Project description:Plants adjust their growth in response to environmental cues by forming new organs in different development contexts. Underground lateral roots initiate from prepatterned cells in the main root, but cells can also bypass the root/shoot trajectory separation and generate shoot-borne-roots through an unknown mechanism. Here, we mapped tomato (Solanum lycoperiscum) shoot-borne-roots development at single-cell resolution and show that they initiate from differentiated phloem-associated cells via a unique transitional stem-cell-like state. This state required the activity of a transcription factor which we named SHOOTBORNE ROOTLESS (SBRL), a function that was deeply conserved in angiosperms. Phylogenetic analysis revealed that SBRL arose in angiosperms as an ancient duplicated superlocus with its paralogs showing root-type-specific transient expression in wound-induced and lateral root initiation. Mutants in all SBRL-like genes completely lost post-embryonic roots. We propose that the activation of a common transition state by context-specific regulators underlies the plasticity of plant root systems.
Project description:We used Ribo-seq (Ribosome profiling) combining with RNA-seq to explore the translational landscape of tomato roots. We generated three biological replicates of RNA-seq and Ribo-seq data for tomato roots. We next used the RNA-seq result for de novo transcriptome assembly and Ribo-seq to identify novel translated open reading frames (ORFs). Our data revealed more than three hundreds of novel translated ORFs on previously unannotated transcripts. Most of the newly identified ORFs are small and difficult to detect with in silico methods. We also identified over thirteen hundreds of upstream ORFs on annotated genes. This data could facilitate gene annotation. Besides, this data also demonstrated that uORFs, miRNAs and antisense RNAs are regulating the expression of associated genes. This study uncovered mechanisms of translational regulation and gene annotation in tomato.
Project description:Arbuscular mycorrhizal symbiosis is a predominant relationship between plant and arbuscular mycorrhizal fungi. To idendify arbuscular mycorrhiza responsive miRNAs, small RNA libraries were constructed in tomato roots colonized with Rhizophagus irregularis and without Rhizophagus irregularis. We identify miRNAs in tomato roots and provide a new profile of tomato miRNAs. And we found that some miRNAs were responsive to arbuscular mycorrhiza by comparing miRNAs in treatment with that in control.
Project description:Arbuscular mycorrhizal symbiosis is a predominant relationship between plant and arbuscular mycorrhizal fungi. To idendify arbuscular mycorrhiza responsive miRNAs, small RNA libraries were constructed in tomato roots colonized with Rhizophagus irregularis and without Rhizophagus irregularis. We identify miRNAs in tomato roots and provide a new profile of tomato miRNAs. And we found that some miRNAs were responsive to arbuscular mycorrhiza by comparing miRNAs in treatment with that in control. Examination of arbuscular mycorrhiza responsive miRNAs in tomato through high-throughput small RNA sequencing of roots with Rhizophagus irregularis and that without Rhizophagus irregularis
Project description:Iron (Fe) deficiency is a yield-limiting factor for a variety of field crops across the world and generally results from the interaction of limited soil Fe bioavailability and susceptible genotype cultivation. Tomato, a Strategy I, model plant for Fe deficiency, is an important economical crop. Tomato responses in order to improve Fe uptake are based on acidification of rhizosphere, reduction of Fe3+ to Fe2+ and transport of Fe2+ into the cells. Transcriptional profile obtained by roots (27-d) of 21-d-old tomato plants starved of iron for an additional week was compared with the transcriptional profile obtained for roots (27-d) of 21-d-old tomato plants grown for an additional week at 100 M-NM-<M Fe. Tomato plants were hydroponically grown in both cases. Three different biological replicates were used for each sample repeating the experiment three times. All samples were obtained pooling roots of six plants (27-d-old).
Project description:To investigate the transcriptional changes induced by the fer mutant in tomato roots, roots from 3-week-old seedlings of fer, cultivated in 1/2 Hoagland’s nutrient solution, along with their respective wild-type control groups, were harvested. RNA-seq analysis was conducted with three biological replicates using the TruSeq RNA Sample Prep Kit.
Project description:Jasmonic acid (JA) is a fatty-acid derived signaling molecule that regulates a wide variety of plant developmental and stress-related responses. We identified a jasmonate-insensitive1 (jai1) mutant of tomato that is defective in the LeCOI1 gene, which plays an essential role in induced resistance of tomato to a broad spectrum of pests, and is also required for maternal control of seed and fruit development. The present study is aimed at identifying genes involved in two JA-signaled processes that have not been studied in other plants. The first specific aim is to identify the set of JA/COI1-regulated genes in tomato reproductive tissues, with emphasis on genes expressed in maternal tissues. We hypothesize that JA/COI1 signaling regulates maternal processes that nurture the developing embryo and seed. The second aim of the study is to identify JA/COI1-regulated genes that are specifically expressed in tomato roots. Although it has been shown that JA promotes root defenses against various pests, virtually nothing is known about the JA-regulated transcriptome in roots. Tomato (Solanum lycopersicum) cv Micro-Tom wild-type and jai1 seed were grown in peat pots and maintained in growth chambers. To identify COI1-regulated genes in reproductive tissues, flower buds, open flowers and immature fruit at 7 and 17 days post-pollination were collected from 8 to 10 week old plants. To identify COI1-regulated genes in roots, 3 week old plants were exposed to exogenous JA by a single soil drench with 0.1mM JA, and roots were collected after 1, 6, 12 and 24 hours. Plants treated with water were used for the 0hr time point. All tissue was snap-frozen in liquid nitrogen, and RNA was extracted and analyzed as described in the TIGR Potato Microarray protocol (phenol method). Three biological replicates were collected for this study. Keywords: Direct comparison