Ontology highlight
ABSTRACT:
PROVIDER: PRJNA640514 | ENA |
REPOSITORIES: ENA
Similar Datasets
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
2012-06-01 | E-GEOD-22079 | biostudies-arrayexpress
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.
2012-06-01 | GSE22079 | GEO
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
2011-09-01 | E-GEOD-26514 | biostudies-arrayexpress
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.
2018-07-20 | GSE117393 | GEO
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.
2011-09-01 | GSE26514 | GEO
Project description:Zanthoxylum armatum (Z. armatum) is one of the most economical trees with the unique numbing taste. However, the underlying regulation mechanism involved in the numbing-taste remains scarce. Thus, uncovering the vital genes associated with numbing-taste biosythesis pathways is critical for revealing the genetic information and breeding the high-quality Z. armatum germplasms. Here, a de novo transcriptome assembly of the five major organs was performed in Z. armatum, including roots, stems, leaf buds, mature leaves and fruits. A total of 111 318 unigenes were generated with an average of 1 014 bp. Meanwhile, a large number of SSR and SNP/Indel loci were obtained to improve our understanding about the phylogenetic and genetic information in Z. armatum. The organ specific unigenes of five major samples were screened and annotated with GO and KEGG enrichment analysis, respectively. Additionally, 53 and 34 unigenes were exclusively up-regulated in fruit samples, and identified as candidate unigenes for terpenoid biosynthesis process and fatty acid biosynthesis, elongation and degradation pathways, respectively. Moreover, he forty days after fertilization (Fr4 stage) could be a important period to accumulate the terpenoid compounds in the fruit development and maturation process of Z. armatum. The Fr4 stage could be a vital point to promote the first few steps of fatty acid biosynthesis process, and the subsequent reactions could be significantly catalyzed at sixty two days after fertilization (Fr6 stage). The present study conducted the de novo transcriptome assembly of the five major organs in Z. armatum. To the best of our knowledge, this study is the first comprehensive analysis to reveal the underlying genes related to the unique numbing taste in Z. armatum. The assembled transcriptome profiles will expand the genetic information and improve our understanding for gene functional studies, which helps in engineering high-quality cultivars of Z. armatum.
2020-02-03 | GSE142491 | GEO