Imprinting In Plants Research Articles

Plant–insect interactions in the Quaternary fossil record of the Azores Archipelago (Portugal)

ABSTRACTThe fossil record of the Azores still lacks evidence of terrestrial invertebrates. Based on a study of the collections of Quaternary fossil plant imprints from the Azores, located in the depositories of public collections and also newly conducted field research, several samples of fossil leaves with traces of plant–animal interactions were found. These are evidence of marginal feeding (Phagophytichnus ekowskii) and anophionome mine (Cuniculonomus isp.). One specimen with traces of boring in fossil wood (Xylonichnus trypetus), previously only briefly mentioned in the literature, was also described in detail. In addition to a detailed description of the found traces, the present study also discusses the possible trace‐makers, using a comparison with the recent phytophagous fauna in relation to the original vegetation of the Azores (that includes laurisilva forest). It is thus possible to consider butterfly caterpillars (group Macrolepidoptera) or locust larvae (Orthoptera/Caelifera) as possible originators of marginal feeding. The ophionome mine could have been caused by the larvae of leaf‐miner flies (Agromyzidae) or moths from the group Microlepidoptera (Gracillariidae). Wood‐destroying beetles could be the cause of the boring in fossil wood.

Sacred plant impressions from Somma-Vesuvius volcanic ash deposits: A medicinal garden in Late Antique Acerra (Naples, Campania, Italy)?

The AD 472 eruption of Somma-Vesuvius widely impacted the northern and eastern territory around the volcano, laying down a complex sequence of pyroclastic fallout and pyroclastic current deposits. During archaeological test excavations conducted in the Acerra locality, Pollena eruption (AD 472) fallout and lahar deposits composed of fine ash containing traces of plant impressions were found. These deposits were sampled and carefully fractured in order to recover the plant imprints. Features of the ash impressions were compared with those of live plants and dried Herbarium specimens. Species identification was based on the characteristics of leaves (maximum width, type of leaf margin, size of midrib, angle of formation of the secondary veins) and fruits. Impressions of Mandragora officinarum L., Rosa canina L. and Hedera helix L. were recognized. This is the first documented discovery of subfossil mandrake specimens. The use of mandrake plants for healing and psychotropic purposes is referred to by Classical authors such as Pliny the Elder and Dioscorides; it was sometimes used mixed with rose. In addition, rose and ivy plants were symbolically important to the ancient Romans and were employed together as medicinal plants. The coexistence of these plants in a restricted area suggests the presence of a garden dedicated to sacred/medicinal plants. In addition, it is interesting to note that the discovery of mandrake plants with fruits supports the hypothesis that the eruptive event took place between the end of summer and the autumn.

Conserved noncoding sequences and de novo Mutator insertion alleles are imprinted in maize.

Genomic imprinting is an epigenetic phenomenon in which differential allele expression occurs in a parent-of-origin-dependent manner. Imprinting in plants is tightly linked to transposable elements (TEs), and it has been hypothesized that genomic imprinting may be a consequence of demethylation of TEs. Here, we performed high-throughput sequencing of ribonucleic acids from four maize (Zea mays) endosperms that segregated newly silenced Mutator (Mu) transposons and identified 110 paternally expressed imprinted genes (PEGs) and 139 maternally expressed imprinted genes (MEGs). Additionally, two potentially novel paternally suppressed MEGs are associated with de novo Mu insertions. In addition, we find evidence for parent-of-origin effects on expression of 407 conserved noncoding sequences (CNSs) in maize endosperm. The imprinted CNSs are largely localized within genic regions and near genes, but the imprinting status of the CNSs are largely independent of their associated genes. Both imprinted CNSs and PEGs have been subject to relaxed selection. However, our data suggest that although MEGs were already subject to a higher mutation rate prior to their being imprinted, imprinting may be the cause of the relaxed selection of PEGs. In addition, although DNA methylation is lower in the maternal alleles of both the maternally and paternally expressed CNSs (mat and pat CNSs), the difference between the two alleles in H3K27me3 levels was only observed in pat CNSs. Together, our findings point to the importance of both transposons and CNSs in genomic imprinting in maize.

Epigenetic modifications potentially controlling the allelic expression of imprinted genes in sunflower endosperm

BackgroundGenomic imprinting is an epigenetic phenomenon mainly occurs in endosperm of flowering plants. Genome-wide identification of imprinted genes have been completed in several dicot Cruciferous plant and monocot crops.ResultsHere, we analyzed global patterns of allelic gene expression in developing endosperm of sunflower which belongs to the composite family. Totally, 691 imprinted loci candidates were identified in 12 day-after-pollination sunflower endosperm including 79 maternally expressed genes (MEG) and 596 paternally expressed genes (PEG), 6 maternally expressed noncoding RNAs (MNC) and 10 paternally expressed noncoding RNAs (PNC). And a clear clustering of imprinted genes throughout the rapeseed genome was identified. Generally, imprinting in sunflower is conserved within a species, but intraspecific variation also was detected. Limited loci in sunflower are imprinted in other several different species. The DNA methylation pattern around imprinted genes were investigated in embryo and endosperm tissues. In CG context, the imprinted genes were significantly associated with differential methylated regions exhibiting hypomethylation in endosperm and hypermethylation in embryo, which indicated that the maternal demethylation in CG context potentially induce the genomic imprinting in endosperm.ConclusionOur study would be helpful for understanding of genomic imprinting in plants and provide potential basis for further research in imprinting in sunflower.

The pottery production from the Deh Dumen Bronze Age graveyard (South-Western Iran): a chemical, mineralogical and physical study

A collection of pottery vessels uncovered during the first season of excavations in the Deh Dumen Bronze Age graveyard (the second half of the third millennium BC) located in south-western Iran were studied by using chemical, mineralogical and physical techniques, with the aim to identify the pottery manufacturing process in this region. The site is located in a region of the Zagros fold and thrust belt that includes carbonate rocks and alluvial deposits. The pottery vessels found in the site present two different fabric types in their fresh surface: bright yellowish hue fabric (TYPE-1) and sandwich-like or black core fabric (TYPE-2) showing presumably different production techniques or workshops. Twenty-four samples from pottery sherds were selected and analysed by X-ray fluorescence (XRF), powder X-ray diffraction (XRD), polarized light microscopy (PLM), and field emission scanning electron microscopy (FESEM). Hydric tests were also performed. Samples were different according to their chemistry having distinguished calcium-rich and calcium-poor ceramics. Al2O3 and Fe2O3 were detected as the other main components of samples besides SiO2 and CaO. The mineralogical and textural characterisation revealed a fine-grained clayey matrix with quartz and feldspar grains in TYPE-1 potteries and large and small calcitic and clayey lumps inclusions in TYPE-2 potteries. Imprints of straw or other plants can be responsible for the higher porosity of some of the potteries. It was found that most of the potteries from the Deh Dumen graveyard were produced by means of a local and traditional pottery manufacturing technique, whilst others may have been produced in different places and transported to the graveyard as ritual offerings.

Potassium isotopic fractionation in a humid and an arid soil–plant system in Hawai‘i

Plants play a critical role in the cycling of potassium (K) and the fractionation of its isotopes. However, little is known about K stable isotopic compositions in natural soil–plant systems and possible fractionation during intra-plant transport and root-soil uptake of K. This study focuses on K isotopic fractionation within a humid and an arid soil–plant system sampled on the windward and leeward sides of Kohala Mountain, Hawai‘i. We determined the K isotopic compositions of < 2-mm bulk soil, soil saturation extraction, and selected plant tissues by multi-collector inductively coupled plasma mass spectrometry and X-ray absorption spectroscopy. We studied soils and individual tissue samples such as roots, stems, barks, shoots (a sum of stems and fresh leaves), leaves (fresh and dead), seeds, and flowers of trees and grasses. The results demonstrated that: (i) tissue δ41K values ranged from −1.06 ± 0.06 to 1.15 ± 0.09‰; (ii) within the same plant, stems (barks), dead leaves, and reproductive tissues (flowers and seeds) were isotopically lighter compared to fresh leaves, and to a lesser extent,roots; (iii) δ41K values of the humid soil (-0.54 ± 0.07 to −0.49 ± 0.06‰) were lower than those of the arid soil (-0.24 ± 0.07 to −0.14 ± 0.06‰); and (iv) soil bioavailable pool δ41K (saturation extracts) ranged from −0.63 ± 0.08 to 0.34 ± 0.08‰ and 0.48 ± 0.08 to 0.54 ± 0.10‰ in the humid and arid soils, respectively. From synchrotron-based analysis of K atoms, we identified two major K-bearing phases co-existing as ionic K+ and K-pectate association of different fractions. Based on K isotopic and synchrotron data, we conclude that two dominant processes are responsible for plant-mediated K isotopic fractionation, including (1) K redistribution during intra-plant circulation and (2) uptake at the root-soil interface. For intra-plant circulation of K, there is a high affinity of isotopically lighter K to organic complexes as K-pectate, and K-pectate is particularly enriched in roots and fresh leaves. For K uptake at root-soil interface, isotopically lighter K is preferentially taken by roots from soil bioavailable pools following a low-affinity (passive) transport path. Soil K budget in two sites reflects strong source mixing effects with limited plant imprints. This work provides exploratory data on the biogeochemical fractionation of K isotopes in the soil–plant system.

The evolution of imprinting in plants: beyond the seed

Genomic imprinting results in the biased expression of alleles depending on if the allele was inherited from the mother or the father. Despite the prevalence of sexual reproduction across eukaryotes, imprinting is only found in placental mammals, flowering plants, and some insects, suggesting independent evolutionary origins. Numerous hypotheses have been proposed to explain the selective pressures that favour the innovation of imprinted gene expression and each differs in their experimental support and predictions. Due to the lack of investigation of imprinting in land plants, other than angiosperms with triploid endosperm, we do not know whether imprinting occurs in species lacking endosperm and with embryos developing on maternal plants. Here, we discuss the potential for uncovering additional examples of imprinting in land plants and how these observations may provide additional support for one or more existing imprinting hypotheses.

Genomic imprinted genes in reciprocal hybrid endosperm of Brassica napus

BackgroundGenomic imprinting results in the expression of parent-of-origin-specific alleles in the offspring. Brassica napus is an oil crop with research values in polyploidization. Identification of imprinted genes in B. napus will enrich the knowledge of genomic imprinting in dicotyledon plants.ResultsIn this study, we performed reciprocal crosses between B. napus L. cultivars Yangyou 6 (Y6) and Zhongshuang 11 (ZS11) to collect endosperm at 20 and 25 days after pollination (DAP) for RNA-seq. In total, we identified 297 imprinted genes, including 283 maternal expressed genes (MEGs) and 14 paternal expressed genes (PEGs) according to the SNPs between Y6 and ZS11. Only 36 genes (35 MEGs and 1 PEG) were continuously imprinted in 20 and 25 DAP endosperm. We found 15, 2, 5, 3, 10, and 25 imprinted genes in this study were also imprinted in Arabidopsis, rice, castor bean, maize, B. rapa, and other B. napus lines, respectively. Only 26 imprinted genes were specifically expressed in endosperm, while other genes were also expressed in root, stem, leaf and flower bud of B. napus. A total of 109 imprinted genes were clustered on rapeseed chromosomes. We found the LTR/Copia transposable elements (TEs) were most enriched in both upstream and downstream of the imprinted genes, and the TEs enriched around imprinted genes were more than non-imprinted genes. Moreover, the expression of 5 AGLs and 6 pectin-related genes in hybrid endosperm were significantly changed comparing with that in parent endosperm.ConclusionThis research provided a comprehensive identification of imprinted genes in B. napus, and enriched the gene imprinting in dicotyledon plants, which would be useful in further researches on how gene imprinting regulates seed development.

Late Bronze Age stamp-seals with negative impressions of seeds from Eastern Hungary

The study of plant imprints has a long history in archaeobotany and it became an essential tool for reconstructing the agricultural practices of the past. However, in some cases these imprints are deliberately structured in a way that may suggest interpreting them as symbols, and therefore understanding their manner of organization would help us to reflect on the way people thought about their plants. This applies to the four stamp-seals that I present here. Three of them were found at Berettyóújfalú-Papp-zug and one was found at Baks-Temetőpart. Each seal is dated to the Gáva period and has negatives of seeds on its active face. This study deals with the identification of the seed negatives and the possibilities of interpreting them.

Evidence of Cosmic Impact at Abu Hureyra, Syria at the Younger Dryas Onset (~12.8 ka): High-temperature melting at >2200\u2009\xb0C

At Abu Hureyra (AH), Syria, the 12,800-year-old Younger Dryas boundary layer (YDB) contains peak abundances in meltglass, nanodiamonds, microspherules, and charcoal. AH meltglass comprises 1.6 wt.% of bulk sediment, and crossed polarizers indicate that the meltglass is isotropic. High YDB concentrations of iridium, platinum, nickel, and cobalt suggest mixing of melted local sediment with small quantities of meteoritic material. Approximately 40% of AH glass display carbon-infused, siliceous plant imprints that laboratory experiments show formed at a minimum of 1200°–1300 °C; however, reflectance-inferred temperatures for the encapsulated carbon were lower by up to 1000 °C. Alternately, melted grains of quartz, chromferide, and magnetite in AH glass suggest exposure to minimum temperatures of 1720 °C ranging to >2200 °C. This argues against formation of AH meltglass in thatched hut fires at 1100°–1200 °C, and low values of remanent magnetism indicate the meltglass was not created by lightning. Low meltglass water content (0.02–0.05% H2O) is consistent with a formation process similar to that of tektites and inconsistent with volcanism and anthropogenesis. The wide range of evidence supports the hypothesis that a cosmic event occurred at Abu Hureyra ~12,800 years ago, coeval with impacts that deposited high-temperature meltglass, melted microspherules, and/or platinum at other YDB sites on four continents.

Genomic imprinting in plants-revisiting existing models.

Genomic imprinting is an epigenetic phenomenon leading to parentally biased gene expression. Throughout the years, extensive efforts have been made to characterize the epigenetic marks underlying imprinting in animals and plants. As a result, DNA methylation asymmetries between parental genomes emerged as the primary factor controlling the imprinting status of many genes. Nevertheless, the data accumulated so far suggest that this process cannot solely explain the imprinting of all genes. In this review, we revisit the current models explaining imprinting regulation in plants, and discuss novel regulatory mechanisms that could function independently of parental DNA methylation asymmetries in the establishment of imprinting.

Identification and Comparison of Imprinted Genes Across Plant Species.

Genomic imprinting is a phenomenon that occurs in flowering plants and mammals, whereby a gene is expressed in a parent-of-origin-specific manner. Although imprinting has now been examined genome-wide in a number of species using RNA-seq, the analyses used to assess imprinting vary between studies, making consistent comparisons between species difficult. Here we present a simple, easy-to-use bioinformatic pipeline for imprinting analyses suitable for any tissue, including plant endosperm. All relevant scripts can be downloaded. As an illustrative example, we reanalyze published data from A. thaliana and Z. mays endosperm using the pipeline and then demonstrate how to use the results to assess the conservation of imprinting between these species. We also introduce the Plant Imprinting Database, a repository for published imprinting datasets in plants that can be used to view, compare, and download data.

Regulation of Parent-of-Origin Allelic Expression in the Endosperm.

Genomic imprinting is an epigenetic phenomenon established in the gametes prior to fertilization that causes differential expression of parental alleles, mainly in the endosperm of flowering plants. The overlap between previously identified panels of imprinted genes is limited. To investigate imprinting, we used high-resolution sequencing data acquired with sequence-capture technology. We present a bioinformatics pipeline to assay parent-of-origin allele-specific expression and report more than 300 loci with parental expression bias in Arabidopsis (Arabidopsis thaliana). In most cases, the level of expression from maternal and paternal alleles was not binary, instead supporting a differential dosage hypothesis for the evolution of imprinting in plants. To address imprinting regulation, we systematically employed mutations in regulative epigenetic pathways suggested to be major players in the process. We established the mechanistic mode of imprinting for more than 50 loci regulated by DNA methylation and Polycomb-dependent histone methylation. However, the imprinting patterns of most genes were not affected by these mechanisms. To this end, we also demonstrated that the RNA-directed DNA methylation pathway alone does not substantially influence imprinting patterns, suggesting that more complex epigenetic pathways regulate most of the identified imprinted genes.

Paleosols and Weathering Crusts of the Middle-Late Devonian in the Mikhailovskii Quarry (Kursk Magnetic Anomaly)

Devonian deposits in the Mikhailovskii Mining and Processing Plant quarry comprising weathering crusts and paleosols have been studied. Comparative analysis of the morphological, geochemical, and mineralogical properties of paleosols and weathering crusts allows revealing differences primarily due to biotic processes in soils and vital activity of plants and microorganisms. The presence of root systems, plant imprints, spore diversity, and horizontal profile manifested in the formation of humus-accumulative horizon, the profile differentiation of clay minerals, and the profile distribution of geochemical indices and ratios are key characteristics classifying the objects of study as paleosols.

Genome-wide screening and analysis of imprinted genes in rapeseed (Brassica napus L.) endosperm.

Species-specific genomic imprinting is an epigenetic phenomenon leading to parent-of-origin-specific differential expression of maternally and paternally inherited alleles. To date, no studies of imprinting have been reported in rapeseed, a tetraploid species. Here, we analysed global patterns of allelic gene expression in developing rapeseed endosperms from reciprocal crosses between inbred lines YN171 and 93275. A total of 183 imprinted genes, consisting of 167 maternal expressed genes (MEGs) and 16 paternal expressed genes (PEGs), were identified from 14,394 genes found to harbour diagnostic SNPs between the parental lines. Some imprinted genes were validated in different endosperm stages and other parental combinations by RT-PCR analysis. A clear clustering of imprinted genes throughout the rapeseed genome was identified, which was different from most other plants. Methylation analysis of 104 out of the 183 imprinted genes showed that 11 genes (7 MEGs and 4 PEGs) harboured differentially methylated regions (DMRs). Unexpectedly, only 1 MEG out of these 11 genes had a DMR that exhibited high CG methylation rate in paternal allele and had big difference between parent alleles. These results extend our understanding of gene imprinting in plants and provide potential avenues for further research in imprinted genes.

Characterization of Imprinted Genes in Rice Reveals Conservation of Regulation and Imprinting with Other Plant Species.

Genomic imprinting is an epigenetic phenomenon by which certain genes display differential expression in a parent-of-origin-dependent manner. Hundreds of imprinted genes have been identified from several plant species. Here, we identified, with a high level of confidence, 208 imprinted gene candidates from rice (Oryza sativa). Imprinted genes of rice showed limited association with the transposable elements, which contrasts with findings from Arabidopsis (Arabidopsis thaliana). Generally, imprinting in rice is conserved within a species, but intraspecific variation also was detected. The imprinted rice genes do not show signatures of selection, which suggests that domestication has had a limited evolutionary consequence on genomic imprinting. Although conservation of imprinting in plants is limited, we show that some loci are imprinted in several different species. Moreover, our results suggest that different types of epigenetic regulation can be established either before or after fertilization. Imprinted 24-nucleotide small RNAs and their neighboring genes tend to express alleles from different parents. This association was not observed between 21-nucleotide small RNAs and their neighboring genes. Together, our findings suggest that the regulation of imprinting can be diverse, and genomic imprinting has evolutionary and biological significance.

Parental-genome dosage effects on the transcriptome of F1 hybrid triploid embryos of Arabidopsis thaliana.

Genomic imprinting in the seed endosperm could be due to unequal parental-genome contribution effects in triploid endosperm tissue that trigger parent-of-origin specific activation and/or silencing of loci prone to genomic imprinting. To determine whether genomic imprinting is triggered by unequal parental-genome contribution effects, we generated a whole-genome transcriptome dataset of F1 hybrid triploid embryos (as mimics of F1 hybrid triploid endosperm). For the vast majority of genes, the parental contributions to their expression levels in the F1 triploid hybrid embryos follow a biallelic and linear expression pattern. While allele-specific expression (ASE) bias was detected, such effects were predominantly parent-of-origin independent. We demonstrate that genomic imprinting is largely absent from F1 triploid embryos, strongly suggesting that neither triploidy nor unequal parental-genome contribution are key triggers of genomic imprinting in plants. However, extensive parental-genome dosage effects on gene expression were observed between the reciprocal F1 hybrid embryos, particularly for genes involved in defence response and nutrient reservoir activity, potentially leading to the seed size differences between reciprocal triploids. We further determined that unequal parental-genome contribution in F1 triploids can lead to overexpression effects that are parent-of-origin dependent, and which are not observed in diploid or tetraploid embryos in which the parental-genome dosage is balanced. Overall, our study demonstrates that neither triploidy nor unequal parental-genome contribution is sufficient to trigger imprinting in plant tissues, suggesting that genomic imprinting is an intrinsic and unique feature of the triploid seed endosperm.

CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data

DNA methylation is important for gene silencing and imprinting in both plants and animals. Recent advances in bisulfite sequencing allow detection of single nucleotide variations (SNVs) achieving high sensitivity, but accurately identifying heterozygous SNVs from partially C-to-T converted sequences remains challenging. We designed two methods, BayesWC and BinomWC, that substantially improved the precision of heterozygous SNV calls from ∼80% to 99% while retaining comparable recalls. With these SNV calls, we provided functions for allele-specific DNA methylation (ASM) analysis and visualizing the methylation status on reads. Applying ASM analysis to a previous dataset, we found that an average of 1.5% of investigated regions showed allelic methylation, which were significantly enriched in transposon elements and likely to be shared by the same cell-type. A dynamic fragment strategy was utilized for DMR analysis in low-coverage data and was able to find differentially methylated regions (DMRs) related to key genes involved in tumorigenesis using a public cancer dataset. Finally, we integrated 40 applications into the software package CGmapTools to analyze DNA methylomes. This package uses CGmap as the format interface, and designs binary formats to reduce the file size and support fast data retrieval, and can be applied for context-wise, gene-wise, bin-wise, region-wise and sample-wise analyses and visualizations. The CGmapTools software is freely available at https://cgmaptools.github.io/. guoweilong@cau.edu.cn. Supplementary data are available at Bioinformatics online.

Global analysis of DNA methylation in young (J1) and senescent (J2) Gossypium hirsutum L. cotyledons by MeDIP-Seq.

DNA methylation is an important epigenetic modification regulating gene expression, genomic imprinting, transposon silencing and chromatin structure in plants and plays an important role in leaf senescence. However, the DNA methylation pattern during Gossypium hirsutum L. cotyledon senescence is poorly understood. In this study, global DNA methylation patterns were compared between two cotyledon development stages, young (J1) and senescence (J2), using methylated DNA immunoprecipitation (MeDIP-Seq). Methylated cytosine occurred mostly in repeat elements, especially LTR/Gypsy in both J1 and J2. When comparing J1 against J2, there were 1222 down-methylated genes and 623 up-methylated genes. Methylated genes were significantly enriched in carbohydrate metabolism, biosynthesis of other secondary metabolites and amino acid metabolism pathways. The global DNA methylation level decreased from J1 to J2, especially in gene promoters, transcriptional termination regions and regions around CpG islands. We further investigated the expression patterns of 9 DNA methyltransferase-associated genes and 2 DNA demethyltransferase-associated genes from young to senescent cotyledons, which were down-regulated during cotyledon development. In this paper, we first reported that senescent cotton cotyledons exhibited lower DNA methylation levels, primarily due to decreased DNA methyltransferase activity and which also play important role in regulating secondary metabolite process.

Paleosol complex in the uppermost Mikhailovian Horizon (Viséan, Lower Carboniferous) in the southern flank of the Moscow Syneclise

The beds composing an unconformity at the boundary of the Mikhailovian and Venevian horizons in the Polotnyanyi Zavod quarry (Kaluga Region) are investigated. A detailed study has shown that, at the base of black “rhizoid” limestone, a pedocomplex of two paleosols of different genesis is formed. From below upwards, rocks of subaerial (Paleosol 1 of the rendzina type), subaerial–subaquatic (Paleosol 2 on bog marl), and palustrine genesis replace each other. Both paleosols display a horizontal structure of profiles; the presence of the root systems, imprints of plants, and traces of animal’s activity; the presence of soil new formations (micritic calcite with a light isotopic composition of C, Fe-concretions ). In paleosols, some geochemical indices (PWI, CIA, CIA-K), the ratios Ba/Sr, Rb/Sr, and concentration of Ga increase. The soil complex was formed under conditions of a warm subhumid climate. In the structure and lateral scale of distribution, the object investigated is comparable to the Everglades marsh landscape of Florida (United States).