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: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.
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:Purpose: We aimed to provide a basis for the adaptive mechanism and a rich resource for the discovery and identification of novel genes involved in the cold stress response in Solenopsis japonica. Retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: Solenopsis japonica was reared at lab condition, and incubated at 2 different temperature for 24h (9, and 25℃) under dark conditions. RNA was extracted using Trizol reagent and Illumina sequencing was performed at Macrogen. Illumina short reads were quality-filtered and Illumina-based de novo transcriptome assembly was performed. Differential Gene Expression Analysis was studied for different tempearture conditions. Results: Totally 89,657 unigenes was obtained which overall 43,375 were annotated with gene descriptions, gene ontology terms, and metabolic pathways. 86 GO functional sub-groups and 25 EggNOG terms resulted. DEGs with FC≥2 and FC≤-2, P-value<0.05 were screened and were compared at two different temperatures. We found 138 DEG down regulated and 271 DEG up regulated when the S. japonica incubated at 9 ℃ and compared with 25℃ treated group. Comparing transcriptome profiles for differential gene expression resulted various DE proteins and genes, including cytochrome P450, NADH dehydrogenase subunit 1, cuticle protein and HSP which have previously been reported to be involved in cold and high temperature resistance. GO analysis revealed that antioxidant activity up-regulated under high temperature stress. Conclusions: we compared the transcriptomes of S. japonica under normal room temperature and low-temperature using RNA-Seq technology based on the high-throughput sequencing. Comparative transcriptome analysis identified many genes and a large number of changes were discovered in metabolic pathway through the GO and KEGG enrichment analysis. Our data will facilitate further molecular investigations and genomic research. Many low-temperature significantly up-regulated genes were first identified in this study. These newly found genes may be important and necessary to S. japonica overwintering and its behavior for adaptation in new environment.
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.
Project description:The transcriptome of a light sensitive tea cultivar ‘Huangjinya’ plants exposed to sunlight and shade were analyzed by high-throughput sequencing followed by de novo assembly.
