Genome of a citrus rootstock and global DNA demethylation caused by heterografting

AbstractGrafting is an ancient technique used for plant propagation and improvement in horticultural crops for at least 1,500 years. Citrus plants, with a seed-to-seed cycle of 5–15 years, are among the fruit crops that were probably domesticated by grafting. Poncirus trifoliata, a widely used citrus rootstock, can promote early flowering, strengthen stress tolerance, and improve fruit quality via scion–rootstock interactions. Here, we report its genome assembly using PacBio sequencing. We obtained a final genome of 303 Mb with a contig N50 size of 1.17 Mb and annotated 25,680 protein-coding genes. DNA methylome and transcriptome analyses indicated that the strong adaptability of P. trifoliata is likely attributable to its special epigenetic modification and expression pattern of resistance-related genes. Heterografting by using sweet orange as scion and P. trifoliata as rootstock and autografting using sweet orange as both scion and rootstock were performed to investigate the genetic effects of the rootstock. Single-base methylome analysis indicated that P. trifoliata as a rootstock caused DNA demethylation and a reduction in 24-nt small RNAs (sRNAs) in scions compared to the level observed with autografting, implying the involvement of sRNA-mediated graft-transmissible epigenetic modifications in citrus grafting. Taken together, the assembled genome for the citrus rootstock and the analysis of graft-induced epigenetic modifications provide global insights into the genetic effects of rootstock–scion interactions and grafting biology.

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DNA methylation: from model plants to vegetable crops

Biochemical Society Transactions ◽

10.1042/bst20210353 ◽

2021 ◽

Author(s):

Wen-Feng Nie

Keyword(s):

Dna Methylation ◽

Target Genes ◽

Developmental Process ◽

Epigenetic Modifications ◽

Dna Demethylation ◽

Leafy Vegetables ◽

Vegetable Crops ◽

Human Beings ◽

Horticultural Crops ◽

Active Dna Demethylation

As a subgroup of horticultural crops, vegetable food is a kind of indispensable energy source for human beings, providing necessary nutritional components including vitamins, carbohydrates, dietary fiber, and active substances such as carotenoids and flavonoids. The developmental process of vegetable crops is not only regulated by environmental stimulations, but also manipulated by both genetic and epigenetic modifications. Epigenetic modifications are composed by several regulatory mechanisms, including DNA methylation, histone modification, chromatin remodeling, and non-coding RNAs. Among these modifications, DNA methylation functions in multiple biological pathways ranging from fundamental development to environmental stimulations by mediating transcriptomic alterations, resulting in the activation or silencing of target genes. In recent years, intensive studies have revealed that DNA methylation is essential to fruit development and ripening, indicating that the epigenome of fruit crops could be dynamically modified according to the specific requirements in the commercial production. Firstly, this review will present the mechanisms of DNA methylation, and update the understanding on active DNA demethylation in Arabidopsis thaliana. Secondly, this review will summarize the recent progress on the function of DNA methylation in regulating fruit ripening. Moreover, the possible functions of DNA methylation on controlling the expansion of edible organs, senescence of leafy vegetables, and anthocyanin pigmentation in several important vegetable crops will be discussed. Finally, this review will highlight the intractable issues that need to be resolved in the application of epigenome in vegetable crops, and provide perspectives for the potential challenges in the further studies.

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Rootstock and scion effects on the leaf nutrient composition of citrus trees

Australian Journal of Experimental Agriculture ◽

10.1071/ea9930363 ◽

1993 ◽

Vol 33 (3) ◽

pp. 363 ◽

Cited By ~ 16

Author(s):

BK Taylor ◽

RT Dimsey

Keyword(s):

Sweet Orange ◽

Nutrient Composition ◽

Poncirus Trifoliata ◽

Navel Orange ◽

Rangpur Lime ◽

Rough Lemon ◽

Valencia Orange ◽

Citrus Rootstock ◽

Leaf N ◽

High Range

Four long-term citrus rootstock trials (navel orange, mandarin, Valencia orange, and lime soil trial) established at Irymple, in the Sunraysia district of Victoria, were tested for leaf nutrient composition in each of 2 years. Scion or rootstock significantly influenced leaf nutrient composition in orange and mandarin trees in all 4 trials. Poncirus trifoliata and citrange rootstocks and Ellendale tangor scion resulted in high to moderate leaf N, P, and K concentrations, while Symons sweet orange rootstock and Dancy mandarin gave low leaf nitrogen (N), phosphorus (P), and potassium (K) concentrations. Potassium concentrations of navel and Valencia oranges on rough lemon rootstock were lower than on most of the other rootstocks tested. For all rootstocks, however, leaf N, P, and K concentrations were in the high range in the navel orange and Valencia orange trials, while leaf K concentrations were in the high range in the mandarin trial. Citrange rootstocks and Ellendale scion also had higher concentrations of leaf magnesium (Mg), while Symons sweet orange, Cox sweet orange, and Rangpur lime had lower leaf Mg concentrations than other rootstocks and scions. In the Valencia rootstock trial, rough lemon and Rangpur lime induced the highest leaf sulfur concentrations, while citrange rootstocks gave the lowest. Soil depth in the lime soil trial influenced foliar P and K levels in Valencia orange trees but these differences were small. In all trials, rootstock, but not scion, strongly influenced chloride (Cl) concentrations of citrus leaves. Poncirus trifoliata rootstock accumulated high concentrations of Cl, and the citrange rootstocks moderate, while Cleopatra mandarin rootstock showed consistently low leaf C1 concentrations in all trials. Rough lemon rootstock was not consistently good at excluding C1, and Rangpur lime showed good C1 exclusion only in the Valencia rootstock trial. There was no evidence of a negative relationship between uptake of N and C1 by citrus rootstocks. Poncirus trifoliata had a lower uptake of sodium (Na) in the Valencia rootstock trial, while Cleopatra and Emperor mandarin rootstocks showed slightly higher leaf Na levels than most other rootstocks tested. The 2 citranges, mandarin, rough lemon, and Rangpur lime rootstocks induced higher boron (B) concentrations in leaves of navel orange compared with other rootstocks but they were still in the adequate range for citrus (Reuter and Robinson 1986), while sweet orange rootstocks had lower levels. Emperor mandarin scion on all rootstocks tested had the lowest B levels. Concentrations of iron and copper were rarely influenced by scion or rootstock. Rootstock significantly influenced leaf manganese (Mn) and zinc (Zn) levels in a number of trials, but scion effects were minor. In comparison with all other rootstocks, rough lemon induced higher Mn levels in some cases; sweet orange rootstocks gave higher leaf Zn levels in other cases; while Rangpur lime induced higher Mn and Zn levels in trees grown in the lime soil trial. In the first 3 trials, concentrations of Zn and Mn were low in many of the rootstocks and scions, indicating a need for a second micronutrient spray per growing season.

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A GENETIC MAP OF CITRUS BASED ON ISOZYMES AND RFLPS.

HortScience ◽

10.21273/hortsci.25.9.1154b ◽

1990 ◽

Vol 25 (9) ◽

pp. 1154b-1154 ◽

Cited By ~ 1

Author(s):

David C. Jarrell ◽

Mikeal L. Roose

Keyword(s):

Genetic Map ◽

Sweet Orange ◽

Poncirus Trifoliata ◽

Citrus Paradisi ◽

Structural Rearrangements ◽

Mendelian Segregation ◽

Dna Libraries ◽

Citrus Rootstock ◽

Multipoint Linkage ◽

Segregating Population

We report a preliminary genetic map of citrus based on segregation of 8 isozyme and at least 33 RFLP loci. The segregating population consisted of 60 plants from a cross of two citrus rootstock, `Sacaton' citrumelo × `Troyer' citrange. This cross represents an intergeneric F2 since `Sacaton' is Citrus paradisi (grapefruit) × Poncirus trifoliata (trifoliate orange) and `Troyer' is C. sinensis (sweet orange) × P. trifoliata. RFLPs were identified using anonymous probes from both cDNA and genomic DNA libraries of citrus. About 20% of the loci deviated significantly from Mendelian segregation. Two-point linkage analysis identified 8 linkage groups in which pairs of loci were within 30 centimorgans. This suggests that we have markers on most of the 9 chromosomes of Citrus. A map based on multipoint linkage estimates will be reported. Evidence for structural rearrangements between Citrus and Poncirus and extension of the map to additional marker and disease resistance loci will be discussed.

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Epigenetic Modulation of TLR4 Expression by Sulforaphane Increases Anti-Inflammatory Capacity in Porcine Monocyte-Derived Dendritic Cells

Biology ◽

10.3390/biology10060490 ◽

2021 ◽

Vol 10 (6) ◽

pp. 490

Author(s):

Xueqi Qu ◽

Christiane Neuhoff ◽

Mehmet Ulas Cinar ◽

Maren Pröll ◽

Ernst Tholen ◽

...

Keyword(s):

Dna Methylation ◽

Dendritic Cells ◽

Epigenetic Modifications ◽

Dna Demethylation ◽

Dependent Manner ◽

Experimental Conditions ◽

Hdac Activity ◽

Protein Levels ◽

Anti Inflammatory ◽

Epigenetic Modulation

Inflammation is regulated by epigenetic modifications, including DNA methylation and histone acetylation. Sulforaphane (SFN), a histone deacetylase (HDAC) inhibitor, is also a potent immunomodulatory agent, but its anti-inflammatory functions through epigenetic modifications remain unclear. Therefore, this study aimed to investigate the epigenetic effects of SFN in maintaining the immunomodulatory homeostasis of innate immunity during acute inflammation. For this purpose, SFN-induced epigenetic changes and expression levels of immune-related genes in response to lipopolysaccharide (LPS) stimulation of monocyte-derived dendritic cells (moDCs) were analyzed. These results demonstrated that SFN inhibited HDAC activity and caused histone H3 and H4 acetylation. SFN treatment also induced DNA demethylation in the promoter region of the MHC-SLA1 gene, resulting in the upregulation of Toll-like receptor 4 (TLR4), MHC-SLA1, and inflammatory cytokines’ expression at 6 h of LPS stimulation. Moreover, the protein levels of cytokines in the cell culture supernatants were significantly inhibited by SFN pre-treatment followed by LPS stimulation in a time-dependent manner, suggesting that inhibition of HDAC activity and DNA methylation by SFN may restrict the excessive inflammatory cytokine availability in the extracellular environment. We postulate that SFN may exert a protective and anti-inflammatory function by epigenetically influencing signaling pathways in experimental conditions employing porcine moDCs.

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Metabolic reprogramming and epigenetic modifications on the path to cancer

Protein & Cell ◽

10.1007/s13238-021-00846-7 ◽

2021 ◽

Author(s):

Linchong Sun ◽

Huafeng Zhang ◽

Ping Gao

Keyword(s):

Immune Cells ◽

Immune Escape ◽

Epigenetic Modification ◽

Epigenetic Modifications ◽

Metabolic Reprogramming ◽

Epigenetic Alterations ◽

Metabolic Alterations ◽

Cancer Hallmarks ◽

Epigenetic Remodeling ◽

Spatial Regionalization

AbstractMetabolic rewiring and epigenetic remodeling, which are closely linked and reciprocally regulate each other, are among the well-known cancer hallmarks. Recent evidence suggests that many metabolites serve as substrates or cofactors of chromatin-modifying enzymes as a consequence of the translocation or spatial regionalization of enzymes or metabolites. Various metabolic alterations and epigenetic modifications also reportedly drive immune escape or impede immunosurveillance within certain contexts, playing important roles in tumor progression. In this review, we focus on how metabolic reprogramming of tumor cells and immune cells reshapes epigenetic alterations, in particular the acetylation and methylation of histone proteins and DNA. We also discuss other eminent metabolic modifications such as, succinylation, hydroxybutyrylation, and lactylation, and update the current advances in metabolism- and epigenetic modification-based therapeutic prospects in cancer.

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Mitochondrial DNA Methylation and Human Diseases

International Journal of Molecular Sciences ◽

10.3390/ijms22094594 ◽

2021 ◽

Vol 22 (9) ◽

pp. 4594

Author(s):

Andrea Stoccoro ◽

Fabio Coppedè

Keyword(s):

Dna Methylation ◽

Mitochondrial Dna ◽

Mitochondrial Genome ◽

Nuclear Dna ◽

Epigenetic Modification ◽

Nuclear Genome ◽

Epigenetic Modifications ◽

Human Diseases ◽

Loop Region ◽

D Loop

Epigenetic modifications of the nuclear genome, including DNA methylation, histone modifications and non-coding RNA post-transcriptional regulation, are increasingly being involved in the pathogenesis of several human diseases. Recent evidence suggests that also epigenetic modifications of the mitochondrial genome could contribute to the etiology of human diseases. In particular, altered methylation and hydroxymethylation levels of mitochondrial DNA (mtDNA) have been found in animal models and in human tissues from patients affected by cancer, obesity, diabetes and cardiovascular and neurodegenerative diseases. Moreover, environmental factors, as well as nuclear DNA genetic variants, have been found to impair mtDNA methylation patterns. Some authors failed to find DNA methylation marks in the mitochondrial genome, suggesting that it is unlikely that this epigenetic modification plays any role in the control of the mitochondrial function. On the other hand, several other studies successfully identified the presence of mtDNA methylation, particularly in the mitochondrial displacement loop (D-loop) region, relating it to changes in both mtDNA gene transcription and mitochondrial replication. Overall, investigations performed until now suggest that methylation and hydroxymethylation marks are present in the mtDNA genome, albeit at lower levels compared to those detectable in nuclear DNA, potentially contributing to the mitochondria impairment underlying several human diseases.

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Nutritional Status Impacts Epigenetic Regulation in Early Embryo Development: A Scoping Review

Advances in Nutrition ◽

10.1093/advances/nmab038 ◽

2021 ◽

Author(s):

Shuang Cai ◽

Shuang Quan ◽

Guangxin Yang ◽

Meixia Chen ◽

Qianhong Ye ◽

...

Keyword(s):

Embryonic Development ◽

Embryo Development ◽

Epigenetic Regulation ◽

Scoping Review ◽

Epigenetic Modification ◽

Reproductive Technologies ◽

Early Embryo ◽

Epigenetic Modifications ◽

Nutrition Status ◽

Early Embryo Development

ABSTRACTWith the increasing maternal age and the use of assisted reproductive technology in various countries worldwide, the influence of epigenetic modification on embryonic development is increasingly notable and prominent. Epigenetic modification disorders caused by various nutritional imbalance would cause embryonic development abnormalities and even have an indelible impact on health in adulthood. In this scoping review, we summarize the main epigenetic modifications in mammals and the synergies among different epigenetic modifications, especially DNA methylation, histone acetylation, and histone methylation. We performed an in-depth analysis of the regulation of various epigenetic modifications on mammals from zygote formation to cleavage stage and blastocyst stage, and reviewed the modifications of key sites and their potential molecular mechanisms. In addition, we discuss the effects of nutrition (protein, lipids, and one-carbon metabolism) on epigenetic modification in embryos and emphasize the importance of various nutrients in embryonic development and epigenetics during pregnancy. Failures in epigenetic regulation have been implicated in mammalian and human early embryo loss and disease. With the use of reproductive technologies, it is becoming even more important to establish developmentally competent embryos. Therefore, it is essential to evaluate the extent to which embryos are sensitive to these epigenetic modifications and nutrition status. Understanding the epigenetic regulation of early embryo development will help us make better use of reproductive technologies and nutrition regulation to improve reproductive health in mammals.

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Screening of ‘King’ Mandarin Hybrids as Tolerant Citrus Rootstocks to Flooding Stress

Horticulturae ◽

10.3390/horticulturae7100388 ◽

2021 ◽

Vol 7 (10) ◽

pp. 388

Author(s):

Mary-Rus Martínez-Cuenca ◽

Amparo Primo-Capella ◽

María Ángeles Forner-Giner

Keyword(s):

Water Relations ◽

Growth Parameters ◽

Chlorophyll Concentration ◽

Co2 Assimilation ◽

Poncirus Trifoliata ◽

Control Treatment ◽

Gene Expressions ◽

Flooding Stress ◽

Citrus Rootstock ◽

Osmotic Potentials

This work compares the tolerance to long-term anoxia conditions (35 days) of five new citrus ‘King’ mandarin (Citrus nobilis L. Lour) × Poncirus trifoliata ((L.) Raf.) hybrids (named 0501XX) and Carrizo citrange (CC, Citrus sinensis (L.) Osb. × Poncirus trifoliata (L.) Raf.), the widely used citrus rootstock in Spain. Growth parameters, chlorophyll concentration, gas exchange and fluorescence parameters, water relations in leaves, abscisic acid (ABA) concentration, and PIP1 and PIP2 gene expressions were assessed. With a waterlogging treatment, the root system biomass of most hybrids went down, and the chlorophyll a and b concentrations substantially dropped. The net CO2 assimilation rates (An) and stomatal conductance (gs) lowered significantly due to flooding, and the transpiration rate (E) closely paralleled the changes in gs. The leaf water and osmotic potentials significantly increased in most 0501 hybrids. As a trend, flooding stress lowered the ABA concentration in roots from most hybrids, but increased in the leaves of CC, 05019 and 050110. Under the control treatment (Ct) conditions, most 0501 hybrids showed higher PIP1 and PIP2 expressions than the control rootstock CC, but were impaired due to the flooding conditions in 05019 and 050110. From this study, we conclude that 0501 genotypes develop some adaptive responses in plants against flooding stress such as (1) stomata closure to prevent water loss likely mediated by ABA levels, and (2) enhanced water and osmotic potentials and the downregulation of those genes regulating aquaporin channels to maintain water relations in plants. Although these traits seemed especially relevant in hybrids 050110 and 050125, further experiments must be done to determine their behavior under field conditions, particularly their influence on commercial varieties and their suitability as flooding-tolerant hybrids for replacing CC, one of the main genotypes that is widely used as a citrus rootstock in Spain, under these conditions.

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Impact of Physical Activity and Exercise on the Epigenome in Skeletal Muscle and Effects on Systemic Metabolism

Biomedicines ◽

10.3390/biomedicines10010126 ◽

2022 ◽

Vol 10 (1) ◽

pp. 126

Author(s):

Julio Plaza-Diaz ◽

David Izquierdo ◽

Álvaro Torres-Martos ◽

Aiman Tariq Baig ◽

Concepción M. Aguilera ◽

...

Keyword(s):

Physical Activity ◽

Skeletal Muscle ◽

Gene Transcription ◽

Histone Modifications ◽

Epigenetic Modification ◽

Epigenetic Modifications ◽

Late Response ◽

Transcriptional Responses ◽

Response To Exercise ◽

The Impact

Exercise and physical activity induces physiological responses in organisms, and adaptations in skeletal muscle, which is beneficial for maintaining health and preventing and/or treating most chronic diseases. These adaptations are mainly instigated by transcriptional responses that ensue in reaction to each individual exercise, either resistance or endurance. Consequently, changes in key metabolic, regulatory, and myogenic genes in skeletal muscle occur as both an early and late response to exercise, and these epigenetic modifications, which are influenced by environmental and genetic factors, trigger those alterations in the transcriptional responses. DNA methylation and histone modifications are the most significant epigenetic changes described in gene transcription, linked to the skeletal muscle transcriptional response to exercise, and mediating the exercise adaptations. Nevertheless, other alterations in the epigenetics markers, such as epitranscriptomics, modifications mediated by miRNAs, and lactylation as a novel epigenetic modification, are emerging as key events for gene transcription. Here, we provide an overview and update of the impact of exercise on epigenetic modifications, including the well-described DNA methylations and histone modifications, and the emerging modifications in the skeletal muscle. In addition, we describe the effects of exercise on epigenetic markers in other metabolic tissues; also, we provide information about how systemic metabolism or its metabolites influence epigenetic modifications in the skeletal muscle.

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PHYTOCHROMES B1/B2 ARE KEY REGULATORS OF EPIGENOME REPROGRAMMING DURING TOMATO FRUIT DEVELOPMENT

10.1101/2020.07.30.227447 ◽

2020 ◽

Author(s):

Ricardo Bianchetti ◽

Nicolas Bellora ◽

Luis A de Haro ◽

Rafael Zuccarelli ◽

Daniele Rosado ◽

...

Keyword(s):

Fruit Development ◽

Epigenetic Modification ◽

Tomato Fruit ◽

Dna Demethylation ◽

Temperature Perception ◽

Genome Wide ◽

Fruit Development And Ripening ◽

Histone Modifying Enzymes ◽

Level Of Understanding ◽

Agronomical Traits

AbstractPhytochrome-mediated light and temperature perception has been shown to be a major regulator of fruit development. Furthermore, chromatin remodelling via DNA demethylation has been described as a crucial mechanism behind the fruit ripening process; however, the molecular basis underlying the triggering of this epigenetic modification remains largely unknown. Here, an integrative analyses of the methylome, siRNAome and transcriptome of tomato fruits from phyA and phyB1B2 null mutants was performed, revealing that PHYB1 and PHYB2 influences genome-wide DNA methylation during fruit development and ripening. The experimental evidence indicates that PHYB1B2 signal transduction relies on a gene expression network that includes chromatin organization factors (DNA methylases/demethylases, histone-modifying enzymes and remodelling factors) and transcriptional regulators, ultimately leading to altered mRNA profile of photosynthetic and ripening-associated genes. This new level of understanding provides insights into the orchestration of epigenetic mechanisms in response to environmental cues affecting agronomical traits in fleshy fruits.

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