scholarly journals DNA Methylation Analysis of Dormancy Release in Almond (Prunus dulcis) Flower Buds Using Epi-Genotyping by Sequencing

2018 ◽  
Vol 19 (11) ◽  
pp. 3542 ◽  
Author(s):  
Ángela Prudencio ◽  
Olaf Werner ◽  
Pedro Martínez-García ◽  
Federico Dicenta ◽  
Rosa Ros ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Prunus Persica ◽  
Prolonged Exposure ◽  
Genotyping By Sequencing ◽  
Fruit Trees ◽  
Prunus Dulcis ◽  
Dormancy Release ◽  
Release Process ◽  
Cold Temperatures ◽  
Reduced Representation

DNA methylation and histone post-translational modifications have been described as epigenetic regulation mechanisms involved in developmental transitions in plants, including seasonal changes in fruit trees. In species like almond (Prunus dulcis (Mill.) D.A: Webb), prolonged exposure to cold temperatures is required for dormancy release and flowering. Aiming to identify genomic regions with differential methylation states in response to chill accumulation, we carried out Illumina reduced-representation genome sequencing on bisulfite-treated DNA from floral buds. To do this, we analyzed almond genotypes with different chilling requirements and flowering times both before and after dormancy release for two consecutive years. The study was performed using epi-Genotyping by Sequencing (epi-GBS). A total of 7317 fragments were sequenced and the samples compared. Out of these fragments, 677 were identified as differentially methylated between the almond genotypes. Mapping these fragments using the Prunus persica (L.) Batsch v.2 genome as reference provided information about coding regions linked to early and late flowering methylation markers. Additionally, the methylation state of ten gene-coding sequences was found to be linked to the dormancy release process.

Host suitability analysis of the bark beetle Scolytus amygdali (Coleoptera: Curculionidae: Scolytinae)

2015 ◽  
Vol 105 (4) ◽  
pp. 434-440
Author(s):  
A. Zeiri ◽  
M.Z. Ahmed ◽  
M. Braham ◽  
M. Braham ◽  
B.-L. Qiu
Keyword(s):  
Development Time ◽  
Prunus Persica ◽  
Insect Pest ◽  
Reproductive Potential ◽  
Fruit Trees ◽  
Prunus Dulcis ◽  
Prunus Armeniaca ◽  
Suitability Analysis ◽  
Prunus Domestica ◽  
Polyphagous Insect

AbstractScolytus amygdali is a polyphagous insect pest that feeds on fruit trees and forest trees. Our study assessed the host preference and reproductive potential of S. amygdali on four tree species: almond (Prunus dulcis), apricot (Prunus armeniaca), peach (Prunus persica), and plum (Prunus domestica). Females of S. amygdali produced maternal galleries that were longer on peach than the other three trees, and female fecundity was highest on peach. Females with longer maternal galleries produced more eggs, indicating a positive correlation between maternal gallery length and female fertility. The under-bark development time of S. amygdali is significantly shorter on plum (45 days) and almond (56 days) than on apricot (65 days) and peach (64 days). Despite this longer development time on peach, our results still suggest that, of the four types of tree tested, peach is the most preferred host for S. amygdali.

scholarly journals Effects of Rootstock and Budding Height on Bacterial Canker in French Prune

Plant Disease ◽  
2002 ◽  
Vol 86 (5) ◽  
pp. 543-546 ◽  
Author(s):  
R. J. Sayler ◽  
S. M. Southwick ◽  
J. T. Yeager ◽  
K. Glozer ◽  
E. L. Little ◽  
...  
Keyword(s):  
Tree Mortality ◽  
Prunus Persica ◽  
Disease Incidence ◽  
Fruit Trees ◽  
Field Trials ◽  
Bacterial Canker ◽  
Prunus Domestica ◽  
Severity Of Disease ◽  
Prunus Cerasifera ◽  
Disease Pressure

Bacterial canker is one of the most economically important diseases of stone fruit trees, including ‘French’ prune (Prunus domestica). Field trials were conducted to evaluate the effect of rootstock selection and budding height on the incidence and severity of bacterial canker in four orchards with low to high disease pressure. Treatments included French prune scions low-grafted on ‘Lovell’ peach (Prunus persica) rootstocks as well as Myrobalan 29C (Prunus cerasifera) plum rootstocks grafted at 15, 50, and 90 cm above the rootstock crown. Another treatment consisted of growing Myrobalan 29C plum rootstocks in the field for one growing season, then field-grafting French prune buds onto rootstock scaffolds. Lovell peach rootstock provided the greatest protection from bacterial canker as measured by disease incidence and tree mortality in all orchards. Field-budded rootstocks and rootstocks grafted at the highest budding height provided moderate levels of resistance to bacterial canker. These treatments reduced the incidence but not the severity of disease.

scholarly journals Umbilical Cord Blood DNA Methylation in Children Who Later Develop Type 1 Diabetes

2021 ◽  
Author(s):  
Essi Laajala ◽  
Ubaid Ullah ◽  
Toni Grönroos ◽  
Omid Rasool ◽  
Viivi Halla-aho ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Type 1 Diabetes ◽  
Cord Blood ◽  
Umbilical Cord ◽  
Umbilical Cord Blood ◽  
Reduced Representation ◽  
Prediction And Prevention ◽  
Develop Type ◽  
Methylation Patterns

Distinct DNA methylation patterns have recently been observed to precede type 1 diabetes in whole blood collected from young children. Our aim was to determine, whether perinatal DNA methylation could be associated with later progression to type 1 diabetes. Reduced representation bisulfite sequencing (RRBS) analysis was performed on umbilical cord blood samples collected within the Type 1 Diabetes Prediction and Prevention (DIPP) study. Children later diagnosed with type 1 diabetes and/or testing positive for multiple islet autoantibodies (N=43) were compared to control individuals (N=79), who remained autoantibody-negative throughout the DIPP follow-up until 15 years of age. Potential confounding factors related to the pregnancy and the mother were included in the analysis. No differences in the cord blood methylation patterns were observed between these cases and controls.

scholarly journals Reversible DNA Hypermethylation of the Interleukin-15 (IL-15) Promoter Induces IL-15 Expression, Drives the Pathogenesis of T-Cell Large Granular Lymphocytic Leukemia and Provides a Potential Therapeutic Approach Using 5-Azacitidine

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 3776-3776
Author(s):  
Jonathan E Brammer ◽  
Amy E Boles ◽  
Anthony Mansour ◽  
Aharon G. Freud ◽  
Monique Mathé-Allainmat ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
T Cell ◽  
Research Funding ◽  
Marked Decrease ◽  
Lymphocytic Leukemia ◽  
Dna Hypermethylation ◽  
Reduced Representation ◽  
Primary Driver ◽  
Interleukin 15

Background and Rationale: T-cell large granular lymphocytic leukemia (T-LGLL) is an incurable clonal proliferation of CD8+ memory T-cells that leads to profound neutropenia and anemia with limited treatment options. The primary driver of T-LGLL is overexpression of interleukin-15 (IL-15), a gamma-chain cytokine. Previously, we have demonstrated that mice overexpressing IL-15 develop DNA hypermethylation and chromosomal instability that leads to the spontaneous development of LGLL (Mishra et al. Cancer Cell 2012). Further, the IL-15 promoter is known to be hypermethylated in cutaneous T-cell lymphoma (CTCL), another IL-15 driven malignancy (Mishra et al. Cancer Discovery 2016). In CTCL patients, the counterintuitive increase in IL-15 mRNA was due to hypermethylation of its promoter at the repressor binding sequences in the IL-15 gene. However, the methylation status of the IL-15 promoter in T-LGLL patients remains unknown. Concept: We hypothesize that the IL-15 promoter is hypermethylated in patients with T-LGLL, leading to aberrant overexpression of IL-15 and that this hypermethylation is a critical event in the leukemogenesis of T-LGLL. If true, demethylation of the IL-15 promoter with a resultant decrease in IL-15 transcripts should lead to apoptosis of T-LGLL cells. Hypomethylation of the IL-15 promoter, therefore, may provide a novel therapeutic approach to inhibiting IL-15, the primary driver of T-LGLL. Results: CD3+/CD8+/CD5-/dim T-cells were purified from peripheral blood of LGLL patient (n=3) and normal donor (ND) (n=3) by flow cytometry sorting. We analyzed DNA methylation and gene expression profiling using reduced representation bisulfite and RNA sequencing. With bioinformatics analysis, we determined differential methylation (1-way ANOVA P= 0.0178) and expression (1-way ANOVA P =0.0059). These data sets revealed significant differential hypermethylation of gene promoters in leukemic samples, compared to controls (Figure 1A). Reduced representation bisulfite sequencing that can identify differentially methylated regions at single base-pair resolutions demonstrated an increase in DNA methylation of the IL-15 promoter in patient samples over controls. To determine the functional significance of this finding, we treated the MOTN-1 T-LGLL cell line in vitro with the hypomethylating agent, 5-azacytidine (5-aza) at concentrations of 0.5 uM, 1 uM, 2.5 uM, and 5 uM. At 24 and 48 hours, a marked decrease in the viability of T-LGLL cells was observed, from 100% to 49.50%, p=0.037; particularly at higher concentrations of 5-aza (100% to 27% +11.30%, p=0.0030). Next, we sought to determine whether 5-aza induced hypomethylation of the IL-15 promoter. IL-15 gene expression in MOTN-1 T-LGLL cells treated with 5-aza was measured in comparison to control treated MOTN-1 cells. A marked decrease in IL-15 expression was observed at all concentrations of 5-aza compared to control (Figure 1B, p=0.0001). These results confirm that 5-aza leads to decreased transcription of the IL-15 gene, possibly due to hypomethylation of the IL-15 promoter. Finally, to determine whether a decrease in IL-15 alone was the cause of increased apoptosis of T-LGLL cells, we exposed MOTN-1 cells to a novel IL-15 inhibitor, IBI-15, and compared cell viability against MOTN-1 cells exposed to an inactive control, IBI-40. Even more profound decrease in cell viability was observed utilizing IBI-15 that targets the binding of IL-15 to its receptor (Figure 1C). Together, these data suggest that hypermethylation of the IL-15 promoter is critical to the pathogenesis of T-LGLL, and that treatment with 5-aza is sufficient to induce hypomethylation of the IL-15 promoter, decrease IL-15 transcription, and induce apoptosis in T-LGLL cells. Conclusions: Hypermethylation of the IL-15 promoter, with subsequent increase in IL-15, is critical to the pathogenesis of T-LGLL. Inhibition of the IL-15 promoter hypermethylation by 5-aza leads to down-regulation of the IL-15 gene transcript, which is sufficient to induce apoptosis of T-LGLL cells. These data suggest that 5-aza induced hypomethylation may be a novel method to induce IL-15 inhibition and a potentially efficacious clinical strategy against T-LGLL. Disclosures Brammer: Bioniz Therapeutics, Inc.: Research Funding; Viracta Therapeutics, Inc.: Research Funding; Verastem, Inc: Research Funding. Porcu:Daiichi: Research Funding; BeiGene: Other: Scientific Board, Research Funding; Spectrum: Consultancy; Viracta: Honoraria, Other: Scientific Board, Research Funding; Innate Pharma: Honoraria, Other: Scientific Board, Research Funding; Kyowa: Honoraria, Other: Scientific Board, Research Funding; ADCT: Research Funding; Incyte: Research Funding. OffLabel Disclosure: IBI-15 IBI-40 IL-15 inhibitor

Monilinia fructicola. [Distribution map].

2010 ◽  
Author(s):  
Keyword(s):  
South Carolina ◽  
Rhode Island ◽  
Prince Edward Island ◽  
Prunus Persica ◽  
New Caledonia ◽  
South Australia ◽  
Fruit Trees ◽  
Eriobotrya Japonica ◽  
Monilinia Fructicola ◽  
Distribution Map

Abstract A new distribution map is provided for Monilinia fructicola (G. Winter) Honey. Ascomycota: Helotiales. Hosts: Rosaceous stone fruit trees (Prunus, Malus, Pyrus spp.), especially peach (Prunus persica). Also grape (Vitis spp.), flowering quinces (Chaenomeles spp.), hawthorns (Crataegus spp.) and loquat (Eriobotrya japonica). Information is given on the geographical distribution in Europe (Austria, Czech Republic, France, Mainland France, Germany, Hungary, Italy, Mainland Italy, Spain, Mainland Spain, Switzerland, UK), Asia (China, Hebei, Shandong, India, Himachal Pradesh, Uttar Pradesh, Japan, Honshu, Korea Republic, Taiwan, Yemen), Africa (Nigeria, Zimbabwe), North America (Canada, Alberta, British Columbia, Manitoba, New Brunswick, Nova Scotia, Ontario, Prince Edward Island, Quebec, Saskatchewan, Mexico, USA, Alabama, Arizona, Arkansas, California, Connecticut, Delaware, District of Columbia, Florida, Georgia, Hawaii, Idaho, Illinois, Indiana, Iowa, Kansas, Kentucky, Louisiana, Maine, Maryland, Massachussetts, Michigan, Minnesota, Mississippi, Missouri, Montana, Nebraska, New Hampshire, New Jersey, New Mexico, New York, North Carolina, Ohio, Oklahoma, Oregon, Pennsylvania, Rhode Island, South Carolina, South Dakota, Tennessee, Texas, Vermont, Virginia, Washington, West Virginia, Wisconsin), Central America and Caribbean (Guatemala, Panama), South America (Argentina, Bolivia, Brazil, Minas Gerais, Parana, Rio Grande do Sul, Sao Paulo, Ecuador, Paraguay, Peru, Uruguay, Venezuela), Oceania (Australia, New South Wales, Queensland, South Australia, Tasmania, Victoria, Western Australia, New Caledonia, New Zealand).

Xylella fastidiosa. [Distribution map].

2006 ◽  
Author(s):  
Keyword(s):  
New York ◽  
South Carolina ◽  
Prunus Persica ◽  
Xylella Fastidiosa ◽  
Acer Rubrum ◽  
Prunus Dulcis ◽  
Wild Plants ◽  
Distribution Map ◽  
Ulmus Americana ◽  
Platanus Occidentalis

Abstract A new distribution map is provided for Xylella fastidiosa Wells et al. Bacteria. Hosts: Grapevine (Vitis vinifera and others), peach (Prunus persica), Citrus, almond (Prunus dulcis), lucerne (Medicago sativa), some wild trees (including Acer rubrum, Platanus occidentalis, Quercus rubra, Ulmus americana), other wild plants and weeds. Information is given on the geographical distribution in Europe (France, Italy), Asia (Taiwan), North America (Canada (Ontario), Mexico, USA (Alabama, Arizona, Arkansas, California, Delaware, District of Columbia, Florida, Georgia, Indiana, Kentucky, Louisiana, Maryland, Mississippi, Missouri, Montana, Nebraska, New Jersey, New Mexico, New York, North Carolina, Pennsylvania, South Carolina, Tennessee, Texas, Virginia, Washington, West Virginia)), Central America and Caribbean (Costa Rica), and South America (Argentina, Brazil (Bahia, Goias, Minas Gerais, Parana, Rio de Janeiro, Rio Grande do Sul, Santa Catarina, Sao Paulo, Sergipe), Paraguay, Venezuela).

scholarly journals Continuous salt stress-induced long non-coding RNAs and DNA methylation patterns in soybean roots

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Rui Chen ◽  
Ming Li ◽  
Huiyuan Zhang ◽  
Lijin Duan ◽  
Xianjun Sun ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Salt Stress ◽  
Bioinformatic Analysis ◽  
Protein Coding ◽  
Reduced Representation ◽  
Soybean Seedlings ◽  
A Genome ◽  
Whole Transcriptome Sequencing ◽  
Soybean Roots ◽  
Non Coding Rnas

Abstract Background Environmental stimuli can activate a series of physiological and biochemical responses in plants accompanied by extensive transcriptional reprogramming. Long non-coding RNAs (lncRNAs), as versatile regulators, control gene expression in multiple ways and participate in the adaptation to biotic and abiotic stresses. Results In this study, soybean seedlings were continuously cultured for 15 days with high salinity solutions started from seed germination. Strand-specific whole transcriptome sequencing and stringent bioinformatic analysis led to the identification of 3030 long intergenic non-coding RNAs (lincRNAs) and 275 natural antisense transcripts (lncNATs) in soybean roots. In contrast to mRNAs, newly identified lncRNAs exhibited less exons, similar AU content to UTRs, even distribution across the genome and low evolutionary conservation. Remarkably, more than 75% of discovered lncRNAs that were activated or up-regulated by continuous salt stress mainly targeted proteins with binding and catalytic activities. Furthermore, two DNA methylation maps with single-base resolution were generated by using reduced representation bisulfite sequencing, offering a genome-wide perspective and important clues for epigenetic regulation of stress-associated lncRNAs and protein-coding genes. Conclusions Taken together, our findings systematically demonstrated the characteristics of continuous salt stress-induced lncRNAs and extended the knowledge of corresponding methylation profiling, providing valuable evidence for a better understanding of how plants cope with long-term salt stress circumstances.

scholarly journals Characterization of Global DNA Methylation in Different Gene Regions Reveals Candidate Biomarkers in Pigs with High and Low Levels of Boar Taint

2020 ◽  
Vol 7 (2) ◽  
pp. 77 ◽  
Author(s):  
Xiao Wang ◽  
Haja N. Kadarmideen
Keyword(s):  
Dna Methylation ◽  
Cpg Island ◽  
Cpg Islands ◽  
Gene Interaction ◽  
Boar Taint ◽  
Reduced Representation ◽  
Gene Interaction Networks ◽  
Reduced Representation Bisulfite Sequencing ◽  
Pathways Analysis ◽  
Porcine Gene

DNA methylation of different gene components, including different exons and introns, or different lengths of exons and introns is associated with differences in gene expression. To investigate the methylation of porcine gene components associated with the boar taint (BT) trait, this study used reduced representation bisulfite sequencing (RRBS) data from nine porcine testis samples in three BT groups (low, medium and high BT). The results showed that the methylation levels of the first exons and first introns were lower than those of the other exons and introns. The first exons/introns of CpG island regions had even lower levels of methylation. A total of 123 differentially methylated promoters (DMPs), 194 differentially methylated exons (DMEs) and 402 differentially methylated introns (DMIs) were identified, of which 80 DMPs (DMP-CpGis), 112 DMEs (DME-CpGis) and 166 DMIs (DMI-CpGis) were discovered in CpG islands. Importantly, GPX1 contained one each of DMP, DME, DMI, DMP-CpGi, DME-CpGi and DMI-CpGi. Gene-GO term relationships and pathways analysis showed DMP-CpGi-related genes are mainly involved in methylation-related biological functions. In addition, gene–gene interaction networks consisted of nodes that were hypo-methylated GPX1, hypo-methylated APP, hypo-methylated ATOX1, hyper-methylated ADRB2, hyper-methylated RPS6KA1 and hyper-methylated PNMT. They could be used as candidate biomarkers for reducing boar taint in pigs, after further validation in large cohorts.

scholarly journals Identification and Characterization of Botryosphaeria spp. Causing Gummosis of Peach Trees in Hubei Province, Central China

Plant Disease ◽  
2011 ◽  
Vol 95 (11) ◽  
pp. 1378-1384 ◽  
Author(s):  
Fan Wang ◽  
Lina Zhao ◽  
Guohuai Li ◽  
Junbin Huang ◽  
Tom Hsiang
Keyword(s):  
Prunus Persica ◽  
Elongation Factor ◽  
Fruit Trees ◽  
Hubei Province ◽  
Central China ◽  
Internal Transcribed Spacer Region ◽  
Fusicoccum Aesculi ◽  
Peach Trees ◽  
Production Areas ◽  
Genomic Regions

Peach (Prunus persica) is one of the most important and widely grown fruit trees in China; however, perennial gummosis on trunks and branches is a major problem in peach orchards of Hubei Province, one of the most important peach production areas of China. In order to identify the gummosis-causing agents, diseased trunks and branches were collected from 11 peach orchards in Hubei Province. Fungal isolates were obtained from these samples, yielding three species: Botryosphaeria dothidea (anamorph Fusicoccum aesculi), B. rhodina (anamorph Lasiodiplodia theobromae), and B. obtusa (anamorph Diplodia seriata). They were identified based on conidial morphology and cultural characteristics, as well as analyses of nucleotide sequences of three genomic regions: the internal transcribed spacer region, a partial sequence of the β-tubulin gene, and the translation elongation factor 1-α gene. Fusicoccum aesculi was found in all 11 orchards but L. theobromae was found only in Shayang County in the Jingmen region and D. seriata only in Gong'an County in the Jingzhou region. Via artificial inoculation using mycelia on wounded twigs or branches, these three species were all found to be pathogenic, causing dark lesions on the twigs and branches and, sometimes, gum exudation from diseased parts. Isolates of L. theobromae were the most virulent and caused the largest lesions and most copious gummosis, and D. seriata had less gum than the other two species. This report represents the first description of L. theobromae and D. seriata as causal agents of gummosis on peach in China.

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