Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana

Maumus, Florian; Quesneville, Hadi

doi:10.1038/ncomms5104

Cited by 77 publications

(101 citation statements)

References 63 publications

(98 reference statements)

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“…As expected, in contrast to genes with low methylation, DNA methylation of Spirodela LTRs is higher (>20% versus 9% genome‐wide average; Figure ). Similar results were found in Arabidopsis, where older repeats were highly methylated (Maumus and Quesneville, ). The high S:I ratio and the presence of old, highly methylated LTRs suggests that Spirodela is still in a dynamic state of genome reduction, which is also reflected in its small genome size, low rDNA repeat number and gene count (Michael, ).…”

Section: Resultssupporting

confidence: 81%

Comprehensive definition of genome features in Spirodela polyrhiza by high‐depth physical mapping and short‐read DNA sequencing strategies

et al. 2017

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Spirodela polyrhiza is a fast-growing aquatic monocot with highly reduced morphology, genome size and number of protein-coding genes. Considering these biological features of Spirodela and its basal position in the monocot lineage, understanding its genome architecture could shed light on plant adaptation and genome evolution. Like many draft genomes, however, the 158-Mb Spirodela genome sequence has not been resolved to chromosomes, and important genome characteristics have not been defined. Here we deployed rapid genome-wide physical maps combined with high-coverage short-read sequencing to resolve the 20 chromosomes of Spirodela and to empirically delineate its genome features. Our data revealed a dramatic reduction in the number of the rDNA repeat units in Spirodela to fewer than 100, which is even fewer than that reported for yeast. Consistent with its unique phylogenetic position, small RNA sequencing revealed 29 Spirodela-specific microRNA, with only two being shared with Elaeis guineensis (oil palm) and Musa balbisiana (banana). Combining DNA methylation data and small RNA sequencing enabled the accurate prediction of 20.5% long terminal repeats (LTRs) that doubled the previous estimate, and revealed a high Solo:Intact LTR ratio of 8.2. Interestingly, we found that Spirodela has the lowest global DNA methylation levels (9%) of any plant species tested. Taken together our results reveal a genome that has undergone reduction, likely through eliminating non-essential protein coding genes, rDNA and LTRs. In addition to delineating the genome features of this unique plant, the methodologies described and large-scale genome resources from this work will enable future evolutionary and functional studies of this basal monocot family.

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Section: Resultssupporting

confidence: 81%

Comprehensive definition of genome features in Spirodela polyrhiza by high‐depth physical mapping and short‐read DNA sequencing strategies

et al. 2017

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“…We propose that such a mechanism would be a previously unidentified aspect of "genetic mimicry," where the host is, for all practical purposes, mimicking pathogen-associated nucleic acid patterns. HSATII and GSAT emanate from the pericentromeres, which harbor new repetitive elements with no known function (48). This region, unlike centromeres or regions critical for structure or regulation, may dynamically produce unusual repetitive elements that can adapt to a particular organism's PRRs.…”

Section: Discussionmentioning

confidence: 99%

Distinguishing the immunostimulatory properties of noncoding RNAs expressed in cancer cells

Tanne

Muniz

Puzio-Kuter

et al. 2015

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

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Recent studies have demonstrated abundant transcription of a set of noncoding RNAs (ncRNAs) preferentially within tumors as opposed to normal tissue. Using an approach from statistical physics, we quantify global transcriptome-wide motif use for the first time, to our knowledge, in human and murine ncRNAs, determining that most have motif use consistent with the coding genome. However, an outlier subset of tumor-associated ncRNAs, typically of recent evolutionary origin, has motif use that is often indicative of pathogenassociated RNA. For instance, we show that the tumor-associated human repeat human satellite repeat II (HSATII) is enriched in motifs containing CpG dinucleotides in AU-rich contexts that most of the human genome and human adapted viruses have evolved to avoid. We demonstrate that a key subset of these ncRNAs functions as immunostimulatory "self-agonists" and directly activates cells of the mononuclear phagocytic system to produce proinflammatory cytokines. These ncRNAs arise from endogenous repetitive elements that are normally silenced, yet are often very highly expressed in cancers. We propose that the innate response in tumors may partially originate from direct interaction of immunogenic ncRNAs expressed in cancer cells with innate pattern recognition receptors, and thereby assign a previously unidentified danger-associated function to a set of dark matter repetitive elements. These findings potentially reconcile several observations concerning the role of ncRNA expression in cancers and their relationship to the tumor microenvironment.noncoding RNA | genome evolution | cancer immunology

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“…Sequence divergence plots were drawn as described by Maumus et al [28]. RIP analyses followed the steps described previously [25].…”

Section: Methodsmentioning

confidence: 99%

Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters

et al. 2017

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BackgroundThe ascomycete fungus Colletotrichum higginsianum causes anthracnose disease of brassica crops and the model plant Arabidopsis thaliana. Previous versions of the genome sequence were highly fragmented, causing errors in the prediction of protein-coding genes and preventing the analysis of repetitive sequences and genome architecture.ResultsHere, we re-sequenced the genome using single-molecule real-time (SMRT) sequencing technology and, in combination with optical map data, this provided a gapless assembly of all twelve chromosomes except for the ribosomal DNA repeat cluster on chromosome 7. The more accurate gene annotation made possible by this new assembly revealed a large repertoire of secondary metabolism (SM) key genes (89) and putative biosynthetic pathways (77 SM gene clusters). The two mini-chromosomes differed from the ten core chromosomes in being repeat- and AT-rich and gene-poor but were significantly enriched with genes encoding putative secreted effector proteins. Transposable elements (TEs) were found to occupy 7% of the genome by length. Certain TE families showed a statistically significant association with effector genes and SM cluster genes and were transcriptionally active at particular stages of fungal development. All 24 subtelomeres were found to contain one of three highly-conserved repeat elements which, by providing sites for homologous recombination, were probably instrumental in four segmental duplications.ConclusionThe gapless genome of C. higginsianum provides access to repeat-rich regions that were previously poorly assembled, notably the mini-chromosomes and subtelomeres, and allowed prediction of the complete SM gene repertoire. It also provides insights into the potential role of TEs in gene and genome evolution and host adaptation in this asexual pathogen.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4083-x) contains supplementary material, which is available to authorized users.

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Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana

Cited by 77 publications

References 63 publications

Comprehensive definition of genome features in Spirodela polyrhiza by high‐depth physical mapping and short‐read DNA sequencing strategies

Comprehensive definition of genome features in Spirodela polyrhiza by high‐depth physical mapping and short‐read DNA sequencing strategies

Distinguishing the immunostimulatory properties of noncoding RNAs expressed in cancer cells

Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters

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