Project description:Comparison of the endogenous small RNA content of tomato leaves and fruits. Size fractionated small RNA from total RNA extracts was ligated to adapters, purified again and reverse transcribed. After PCR amplification the sample was subjected to 454 high throughput pyrosequencing. Please see www.454.com for details of the sequencing technology. Note: Raw data files were not available from 454 at the time this experiment was carried out.
Project description:Comparison of endogenous small RNA profiles from different developmental stages of tomato fruits Size fractionated small RNA from total RNA extracts was ligated to adaptors, purified again and reverse transcribed. After PCR amplification the sample was subjected to Solexa/Illumina high throughput pyrosequencing. Please see www.illumina.com for details of the sequencing technology.
Project description:To provide insights into how SUN regulates shape and whether this is accompanied with shifts in transcript profiles, we identified differentially expressed genes in eight pairwise comparisons of SUN and wild-type fruit tissues and time points. Lines nearly isogenic for SUN in the cultivated background Solanum lycopersicum c.v. SUN1642 were grown in the greenhouse in a completely randomized design. SA4 is like SUN1642 and SA3 is like WT LA1589 at SUN locus. Flowers at anthesis were tagged and self-pollinated on successive days. Anthesis is defined as when the flower opens. Pollination of flowers was staggered so fruit of all developmental stages would be harvested on the same day. Fruits at stage four, seven, and ten days post anthesis (dpa) were harvested and brought back to the laboratory. Septum, seed, and pericarp tissue were isolated and frozen in liquid nitrogen. Four dpa septum tissues is a mixture of septum and seed tissue. Four dpa pericarp is a mixture of pericarp and exocarp tissue due to small size of four dpa fruits. Seven and 10 dpa pericarp dont contain the exocarp (epidermal) tissues. Four replicates were collected. RNA was extracted using Trizol and Stand-specific libraries were prepared from total RNA and sequences of 51 bp were generated on an Illumina HiSeq2000.
Project description:RNA sequencing in tomato for detect mRNA expression of Solanum lycopersicum flower.The two cultivars (monomaker, raceme) had three different flowering stages (budlet, Flower bud, Full bloom) for transcriptome sequencing
Project description:RKNs are economically most damaging, obligate sedentary endoparasites that form giant cells within host roots to obtain nutrition and complete their life cycle. We report genome-wide identification of miRNAs from both host and RKN using RKN-infected susceptible tomato roots through high-throughput sequencing. Eleven small RNA libraries were made from five disease development stages, their five corresponding uninfected development stages and uninfected development stage 0. A total of 52 conserved miRNAs, 4 variants of conserved miRNAs and 281 novel miRNAs of host were identified. A significantly upregulated expression of majority of the miRNAs was observed during susceptible response and downregulated expression during resistance response through qRT-PCR. The miRNA targets were predicted and validated through 5’RLM-RACE. Furthermore, correlation between the expression profile of selected conserved miRNAs viz., miR164, miR156, miR396, miR159, and novel Sly_miRNA996 with their target transcription factors viz., NAC, SBP, GRF1, GAMYB-like, and MYB-like, respectively was also determined. This study suggests a potential role of host miRNAs in regulating transcription factor genes involved in plant developmental processes and defense responses during RKN infection. Additionally, 328 RKN miRNAs including 38 conserved miRNAs, 106 novel miRNAs, and 184 candidate novel miRNAs were identified from same dataset. The differential expression of conserved and RKN-specific miRNAs at different development stages of nematode in tomato roots suggests their probable role during nematode development and adaptation to parasitic behavior. This is the most comprehensive study reporting the identification and characterization of miRNAs from both tomato and RKN in five different disease development stages under soil grown conditions and their potential roles during RKN infection in tomato roots.