Project description:The leaf transcriptome of the nickel hyperaccumulator Phyllanthus luciliae (Phyllanthaceae) endemic from New Caledonia was compared to the related non-accumulator Phyllanthus conjugatus var. ducosensis, living respectively on ultramafic and sedimentary soil, to identity differentially expressed genes potentially involved in Ni hyperaccumulation.
Project description:To understand the biosynthesis of C. majus BIAs, we performed de novo transcriptome sequencing of leaf and root tissues of C. majus using Illumina high-throughput sequencing technology.
Project description:We first report the use of next-generation massively parallel sequencing technologies and de novo transcriptome assembly to gain insight into the wide range of transcriptome of Hevea brasiliensis. The output of sequenced data showed that more than 12 million sequence reads with average length of 90nt were generated. Totally 48,768 unigenes (mean size = 488 bp) were assembled through transcriptome de novo assembly, which represent more than 3-fold of all the sequences of Hevea brasiliensis deposited in the GenBank. Assembled sequences were annotated with gene descriptions, gene ontology and clusters of orthologous group terms. Total 37,373 unigenes were successfully annotated and more than 10% of unigenes were aligned to known proteins of Euphorbiaceae. The unigenes contain nearly complete collection of known rubber-synthesis-related genes. Our data provides the most comprehensive sequence resource available for study rubber tree and demonstrates the availability of Illumina sequencing and de novo transcriptome assembly in a species lacking genome information. The transcriptome of latex and leaf in Hevea brasiliensis
Project description:In this study, we aim to present a global transcriptome analysis of medicinal plant, Catharanthus roseus. We generated about 343 million high-quality reads from three tissues (leaf, root and flower) using Illumina platform. We performed an optimized de novo assembly of the reads and estimated transcript abundance in different tissue samples. The transcriptome dynamics was studied by differential gene expression analyses among tissue samples. We collected different tissue samples from the mature plants. Total RNA isolated from these tissue samples was subjected to Illumina sequencing. The sequence data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were used for de novo assembly optimization. The reads were further mapped to the Catharanthus transcripts via CLC Genomics Workbench and differential gene expression analysis was performed using DESeq software.
Project description:In this study, we have performed Illumina based RNA sequencing to characterize the transcriptome and expression profiles of genes expressed in 5 tissues of P. japonicus. RNA sequencing and de novo transcriptome assembly for P. japonicus resulted in a total of 135,235 unigenes with 78,794 (58.24%) unigenes being annotated using NCBI-nr database. Transcriptome profile and GO enrichment analysis for 5 tissues of P. japonicus showed that although each tissue was characterized by several unique unigenes with leaf showing the most unique unigenes among all, overall processes were evenly conserved across all tissues. Examination of 5 tissues of Panax japonicus
Project description:In this study, we have performed Illumina based RNA sequencing to characterize the transcriptome and expression profiles of genes expressed in 5 tissues of P. japonicus. RNA sequencing and de novo transcriptome assembly for P. japonicus resulted in a total of 135,235 unigenes with 78,794 (58.24%) unigenes being annotated using NCBI-nr database. Transcriptome profile and GO enrichment analysis for 5 tissues of P. japonicus showed that although each tissue was characterized by several unique unigenes with leaf showing the most unique unigenes among all, overall processes were evenly conserved across all tissues.
Project description:We describe an application of deep sequencing and de novo assembly of short RNA reads to investigate small interfering (si)RNAs mediated immunity in leaf samples from eight tree taxa naturally occurring in Wytham Woods, Oxfordshire, UK. BLAST search for homologues of contigs in the GenBank identified siRNA populations against a number of RNA viruses and a Ty1-copia retrotransposons in these tree species. Small RNA sequencing and de novo assembly
Project description:In this study, we aim to present a global transcriptome analysis of medicinal plant, Catharanthus roseus. We generated about 343 million high-quality reads from three tissues (leaf, root and flower) using Illumina platform. We performed an optimized de novo assembly of the reads and estimated transcript abundance in different tissue samples. The transcriptome dynamics was studied by differential gene expression analyses among tissue samples.
