Project description:This research uses terminal branches from a wild poplar tree to track somatic genetic, epigenetic, and transcriptional changes. Using a multi-omics approach, we aim to identify and describe mutations which arise during the lifetime of a long-lived perennial plant.
Project description:TA inhibits cellulose synthesis but its actual mode of action is unknown. Addition of TA to hybrid poplar (Populus trichocarpa x Populus deltoides) cell suspensions can activate a cellular program leading to cell death. In contrast, it is possible to habituate hybrid poplar cell cultures to grow in the presence of TA levels that would normally induce cell death. This habituation was performed by adding increasing levels of TA to cell cultures at the time of subculture over a period of 12 months. TA-habituated cells were then cultured in the absence of TA for more than 18 months. These cells displayed a reduced size and growth compared to control cells and had fragmented vacuoles filled with electron-dense material. Habituation to TA was associated with changes in the cell wall composition, with a reduction in cellulose and an increase in pectin levels. Remarkably, high level of resistance to TA was maintained in TA-habituated cells even after being cultured in the absence of TA. Moreover, these cells exhibited enhanced resistance to two other inhibitors of cellulose biosynthesis, dichlobenil and isoxaben. Analysis of gene expression in TA-habituated cells using Affymetrix GeneChip Poplar Genome Array revealed that durable resistance to TA is associated with a major and complex reprogramming of gene expression implicating processes such as cell wall synthesis and modification, lignin and flavonoid synthesis, as well as DNA and chromatin modifications. Experiment Overall Design: Each sample was taken from an individual flask of control cells or TA-habituated resistant cells grown without the toxin for 18 months (TA(-)hab cells) that had grown for 5 d after subculture. Six arrays were hybridized, representing 3 arrays per cell type.
Project description:This research uses terminal branches from a wild poplar tree to track somatic genetic, epigenetic, and transcriptional changes. Using a multi-omics approach, we aim to identify and describe mutations which arise during the lifetime of a long-lived perennial plant.
Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Populus trichocarpa tissues (including leaves, xylem and mechanically-treated xylem). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.
Project description:To obtain genes expression in different parts of 84k poplar stems, transcriptome sequencing was performed using Illumina Novaseq 6000 second-generation sequencing platform from Shanghai BIOZERON Co. Ltd (www.biozeron.com). Selecte three stem segments of plants REPEAT 1, 2 and 3 with good and similar growth to use: 2nd-3rd internodes (poplar stem top: PST1, PST2, PST3); 9th-10th internodes (poplar stem middle: PSM1, PSM2, PSM3); 14th-15th internodes (poplar stem bottom: PSB1, PSB2, PSB3). [Or the three repeating organisms are also called poplar A, B, C. From top to bottom, the three parts of the stem are also called stem 1, 2, 3.]
Project description:This research uses terminal branches from a wild poplar tree to track somatic genetic, epigenetic, and transcriptional changes. Using a multi-omics approach, we aim to identify and describe mutations which arise during the lifetime of a long-lived perennial plant.
