The bright side of transposons in crop evolution

Vitte, Clémentine; Fustier, Margaux-Alison; Alix, Karine; Tenaillon, Maud I.

doi:10.1093/bfgp/elu002

Cited by 115 publications

(96 citation statements)

References 144 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…We noticed that some of the other densely methylated species, like maize and tomato, had similar TE contents (84.2% and 64.2%, respectively) to Norway spruce (70%) (Fig. 3A) (24). Recently, Takuno et al showed that gene body CG and CHG methylation levels were correlated with genome sizes by sampling more than 14 species.…”

Section: Single-base Resolution Landscapes Of Dna Methylation In Norwaymentioning

confidence: 68%

DNA methylome of the 20-gigabase Norway spruce genome

Ausín

Feng

et al. 2016

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

View full text Add to dashboard Cite

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...

show abstract

Section: Single-base Resolution Landscapes Of Dna Methylation In Norwaymentioning

confidence: 68%

DNA methylome of the 20-gigabase Norway spruce genome

Ausín

Feng

et al. 2016

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

View full text Add to dashboard Cite

show abstract

“…Higher redundancy of Gypsy REs compared to Copia ones already has been reported in P. trichocarpa (Tuskan et al 2006;Cossu et al 2012). In angiosperms, different ratios between Gypsy and Copia RE frequencies were reported, ranging from 5:1 in papaya to 1:2 in grapevine (Vitte et al 2014). Species of the Gossypium genus show a variable proportion of Gypsy versus Copia elements, with Gypsy elements prevailing in species with larger genome sizes (Hawkins et al 2006).…”

Section: Discussionmentioning

confidence: 87%

A survey of Gypsy and Copia LTR-retrotransposon superfamilies and lineages and their distinct dynamics in the Populus trichocarpa (L.) genome

Natali

Cossu

Mascagni

et al. 2015

Tree Genetics & Genomes

View full text Add to dashboard Cite

In this work, we report a comprehensive study of\ud long terminal repeat retrotransposons of Populus trichocarpa.\ud Our research group studied the retrotransposon component of\ud the poplar genome in 2012, isolating 1479 putative full-length\ud elements. However, in that study, it was not possible to identify\ud the superfamily to which the majority of isolated full-length\ud elements belonged. Moreover, during recent years, the genome\ud sequence of P. trichocarpa has been updated, deciphering thek\ud sequences of a number of previously unresolved loci. In this\ud work, we performed a complete scan of the updated version of\ud the genome sequence to isolate full-length retrotransposons\ud based on sequence and structural features. The new dataset\ud showed a reduced number of elements (958), and 21 fulllength\ud elements were discovered for the first time. The majority\ud of retroelements belonged to the Gypsy superfamily (57%),\ud while Copia elements amounted to 41.1% of the dataset. Fulllength\ud elements were dispersed throughout the chromosomes.\ud However, Gypsy and, to a lesser extent, Copia elements accumulated\ud preferentially at putative centromeres. Gypsy elements\ud were more active in retrotransposition than Copia elements,\ud with the exception of during the past million years, in which\ud Copia elements were the most active. Improved annotation\ud procedures also allowed us to determine the specific lineages\ud to which isolated elements belonged. The three Gypsy lineages,\ud Athila, OGRE, and Chromovirus (in the decreasing order),\ud were by far the most abundant. On the other hand, each\ud identified Copia lineage represented less than 1 % of the genome.\ud Significant differences in the insertion age were found\ud among lineages, suggesting specific activation mechanisms.\ud Moreover, different chromosomal regions were affected by\ud retrotransposition in different ages. In all chromosomes, putative\ud pericentromeric regions were filled with elements older\ud than themean insertion age. Overall, results demonstrate structural\ud and functional differences among plant retrotransposon\ud lineages and further support the view of retrotransposons as a\ud community of different organisms in the genome

show abstract

“…A large fraction of most plant genomes is composed of TEs, roughly proportional to genome size variation (Tenaillon et al, 2010;Vitte et al, 2014). Comparisons of the DNA methylation content of several plant species with different TE percentages have shown that the global methylation level clearly follows the TE density of a genome (Mirouze and Vitte, 2014).…”

Section: Tes Shape Plant Methylomesmentioning

confidence: 99%

A Comparative Epigenomic Analysis of Polyploidy-Derived Genes in Soybean and Common Bean

et al. 2015

View full text Add to dashboard Cite

Soybean (Glycine max) and common bean (Phaseolus vulgaris) share a paleopolyploidy (whole-genome duplication [WGD]) event, approximately 56.5 million years ago, followed by a genus Glycine-specific polyploidy, approximately 10 million years ago. Cytosine methylation is an epigenetic mark that plays an important role in the regulation of genes and transposable elements (TEs); however, the role of DNA methylation in the fate/evolution of genes following polyploidy and speciation has not been fully explored. Whole-genome bisulfite sequencing was used to produce nucleotide resolution methylomes for soybean and common bean. We found that, in soybean, CG body-methylated genes were abundant in WGD genes, which were, on average, more highly expressed than single-copy genes and had slower evolutionary rates than unmethylated genes, suggesting that WGD genes evolve more slowly than single-copy genes. CG body-methylated genes were also enriched in shared single-copy genes (single copy in both species) that may be responsible for the broad and high expression patterns of this class of genes. In addition, diverged methylation patterns in non-CG contexts between paralogs were due mostly to TEs in or near genes, suggesting a role for TEs and non-CG methylation in regulating gene expression post polyploidy. Reference methylomes for both soybean and common bean were constructed, providing resources for investigating epigenetic variation in legume crops. Also, the analysis of methylation patterns of duplicated and single-copy genes has provided insights into the functional consequences of polyploidy and epigenetic regulation in plant genomes.

show abstract

The bright side of transposons in crop evolution

Cited by 115 publications

References 144 publications

DNA methylome of the 20-gigabase Norway spruce genome

DNA methylome of the 20-gigabase Norway spruce genome

A survey of Gypsy and Copia LTR-retrotransposon superfamilies and lineages and their distinct dynamics in the Populus trichocarpa (L.) genome

A Comparative Epigenomic Analysis of Polyploidy-Derived Genes in Soybean and Common Bean

Contact Info

Product

Resources

About