ABSTRACT: RNA-seq of lime (Citrus aurantifolia) using long-read sequencing under ethylene and abscisic acid treatments. Transcriptomic analyses were carried out on the leaves of lime plants to determine the expression of genes involved lime plants were induced by plant growth regulators, namely ethylene and abscisic acid.
Project description:Background: Witches’ broom disease of Mexican lime (Citrus aurantifolia L.), which is caused by the phytoplasma “Candidatus Phytoplasma aurantifolia”, is a devastating disease that results in significant economic losses. Plants adapt to abiotic stresses by regulating gene expression at the transcriptional and post-transcriptional levels. MicroRNAs (miRNAs) are a recently identified family of molecules that regulate plant responses to environmental stresses through post-transcriptional gene silencing. Methods: Using a high-throughput approach to sequence small RNAs, we compared the expression profiles of miRNAs in healthy Mexican lime trees and in plants infected with “Ca. Phytoplasma aurantifolia”. Results: Our results demonstrated the involvement of different miRNAs in the response of Mexican lime trees to infection by “Ca. Phytoplasma aurantifolia”. We identified miRNA families that are expressed differentially upon infection with phytoplasmas. Most of the miRNAs had variants with small sequence variations (isomiRs), which are expressed differentially in response to pathogen infection. Conclusions: It is likely that the miRNAs that are expressed differentially in healthy and phytoplasma-infected Mexican lime trees are involved in coordinating the regulation of hormonal, nutritional, and stress signalling pathways, and the complex interactions between them. Future research to elucidate the roles of these miRNAs should improve our understanding of the level of diversity of specific plant responses to phytoplasmas.
Project description:Background: WitchesM-bM-^@M-^Y broom disease of Mexican lime (Citrus aurantifolia L.), which is caused by the phytoplasma M-bM-^@M-^\Candidatus Phytoplasma aurantifoliaM-bM-^@M-^], is a devastating disease that results in significant economic losses. Plants adapt to abiotic stresses by regulating gene expression at the transcriptional and post-transcriptional levels. MicroRNAs (miRNAs) are a recently identified family of molecules that regulate plant responses to environmental stresses through post-transcriptional gene silencing. Methods: Using a high-throughput approach to sequence small RNAs, we compared the expression profiles of miRNAs in healthy Mexican lime trees and in plants infected with M-bM-^@M-^\Ca. Phytoplasma aurantifoliaM-bM-^@M-^]. Results: Our results demonstrated the involvement of different miRNAs in the response of Mexican lime trees to infection by M-bM-^@M-^\Ca. Phytoplasma aurantifoliaM-bM-^@M-^]. We identified miRNA families that are expressed differentially upon infection with phytoplasmas. Most of the miRNAs had variants with small sequence variations (isomiRs), which are expressed differentially in response to pathogen infection. Conclusions: It is likely that the miRNAs that are expressed differentially in healthy and phytoplasma-infected Mexican lime trees are involved in coordinating the regulation of hormonal, nutritional, and stress signalling pathways, and the complex interactions between them. Future research to elucidate the roles of these miRNAs should improve our understanding of the level of diversity of specific plant responses to phytoplasmas. Small mRNA profiles of healthy (H) and Phytoplasma-infected Mexican lime trees were generated by deep sequencing, six replicate, using Illumina Hiseq2000
Project description:The transcriptional response of the Mexican Lime to two different isolates of the Citrus Tristeza Virus was evaluated. Virus Isolates were T305, which provokes severe symptoms in Lime plants, and isolate T385 which does not result in any visible symptoms. Five Lime plants were inoculated with each virus isolate, and four healthy plants were used to create a pooled control. Citrus custom arrays were hybridized with an infected sample and the pooled control, using a dyeswap design. In total, the experiment comprised hybridizations with twenty microarrays, ten for each virus isolate, including five biological replicates, each technically duplicated by dye-swapping.
Project description:Being a sessile organism, plants are constantly confronted by various biotic (pest and pathogen) and abiotic (drought, salinity, flood, extreme temperatures, etc.) stresses. In response to these environmental stresses, plants have developed numerous defense mechanisms. One of the basal defense responses in plants are mediated by trypsin inhibitors (TIs). Putranjiva roxburghii trypsin inhibitor (PRTI), a potent trypsin inhibitor from P. roxburghii showing sequence similarity with a group of genes known to have defense and storage function such as wound inducible (WIN) proteins, vegetative storage proteins (VSPs), and Bark storage protein (BSPs) was overexpressed in Citrus aurantifolia. PRTI overexpressing lines were tolerant to various abiotic stresses (salinity, drought, and alkalinity) and two pests namely, Scirtothrips citri and Papilio demoleus. The molecular insights underlying the heterologous overexpression of PRTI at the transcriptomic level reveals the upregulation of stress responsive genes and involvement of hormonal signal transduction and transporters. Further, genes related to DNA repair, amino acid synthesis, and development were also found to be upregulated. Our study also reveals the nuclear-cytoplasmic localization and alteration phytohormone profile by PRTI overexpression in transgenic lines as compared to wild-type which clearly indicates the role of abscisic acid ABA in stress tolerance.
Project description:We developed and performed LIMe-ID to simultaneously measure lamina association and DNA methylation in one experimental workflow. We then conducted LIMe-ID following perturbations of PRC2 to better understand the influence of H3K27me3 on lamina association.
Project description:Phytohormones are involved in diverse aspects of plant life including the regulation of plant growth, development and reproduction, as well as governing stress and defence responses. We have generated a comprehensive transcriptional reference map of the early potato responses to exogenous application of the defence hormones abscisic acid, brassinosteroid, ethylene, salicylic acid and jasmonic acid. Amongst microarray probes representing the 39000 predicted genes, a total of 3175 and 2873 probes were significantly differentially expressed at 1 h and 6 h after hormone treatment, respectively. Marker genes identified for the early hormone responses in potato include: a homeodomain 20 transcription factor (DMG400000248) for abscisic acid; a SAUR gene (DMG400016561) induced in Epibrassinolide treated plants at 6 hours; an osmotin gene (DMG400003057) specifically enhanced by the ethylene precursor aminocyclopropanecarboxylic acid; a gene weakly similar to AtWRKY40 (DMG402007388) that was induced by salicylic acid and; a jasmonate ZIM-domain protein 1 (DMG400002930) which was specifically activated by methyl jasmonate. An online database has been set up to query the expression patterns of potato genes represented on the microarray that can also incorporate future microarray or RNAseq-based expression studies.
Project description:We developed and performed LIMe-Hi-C in order to assess lamina association, DNA methylation, and chromosome conformation in one experimental workflow. We combined LIMe-Hi-C with chemcial inhibition of EZH2 and DNMT1 to better understand the influence of H3K27me3 and DNA methylation on 3D genome organization.
Project description:Using RNA-seq, we recently investigated the transcriptomic dynamics of rose flower under treatment of various plant hormones, including ethylene, 2,4-D, NAA, cytok, gibberellins, abscisic acid, brassinosteroids, salicylic acid, jasmonates, as well as ethylene inhibitor 1-MCP and AgNO. We obtained approximately 240GB data and dissected the transcriptional network with the aim of exploring the transcriptional variation of rose responses towards those plant hormones. Our data will be useful to all those working with the analysis of rose gene expression.