Project description:In this work, we have used deep sequencing to study the viral small RNA (vsiRNA) populations from different mycoviruses infecting field isolates of Botrytis spp. The mycoviruses under study belong to different genera and species and have different type of genome (dsRNA, (+)ssRNA, and (-)ssRNA). In general, vsiRNAs derived from mycoviruses are mostly of 21, 20 and 22 nucleotides in length, possess sense or antisense orientation either in a similar ratio or with a predominance of sense polarity depending on the virus species, have predominantly U at their 5' end, and are unevenly distributed along the viral genome showing conspicuous hotspots of vsiRNA accumulation. These characteristics reveal striking concomitances with vsiRNAs produced by plant viruses suggesting similar pathways of viral targeting in plants and fungi
Project description:The Xenopus genus is well known for the high degree of polyploidy observed in its constituent species, but there is minimal information about transcriptional changes observed in these highly polyploid vertebrates. Xenopus andrei, an octoploid species within the Xenopus genus, presents a novel system for assessing a polyploid transcriptome during vertebrate development. RNA-Seq data was generated at nine different developmental stages ranging from unfertilized eggs through late tailbud stages. Additionally, using Trinity, RNA-seq data from all nine stages was pooled to create a draft de novo assembly of the transcriptome. This represents the first published assembly of an octoploid vertebrate transcriptome. This RNA-Seq and transcriptome data will be useful in comparing polyploid transcriptomes across Xenopus species, as well as understanding evolutionary implications of whole-genome duplication in vertebrates.
Project description:Tricoderma genus fungi are referred to as "biostimulants" because they promote plant development and provide disease resistance. In this study, utilizing a conventional transcriptome analysis and gene co-expression network analysis after conventionally stimulating Arabidopsis thaliana with Trichoderma atroviride or Trichoderma virens. We found by differential expression and functional enrichment analyses that the transcriptome analysis of the plant during interactions, T. atroviride and T. virens, were involved in the reduction of reactive oxygen species, defense mechanisms against pathogens, and hormone signaling pathways. T. virens, as opposed to T. atroviride, was more effective at downregulating genes related to terpenoid metabolism, root development, and chemical homeostasis. We were able to find functional gene modules through network analysis that closely link plant defense mechanisms with hypoxia mechanisms. We discovered a transcription factor (locus AT2G47520) with two functional domains of interest: a DNA-binding domain and an N-terminal cysteine needed for protein stability under hypoxia. We discovered that the transcription factor can bind to the promoter sequence of the GCC-box gene that is connected to pathogenesis by positioned weight matrix analysis.
Project description:Ectomycorrhizal (ECM) fungi are crucial for tree nitrogen (N) nutrition, however, mechanisms governing N transfer from fungal tissues to the host plant are not well understood. ECM fungal isolates, even from the same species, vary considerably in their ability to support tree N nutrition resulting in a range of often unpredictable symbiotic outcomes. In this study, we used isotopic labelling to quantify the transfer of N to the plant host by isolates from the ECM genus Pisolithus known to have significant variability in colonisation and transfer of nutrients to a host. We considered the metabolic fate of N acquired by the fungi and found that the percentage of plant N acquired through symbiosis significantly correlated to the concentration of free amino acids present in the ECM extra-radical mycelium. Transcriptomic analyses complemented these findings with isolates having high amino acid content and N transfer showing increased expression of genes in amino acid transport and catabolic pathways. These results suggest that fungal N metabolism drives transfer to the host plant in this interaction and that relative N transfer may be possible to predict through basic biochemical analyses.
Project description:We present the de novo transcriptome sequencing, analysis and microarray development for a vertebrate herbivore, the woodrat (Neotoma spp.). This genus is of ecological and evolutionary interest, especially with respect to ingestion and hepatic metabolism of potentially toxic plant secondary compounds. We generated a liver transcriptome of the desert woodrat (Neotoma lepida) with the Roche 454 platform. The assembled contigs were well annotated using rodent references (99.7% annotation), and biotransformation function was reflected in the gene ontology. The transcriptome was used to develop a custom microarray (eArray, Agilent). To compare the effect of native diet/habitat and phylogenetic similarity, we performed 3 experiments with the Neotoma probes only: one across species with similar habitat niches (N. lepida versus N. bryanti, Palm Springs), one across species with different habitat niches (N. lepida versus N. bryanti, Caspers Wilderness), and one across populations within a species (N. bryant Palm Springs versus Caspers Wilderness). The resulting one-color arrays had high technical and biological quality. Probes designed from the woodrat transcriptome performed significantly better than functionally similar probes from the Norway rat (Rattus norvegicus). Biotransformation processes and functions were highly represented in the results. Comparisons between ecologically similar woodrat species revealed fewer gene expression differences than ecologically different woodrat species. The conspecific comparison had overall fewest differences.
Project description:A computational metabolomics approach delineates main trends in the diversification of specialized metabolism in the genus Nicotiana.
Samples of 20 different Nicotiana species from the tissues leaf, induced leaf, exudate, roots and calyx.
Project description:We present the de novo transcriptome sequencing, analysis and microarray development for a vertebrate herbivore, the woodrat (Neotoma spp.). This genus is of ecological and evolutionary interest, especially with respect to ingestion and hepatic metabolism of potentially toxic plant secondary compounds. We generated a liver transcriptome of the desert woodrat (Neotoma lepida) with the Roche 454 platform. The assembled contigs were well annotated using rodent references (99.7% annotation), and biotransformation function was reflected in the gene ontology. The transcriptome was used to develop a custom microarray (eArray, Agilent). To compare the effect of native diet/habitat and phylogenetic similarity, we performed 3 experiments with the Neotoma probes only: one across species with similar habitat niches (N. lepida versus N. bryanti, Palm Springs), one across species with different habitat niches (N. lepida versus N. bryanti, Caspers Wilderness), and one across populations within a species (N. bryant Palm Springs versus Caspers Wilderness). The resulting one-color arrays had high technical and biological quality. Probes designed from the woodrat transcriptome performed significantly better than functionally similar probes from the Norway rat (Rattus norvegicus). Biotransformation processes and functions were highly represented in the results. Comparisons between ecologically similar woodrat species revealed fewer gene expression differences than ecologically different woodrat species. The conspecific comparison had overall fewest differences. Gene expression was compared across 3 groups of woodrats: Neotoma lepida (n=4), N. bryanti Palm Springs (n=4), and N. bryanti Caspers Wilderness (n=4). Animals were fed a rabbit chow diet, called control; intake was monitored over 10 days, after which RNA was extracted from hepatic tissue. One-color arrays were performed.
Project description:Arbuscular mycorrhiza (AM) interactions between plants and Glomeromycota fungi primarily support phosphate aquisition of most terrestrial plant species. To unravel gene expression in Medicago truncatula root colonization by AM fungi, we used genome-wide transcriptome profiling based on whole mycorrhizal roots. We used GeneChips to detail the global programme of gene expression in response to colonization by arbuscular mycorrhizal fungi and in response to a treatment with phosphate and identified genes differentially expressed during this process. Medicago truncatula roots were harvested at 28 days post inoculation with the two different arbuscular mycorrhizal fungi Glomus intraradices (Gi-Myc) and Glomus mosseae (Gm-Myc) under low phosphate conditions (20 µM phosphate) or after a 28 days treatment with 2 mM phosphate in the absence of arbuscular mycorrhizal fungi (2mM-P). As a control, uninfected roots grown under low phosphate conditions (20 µM phosphate) were used (20miM-P). Three biological replicates consisting of pools of five roots were used for RNA extraction and hybridization on Affymetrix GeneChips.