Comparative Metabolomics of Early Development of the Parasitic Plants Phelipanche aegyptiaca and Triphysaria versicolor.

Parasitic weeds of the family Orobanchaceae attach to the roots of host plants via haustoria capable of drawing nutrients from host vascular tissue. The connection of the haustorium to the host marks a shift in parasite metabolism from autotrophy to at least partial heterotrophy, depending on the level of parasite dependence. Species within the family Orobanchaceae span the spectrum of host nutrient dependency, yet the diversity of parasitic plant metabolism remains poorly understood, particularly during the key metabolic shift surrounding haustorial attachment. Comparative profiling of major metabolites in the obligate holoparasite Phelipanche aegyptiaca and the facultative hemiparasite Triphysaria versicolor before and after attachment to the hosts revealed several metabolic shifts implicating remodeling of energy and amino acid metabolism. After attachment, both parasites showed metabolite profiles that were different from their respective hosts. In P. aegyptiaca, prominent changes in metabolite profiles were also associated with transitioning between different tissue types before and after attachment, with aspartate levels increasing significantly after the attachment. Based on the results from 15N labeling experiments, asparagine and/or aspartate-rich proteins were enriched in host-derived nitrogen in T. versicolor. These results point to the importance of aspartate and/or asparagine in the early stages of attachment in these plant parasites and provide a rationale for targeting aspartate-family amino acid biosynthesis for disrupting the growth of parasitic weeds

Transcriptome-wide functional characterization reveals novel relationships among differentially expressed transcripts in developing soybean embryos

Sense and antisense transcripts and primers chosen for validation of RNA-Seq-based expression level changes. Sense and antisense transcripts are shown with the corresponding annotation, primer pairs used for qPCR, time points of differential expression, and notes on the presence of additional melt curve peaks. (PPTX 39 kb

Homogentisate Phytyltransferase Activity Is Limiting for Tocopherol Biosynthesis in Arabidopsis

Tocopherols are essential components of the human diet and are synthesized exclusively by photosynthetic organisms. These lipophilic antioxidants consist of a chromanol ring and a 15-carbon tail derived from homogentisate (HGA) and phytyl diphosphate, respectively. Condensation of HGA and phytyl diphosphate, the committed step in tocopherol biosynthesis, is catalyzed by HGA phytyltransferase (HPT). To investigate whether HPT activity is limiting for tocopherol synthesis in plants, the gene encoding Arabidopsis HPT, HPT1, was constitutively overexpressed in Arabidopsis. In leaves, HPT1 overexpression resulted in a 10-fold increase in HPT specific activity and a 4.4-fold increase in total tocopherol content relative to wild type. In seeds, HPT1 overexpression resulted in a 4-fold increase in HPT specific activity and a total seed tocopherol content that was 40% higher than wild type, primarily because of an increase in γ-tocopherol content. This enlarged pool of γ-tocopherol was almost entirely converted to α-tocopherol by crossing HPT1 overexpressing plants with lines constitutively overexpressing γ-tocopherol methyltransferase. Seed of the resulting double overexpressing lines had a 12-fold increase in vitamin E activity relative to wild type. These results indicate that HPT activity is limiting in various Arabidopsis tissues and that total tocopherol levels and vitamin E activity can be elevated in leaves and seeds by combined overexpression of the HPT1 and γ-tocopherol methyltransferase genes

Additional file 3: Figure S2. of CoSpliceNet: a framework for co-splicing network inference from transcriptomics data

The k-means clusters. The set of 7960 differentially expressed transcripts was clustered into 50 clusters using k-means algorithm. (PDF 1583 kb

Additional file 19: Figure S4. of CoSpliceNet: a framework for co-splicing network inference from transcriptomics data

Step-by-step bioinformatics pipeline for co-splicing network construction from expression data (PDF 102 kb

Additional file 1: Figure S1. of CoSpliceNet: a framework for co-splicing network inference from transcriptomics data

Protein diversity analysis of the set of differentially expressed transcripts expressed during Arabidopsis embryo development. Two thousand three hundred forty-five genes were alternatively spliced. Protein diversity analysis was performed on 3008 SV pairs of these genes. a Effect of coding potential on peptide length differences of protein isoforms. b Relationship between the domain composition and coding potential. c Relationship between the peptide length ratio and coding potential. (PDF 130 kb

Additional file 12: Table S9. of CoSpliceNet: a framework for co-splicing network inference from transcriptomics data

Enriched motifs in R regions of targets of each RBP. The motifs are shown as regular expressions from the MEME analysis. (XLSX 50 kb