Project description:In this study, we used the illumina high throughput sequencing approach (Sequencing-By-Synthesis, or SBS) to develop the sequence resource of black pepper. To identify micro RNAs functioning in stress response of the black pepper plant, small RNA libraries were prepared from the leaf and root of Phytophthora capsici infected plants, leaves from drought stressed and control plants.
Project description:The experiments were performed to elucidate the enigmatic enzymatic formation of the pungent principle, piperine, from black pepper (Piper nigrum L.), the world´s most popular spice. Based a differential RNA-Seq approach including immature fruits, flowers, and leaves, the gene encoding piperine synthase, encoding a BAHD-type acyltransferase and several other candidate genes encoding various enzymatic functions in the biosynthetic pathway were identified. Recombinant piperine synthase and additional promiscuous piperamide synthases were used to facilitate the microbial production of a broad range of medicinally relevant piperamides. Subsequent investigations will also include the identification of enzymatic steps in the phenylpropanoid pathway and the amino acid derived biosynthesis of piperidine Based on the assumption that piperine encoding genes are highly expressed shortly before the slope of piperine accumulation reaches its maximum, RNA from greenhouse grown black pepper plants was extracted from young fruits at two different stages of development, flowers, and leaves were harvested for a differential RNA-Seq approach. Candidate transcripts associated with piperine biosynthesis were identified by comparative transcript abundance and sequence annotation tools.
Project description:Genome-wide analysis of skin color-related lncRNA and mRNA expression in Koi carp, Cyprinus carpio L. LncRNAs information linked to fish skin color regulation is over-limited. In this study, Illumina sequencing and bioinformatics were primarily conducted on black, white and red skin colors of Koi carp. A total of 590,415,050 clean reads, 446,614 putative transcripts, 4,252 known and 72,907 novel lncRNAs were simultaneously obtained, respectively. Out of these genes, 92 significant differentially expressed lncRNAs and 722 mRNAs were excavated. Ccr_lnc5622441, Ccr_lnc765201 were found up-regulated in black and red skins; Ccr_lnc14074601 were up-regulated in white skin; and premelanosome proteins a (Pmela), tyrosinase (Tyr) were up-regulated in black skin, etc. Quantitative real-time PCR (qRT-PCR) further validated 12 differentially expressed genes were consistent with RNA-seq. Moreover, 70 lncRNAs on 107 target mRNAs in cis and 79 lncRNAs on 41,625 target mRNAs in trans were investigated, the networks revealed one lncRNAs can connected with numerous mRNAs, vice versa. These findings broadened the lncRNAs landscape of skin colors and provided new insights into the mechanisms underlying lncRNAs mediated pigmentation and differentiation in Koi carp.
Project description:In this study, we have evaluated the proteomic changes that occur in Piper nigrum L.(black pepper) after infection by the pathogen Phytophthora capsici. We report novel leaf proteins from black pepper identified by an integrated transcriptome-assisted label-free quantitative proteomics pipeline. Several previously described methods were used to create this data set. Detached leaves were inoculated with either mock treatment, or the oomycete pathogen and small tissue samples only around the site of inoculation were collected for protein sample preparations. In order to quantify protein abundance in the samples being compared, we used a label free method of spiking samples with a known ratio of pre-digested peptide samples to normalize endogenous protein abundance in the MS detection. Our study attempts to explain the basal immune components of black pepper when challenged with P. capsici.
Project description:Chinese cordyceps is of particular interest for its confined distribution, mysterious lifecycle, ecological importance and developmental biology. The large scale artificial cultivation of this fungus has been succeeded in China until recently but with low efficiency and high cost being ascribed to too much unsolved biological issues, such as gene expression during development and the sexuality reproduction. The success of artificial cultivation provides the convenient for sampling during the different development stages.
Project description:Using the HiSeqTM 2000 sequencing platform, the anther transcriptome of photo thermo sensitive genic male sterile lines (PTGMS) rice Y58S and P64S (Peiâai 64S) were analyzed at the fertility sensitive stage under cold stress.These datas would be most beneficial for further studies investigating the molecular mechanisms of rice responses to cold stress.
Project description:In order to shed light on the DNA methylation pathway mediating Pi starvation-induced changes in DNA methylation, the phosphate starvation experiment was repeated using an RNAi line that knocks DCL3a, a key factor involved in the canonical RdDM pathway.
Project description:We performed RNA-Seq of P. trichocarpa calluses that were firstly induced from roots. Then the total RNAs were isolated from the control and salt-stressed calluses (200 mM NaCl for 6, 12, 24, and 48 h) using a CTAB procedure. Note: All samples in SRA were assigned the same sample accession (SRS938530). This is incorrect as there are different samples, hence âSource Nameâ was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.
Project description:Phosphate (Pi) deficiency alters root hair length and frequency as a means of increasing the absorptive surface area of roots. Three partly redundant single R3 MYB proteins, CAPRICE (CPC), ENHANCER OF TRY AND CPC1 (ETC1) and TRIPTYCHON (TRY), positively regulate the root hair cell fate by participating in a lateral inhibition mechanism. To identify putative targets and processes that are controlled by these three transcription factors (TFs), we conducted transcriptional profiling of roots from Arabidopsis thaliana wild-type plants, and cpc, etc1 and try mutants grown under Pi-replete and Pi-deficient conditions using RNA-seq.