Project description:Here, we performed deep transcriptome sequencing for the aerial-tissues and the roots of S. japonica, generating over 2 billion raw reads with an average length of 101 nt by using an Illumina paired-end sequencing by HiSeq2000 platform. Using a combined approach of three popular assemblers, de novo transcriptome assembly for S. japonica was obtained, yielding in 81,729 unigenes with an average length as 884bps and N50-value as 1,452bps, with 46,963 unigenes being annotated based on the sequence similarity against NCBI-nr protein database. Transcriptome profiling of the aerial-tissues and the roots of Swertia japonica
Project description:Saccharina japonica is one of the most important marine economic crops worldwide. Blue light usually plays a significant role in the lives of Saccharina that may be beneficial to the culture system. Here we applied high-throughput paired-end RNA-sequencing (RNA-Seq) to the transcriptome of Saccharina japonica with blue light and dark exposure respectively. Comparative analysis of gene expression was conducted to understand the underlying molecular mechanisms. RNA-seq analysis yielded 70,497 non-redundant unigenes. 25,924 unigenes of them had good comparability with known gene sequences in existing species. Based on the values of RPKM, 11,660 differentially expressed unigenes were detected in expression profiles between blue light and dark exposed samples. Our results provide clues to potential genes identification in the species and lay the foundation for future functional genomics study. mRNA expression of Saccharina japonica with 2 different treatment (sample exposed to Dark condition, and sample exposed to blue light respectively) was determined by method of RNA-Seq
Project description:Saccharina japonica is one of the most important marine economic crops worldwide. Blue light usually plays a significant role in the lives of Saccharina that may be beneficial to the culture system. Here we applied high-throughput paired-end RNA-sequencing (RNA-Seq) to the transcriptome of Saccharina japonica with blue light and dark exposure respectively. Comparative analysis of gene expression was conducted to understand the underlying molecular mechanisms. RNA-seq analysis yielded 70,497 non-redundant unigenes. 25,924 unigenes of them had good comparability with known gene sequences in existing species. Based on the values of RPKM, 11,660 differentially expressed unigenes were detected in expression profiles between blue light and dark exposed samples. Our results provide clues to potential genes identification in the species and lay the foundation for future functional genomics study. Overall design: mRNA expression of Saccharina japonica with 2 different treatment (sample exposed to Dark condition, and sample exposed to blue light respectively) was determined by method of RNA-Seq
Project description:Blue light (BL) is an important environmental factor that plays critical role in algae growth and development. Saccharina japonica, as a typical brown alga, showed greatly affected by BL. However, little has been known about the regulation pathway of BL response in algae. microRNAs (miRNAs) participated in great number of life process regulation and may be also involved in the BL response in plants. To identify miRNAs from S. japonica and characterize their probable roles in BL response, we sequenced and compared small RNA libraries under BL irradiation and dark conditions. 20 potential novel miRNAs were identified from S. japonica. Bioinformatics analysis of the miRNAs indicated that their potential targets were involved in various biological processes. Based on differential expression analysis and qRT-PCR experiment, some probable miRNAs related to BL responses were selected for further verification of their function, such as miR398. Our results demonstrated that miRNAs might play vital roles in metabolism of S. japonica, including BL responses. Overall design: microRNA profiling of two samples treated by blue light (BL) and dark (DK) by high-throughput sequencing
Project description:Moso bamboo is well known with its rapid growth rate. In order to shed light on the underlying mechanism of growth, we applied Gibberellin (GA) to mimic the fast development process in bamboo and found that exogenous GA can significantly increase the length of internode of moso bamboo. Subsequently, we sequenced the transcriptome by high-through sequencing and identified 5,148 different expressed genes (DEG) and find out 22 genes that take part in GA signaling pathway is significantly differently expressed, including GID1A, GID1B and GAI. From GO analysis, a group of genes related to response hormone stimulus are enriched in up-regulated DEGs and 178 GA-responded genes are involved in other plant hormone signaling pathway, of which genes MYB74 and NCED5 are belong to both two pathways. Besides, clusters of genes about photosynthesis are enriched in down-regulated DEGs. By looking into the content of chlorophyll, we find out that the concentrations of chlorophyll are obviously decreased which verify that photosynthesis do weakened after GA treatment. Through method of slicing by hand, it appears that an increased condensation of lignin after GA treatment. The results imply a functional role of GA in bamboo growth, and maybe major in cell wall formation, and photosynthesis. Differential AS alternative splicing (AS) events upons GA induce suggested that post-transcriptional regulation is involved in the GA response. Overall design: triplicates
Project description:Whole Genome Metabolism of "Oryza sativa Japonica Group"
This is a whole genome metabolism model of Oryza sativa Japonica Group.
This model has been automatically generated by the SuBliMinaL Toolbox
and libAnnotationSBML using information coming from from KEGG (release 66, April 2013, accessed via the resource's web services interface) and, where relevant, augmented with metabolic pathway information extracted from MetaCyc (version 17.0, March 2013).
This model has been produced by the path2models
project and is currently hosted on BioModels Database
and identified by: BMID000000141346
Other models with the same genus include BMID000000022012 BMID000000022013 BMID000000022014 BMID000000022015 BMID000000022016 BMID000000022017 BMID000000022018 BMID000000022019 BMID000000022020 BMID000000022021 BMID000000022022 BMID000000022023 BMID000000022024 BMID000000022025 BMID000000022026 BMID000000022027 BMID000000022028 BMID000000022029 BMID000000022030 BMID000000022031 BMID000000022032 BMID000000022033 BMID000000022034 BMID000000022035 BMID000000022036 BMID000000022037 BMID000000022038 BMID000000022039 BMID000000022040 BMID000000022041 BMID000000118664 BMID000000118665 BMID000000118666 BMID000000118667 BMID000000118668 BMID000000118669 BMID000000118670 BMID000000118671 BMID000000118672 BMID000000118673 BMID000000118674 BMID000000118675 BMID000000118676 BMID000000118677 BMID000000118678 BMID000000118679 BMID000000118680 BMID000000118681 BMID000000118682 BMID000000118683 BMID000000118684 BMID000000118685 BMID000000118686 BMID000000118687 BMID000000118688 BMID000000118689 BMID000000118690 BMID000000118691 BMID000000118692 BMID000000118693 BMID000000118694 BMID000000118695 BMID000000118696 BMID000000118697 BMID000000118698 BMID000000118699 BMID000000118700 BMID000000118701 BMID000000118702 BMID000000118703 BMID000000118704 BMID000000118705 BMID000000118706 BMID000000118707 BMID000000118708 BMID000000118709 BMID000000118710 BMID000000118711 BMID000000118712 BMID000000118713 BMID000000118714 BMID000000118715 BMID000000118716 BMID000000118717 BMID000000118718 BMID000000118719 BMID000000118720 BMID000000118721 BMID000000118722 BMID000000118723 BMID000000118724 BMID000000118725 BMID000000118726 BMID000000118727 BMID000000118728 BMID000000118729 BMID000000118730 BMID000000118731 BMID000000118732 BMID000000118733 BMID000000118734 BMID000000118735 BMID000000118736 BMID000000118737 BMID000000118738 BMID000000118739 BMID000000118740 BMID000000118741 BMID000000118742 BMID000000118743 BMID000000118744 BMID000000118745 BMID000000118746 BMID000000118747 BMID000000118748 BMID000000118749 BMID000000118750 BMID000000118751 BMID000000142467 .
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
Project description:In this study, we performed de novo transcriptome assembly for L. japonica, representing transcripts from nine different tissues. A total of 22Gbps clean RNA-seq reads from nine tissues of L. japonica were used, resulting in 243,185 unigenes, with 99,938 unigenes annotated based on homology search using blastx against NCBI-nr protein database. Unsupervised principal component analysis and correlation studies using transcripts expression data from all nine tissues of L. japonica showed relationships between tissues explaining their association at different developmental stages. Homologs for all genes associated with chlorogenic acid, luteolin, and secoiridoid biosynthesis pathways were identified in the L. japonica transcriptome assembly. Expression of unigenes associated with chlorogenic acid were enriched in stem and leaf-2, unigenes from luteolin were enriched in stem and flowers, while unigenes from secoiridoid metabolic pathways were enriched in leaf-1 and shoot apex. Our results showed that different tissues of L. japonica are enriched with sets of unigenes associated with a specific pharmaceutically important metabolic pathways, and therefore, possess unique medicinal properties. Present study will serve as a resource for future attempts for functional characterization of enzyme coding genes within key metabolic processes. De novo transcriptome assembly and characterization, and transcriptome profiling for nine tissues of Lonicera japonica
Project description:Auxin is essential for plant growth and development by altering downstream gene expression. Although large progresses have been made on auxin-concentration, distribution and signaling pathways in model plants like Arabidopsis and rice, little is known in moso bamboo which belongs to grass family, and has great economic and social value. Here we performed genome-wide analysis of the key components related to auxin action, and identified 13 YUCCA genes for auxin synthesis, 14 PIN-FORMED/PIN-like (PIN/PILS) proteins 7 AUXIN1/LIKE-AUX1 (AUX1/LAX) family members for auxin transport, 10 auxin binding factors (AFB) for auxin perception, 43 auxin/indole-3-aceticacid (AUX/IAA) and 41 auxin response transcription factors (ARF) genes for auxin signaling in moso bamboo genome. We further performed phylogenetic analysis of those auxin action related genes from Arabidopsis, Oryza sativa and moso bamboo. To know those genes’ ability to response exogenous auxin and to generate a comprehensive transcriptome overview of auxin response in moso Bamboo, we performed RNA_seq analysis. Our data showed that auxin regulates genes related its biosynthesis, transport, signaling. Moreover, we present the interaction between auxin and other phytohormones at the level of transcription. In summary, we identified the key gene families involved in the auxin action pathways in moso bamboo, and generated a transcriptional overview of the auxin response in moso bamboo. Our data open up an opportunity to uncover the precise roles of auxin action pathways in this important species. Overall design: bamboo (Phyllostachys heterocycla) one-month-old seedlings were sprayed with 5μM NAA for 4 hours with 1-hour interval, and the root part were dissected for RNA extraction.
Project description:We applied Illumina sequencing to identify microRNAs (miRNAs) and piwi-interacting small RNAs (piRNAs) in Dugesia japonica. Dugesia were cut up after seven day’s starvation. DJ1 is the whole Dugesia body, DJ2 is the head part, DJ3 is the tail part, DJ4 is the left part and DJ5 is the right part. Total RNA was extracted by Trizol, and preserved in ethanol, stored at -80°C until further use. 5 samples examined：DJ1,DJ2,DJ3,DJ4,DJ5. SRA study (not submitted by GEO): SRP017693
Project description:Aluminum (Al) toxicity in plants is one of the primary constraints in crop production. Al³⁺, the most toxic form of Al, is released into soil under acidic conditions and causes extensive damage to plants, especially in the roots. In rice, Al tolerance requires the ASR5 gene, but the molecular function of ASR5 has remained unknown. This data establish a comparative study of miRNAome profiles in ASR5 knockdown rice plants (ssp. Japonica cv. Nipponbare) under Al stress conditions. Overall design: microRNA profiles in 4 different shoot libraries of Oryza sativa (ssp. Japonica cv. Nipponbare) by deep sequencing (Illumina HiSeq2000).