Nucleotide distribution in gymnosperm nuclear sequences suggests a model for GC-content change in land-plant nuclear genomes

Jansson, Stefan; Meyer-Gauen, Gilbert; Cerff, Rüdiger; Martin, William

doi:10.1007/bf00178247

Cited by 41 publications

(19 citation statements)

References 75 publications

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“…Norway spruce belongs to conifers that are the predominant gymnosperm (comprising approximately two-thirds of all of the gymnosperms) and mainly occupy the forests of the Northern Hemisphere. In recent years, sequence analyses in conifers have led to identification of conifer genes and sequencing of conifer genomes (23,(26)(27)(28)(29)(30)(31). Because their genomes are so large (often more than 20 Gbp) compared with other eukaryotes, and because of their high content of transposons together with the role of DNA methylation in transposon silencing, it is of interest to study DNA methylation in gymnosperm genomes.…”

Section: Discussionmentioning

confidence: 99%

DNA methylome of the 20-gigabase Norway spruce genome

Ausín

Feng

et al. 2016

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

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DNA methylation plays important roles in many biological processes, such as silencing of transposable elements, imprinting, and regulating gene expression. Many studies of DNA methylation have shown its essential roles in angiosperms (flowering plants). However, few studies have examined the roles and patterns of DNA methylation in gymnosperms. Here, we present genome-wide high coverage single-base resolution methylation maps of Norway spruce (Picea abies) from both needles and somatic embryogenesis culture cells via whole genome bisulfite sequencing. On average, DNA methylation levels of CG and CHG of Norway spruce were higher than most other plants studied. CHH methylation was found at a relatively low level; however, at least one copy of most of the RNA-directed DNA methylation pathway genes was found in Norway spruce, and CHH methylation was correlated with levels of siRNAs. In comparison with needles, somatic embryogenesis culture cells that are used for clonally propagating spruce trees showed lower levels of CG and CHG methylation but higher level of CHH methylation, suggesting that like in other species, these culture cells show abnormal methylation patterns.NA methylation is the most studied stable and heritable epigenetic modification of eukaryotes, and plays important roles in transcriptional regulation and silencing of repetitive elements and transposons (1). In plants, DNA methylation occurs in three contexts, CG, CHG (H is A, T, or C), and CHH (2-4). In Arabidopsis, forward genetic screens have uncovered many components that are required for DNA methylation. For example, the maintenance of CG, CHG, and a subset of CHH DNA methylation is mediated by METHYLTRANSFERASE 1 (MET1), CHRO-MOMETHYLASE (CMT) 3, and CMT2, respectively, whereas the de novo establishment of DNA methylation in all three contexts and the maintenance of the rest of the CHH methylation is mediated by the RNA-directed DNA methylation (RdDM) pathway that employs DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) (5).Genome-wide methylome studies have been performed in many plant species, such as Arabidopsis, tomato, poplar, soybean, rice, and cassava (2, 3, 6-11). These studies uncovered conserved DNA methylation patterns in genic regions and transposable element regions across plant genomes. However, the DNA methylation landscapes of gymnosperm species that have large genome sizes and high repeat content are relatively understudied. Takuno et al. have demonstrated that genic CHG methylation was correlated with genome size by studying gene body methylation in selected gymnosperm species (12). However, genome-wide high coverage single-base resolution DNA methylation maps of any gymnosperm are still lacking. It is known that transposable elements (TEs) are the main targets of DNA methylation. However, the roles of DNA methylation in TE-abundant gymnosperm species, for example Norway spruce (Picea abies), whose TEs comprise more than 70% of the genome, have not been studied in detail. Using next generation sequencing technology, the genome o...

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Section: Discussionmentioning

confidence: 99%

DNA methylome of the 20-gigabase Norway spruce genome

Ausín

Feng

et al. 2016

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

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“…Plants in the order Poales of class Commelinanae have the best-studied monocot genomes, leading some authors to extrapolate the genomic characteristics of the Poales to all monocots (Jansson et al, 1994;Wong et al, 2002). However, our expressed sequence and genomic comparisons among the Asparagales vegetables, rice, and Arabidopsis indicate that the Asparagales are more similar to Arabidopsis than to rice for codon usage and mean GC content, GC distribution, and relative GC content at each codon position and across 5Ј to 3Ј sliding windows for homologous coding regions.…”

Section: Comparisons Among the Commelinanae And Asparagales Nuclear Gmentioning

confidence: 99%

“…Once established, these transitions have been maintained over millions of years. In plants, the gymnosperms possess coding regions with relatively high GC contents, although lower than those of the Poales (Jansson et al, 1994). Although onion is a monocot, it is much more similar to the eudicots than to the Poales, with lower GC mean values for coding regions and a narrow symmetrical distribution (Figure 2) (Salinas et al, 1988;Matassi et al, 1989;Carels et al, 1998).…”

Section: Comparisons Among the Commelinanae And Asparagales Nuclear Gmentioning

confidence: 99%

“…The similar GC compositions between the Asparagales and eudicots suggest that the progenitor state for angiosperms was a more uniform GC content and that the shift toward higher GC content in the Poales is the derived state. Another possibility is that GC similarities between onion and Arabidopsis are attributable to convergent evolution, with basal angiosperms having GC compositions similar to those of the Poales (Jansson et al, 1994). Additional evaluations of other Asparagales and non-Poales monocots, such as the basal genus Acorus, are required to determine the polarity of large-scale genomic GC transitions among the eudicots and monocots.…”

Section: Comparisons Among the Commelinanae And Asparagales Nuclear Gmentioning

confidence: 99%

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A Unique Set of 11,008 Onion Expressed Sequence Tags Reveals Expressed Sequence and Genomic Differences between the Monocot Orders Asparagales and Poales[W]

Kuhl

Cheung²,

Yuan³

et al. 2004

The Plant Cell

156

151

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Enormous genomic resources have been developed for plants in the monocot order Poales; however, it is not clear how representative the Poales are for the monocots as a whole. The Asparagales are a monophyletic order sister to the lineage carrying the Poales and possess economically important plants such as asparagus, garlic, and onion. To assess the genomic differences between the Asparagales and Poales, we generated 11,008 unique ESTs from a normalized cDNA library of onion. Sequence analyses of these ESTs revealed microsatellite markers, single nucleotide polymorphisms, and homologs of transposable elements. Mean nucleotide similarity between rice and the Asparagales was 78% across coding regions. Expressed sequence and genomic comparisons revealed strong differences between the Asparagales and Poales for codon usage and mean GC content, GC distribution, and relative GC content at each codon position, indicating that genomic characteristics are not uniform across the monocots. The Asparagales were more similar to eudicots than to the Poales for these genomic characteristics.

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“…The GapA1 promoter is relatively strong and generates about 0.5~o of the total steady-state mRNA population in maize seedlings [11]. The first two introns of maize GapA genes are located in the transit peptidecoding region [26].…”

Section: Introductionmentioning

confidence: 99%

Intron-dependent transient expression of the maize GapA1 gene

et al. 1995

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Transient expression experiments show that the maize GapA1 promoter exhibits a requirement for sequences contained within intron 1 and surrounding exon border regions for expression in maize Black Mexican Sweet cells. Maize GapA1-promoter constructs lacking intron 1 are inactive. Intron 1 and its exon border sequences, when reintroduced into constructs lacking introns, restore gene activity whereas intron 2 and its exon borders to not. The minimal promoter so defined encompasses roughly 250 bp upstream of the in vivo transcription start and appears also to include intron 1. An octameric sequence was identified in intron 1 of maize GapA1 which is similar to sequence motifs found in other maize introns known to increase transient expression. Partial restoration of gene expression in GapA1 constructs lacking intron 1 was achieved through insertion of the identified octameric sequence.

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Nucleotide distribution in gymnosperm nuclear sequences suggests a model for GC-content change in land-plant nuclear genomes

Cited by 41 publications

References 75 publications

DNA methylome of the 20-gigabase Norway spruce genome

DNA methylome of the 20-gigabase Norway spruce genome

A Unique Set of 11,008 Onion Expressed Sequence Tags Reveals Expressed Sequence and Genomic Differences between the Monocot Orders Asparagales and Poales[W]

Intron-dependent transient expression of the maize GapA1 gene

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