Epidendroideae. Our findings expand understanding of the diversity of orchid chloroplast genomes and provide a reference for study of the molecular systematics of this family.

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Section: Discussionmentioning

confidence: 99%

Comparative Chloroplast Genomes of Photosynthetic Orchids: Insights into Evolution of the Orchidaceae and Development of Molecular Markers for Phylogenetic Applications

et al. 2014

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“…The extent of RNA editing greatly varies between the main lineages of land plants: whereas basal land plants, like bryophytes, might posses several hundreds of editing sites in their chloroplast genome [13][14][15][16][17], flowering plants usually harbor some 30-40 editing sites [18][19][20][21][22] (Fig. 2).…”

Section: The 'In' Of Rna Editing In Land Plantsmentioning

confidence: 99%

“…Most of the data show that editing sites are defined as such by some 20 nucleotides in the upstream direction [28][29][30][31][32]. Comparison of the cis-elements of different editing sites from seed plant chloroplasts usually yields no [33][34][35] or only limited sequence similarity [21,36,37]. This was seen early on as an indication that most editing sites might require site-specific factors (Fig.…”

Section: The 'In' Of Rna Editing In Land Plantsmentioning

confidence: 99%

The ins and outs of editing and splicing of plastid RNAs: lessons from parasitic plants

Tillich¹,

Krause²

2010

New Biotechnology

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“…Plastid RNA editing was first reported in the maize rpl2 transcript, in which the ACG codon is changed to the start codon AUG (Hoch et al, 1991). So far, RNA editing has been systematically investigated for the chloroplast protein-coding transcripts in the following species: Anthoceros formosae (Kugita et al, 2003), Adiantum capillus-veneris (Wolf et al, 2004), Pinus thunbergii (Wakasugi et al, 1996), Pisum sativum (Inada et al, 2004), Nicotiana tabacum (Sasaki et al, 2003(Sasaki et al, , 2006, Arabidopsis thaliana (Lutz and Maliga, 2001), Atropa belladonna (Schmitz-Linneweber et al, 2002), Solanum lycopersicum (Kahlau et al, 2006), four species of Cucurbitaceae family (Guzowska-Nowowiejska et al, 2009), Phalaenopsis aphrodite (Zeng et al, 2007), Zea mays (Maier et al, 1995), Oryza sativa (Corneille et al, 2000), and Saccharum officinarum (Calsa et al, 2004). Most angiosperms have a relatively constant number of chloroplast RNA editing sites, anywhere from 21 to 44.…”

Section: Introductionmentioning

confidence: 99%

“…Most angiosperms have a relatively constant number of chloroplast RNA editing sites, anywhere from 21 to 44. In closely related taxa, the number of shared editing sites increases (Guzowska-Nowowiejska et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Identification of RNA editing sites in cotton (Gossypium hirsutum) chloroplasts and editing events that affect secondary and three-dimensional protein structures

Jiang¹,

Fan²,

Song³

et al. 2012

Genet. Mol. Res.

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ABSTRACT. RNA editing can alter individual nucleotides in primary transcripts, which can cause the amino acids encoded by edited RNA to deviate from the ones predicted from the DNA template. We investigated RNA editing sites of protein-coding genes from the chloroplast genome of cotton. Fifty-four editing sites were identified in 27 transcripts, which is the highest editing frequency found until now in angiosperms. All these editing sites were C-to-U conversion, biased toward ndh genes and U_A context. Examining published editotypes in various angiosperms, we found that RNA editing mostly converts amino acid from hydrophilic to hydrophobic and restores evolutionary conserved amino acids. Using bioinformatics to analyze the effect of editing events on protein secondary and three-dimensional structures, we found that 21 editing sites can affect protein secondary structures and seven editing sites can alter three-dimensional protein structures. These results imply that 24 editing sites in cotton chloroplast transcripts may play an important role in their protein structures and functions.

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Cucumber, melon, pumpkin, and squash: Are rules of editing in flowering plants chloroplast genes so well known indeed?

Cited by 23 publications

References 52 publications

Comparative Chloroplast Genomes of Photosynthetic Orchids: Insights into Evolution of the Orchidaceae and Development of Molecular Markers for Phylogenetic Applications

Comparative Chloroplast Genomes of Photosynthetic Orchids: Insights into Evolution of the Orchidaceae and Development of Molecular Markers for Phylogenetic Applications

The ins and outs of editing and splicing of plastid RNAs: lessons from parasitic plants

Identification of RNA editing sites in cotton (Gossypium hirsutum) chloroplasts and editing events that affect secondary and three-dimensional protein structures

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