RNA-seq analysis of Rubus idaeus cv. Nova: transcriptome sequencing and de novo assembly for subsequent functional genomics approaches

Publication Overview
TitleRNA-seq analysis of Rubus idaeus cv. Nova: transcriptome sequencing and de novo assembly for subsequent functional genomics approaches
AuthorsHyun TK, Lee S, Kumar D, Rim Y, Kumar R, Lee SY, Lee CH, Kim JY
TypeJournal Article
Journal NamePlant cell reports
Year2014
CitationHyun TK, Lee S, Kumar D, Rim Y, Kumar R, Lee SY, Lee CH, Kim JY. RNA-seq analysis of Rubus idaeus cv. Nova: transcriptome sequencing and de novo assembly for subsequent functional genomics approaches. Plant cell reports. 2014 Jul 15.

Abstract

KEY MESSAGE
Using Illumina sequencing technology, we have generated the large-scale transcriptome sequencing data containing abundant information on genes involved in the metabolic pathways in R. idaeus cv. Nova fruits. Rubus idaeus (Red raspberry) is one of the important economical crops that possess numerous nutrients, micronutrients and phytochemicals with essential health benefits to human. The molecular mechanism underlying the ripening process and phytochemical biosynthesis in red raspberry is attributed to the changes in gene expression, but very limited transcriptomic and genomic information in public databases is available. To address this issue, we generated more than 51 million sequencing reads from R. idaeus cv. Nova fruit using Illumina RNA-Seq technology. After de novo assembly, we obtained 42,604 unigenes with an average length of 812 bp. At the protein level, Nova fruit transcriptome showed 77 and 68 % sequence similarities with Rubus coreanus and Fragaria versa, respectively, indicating the evolutionary relationship between them. In addition, 69 % of assembled unigenes were annotated using public databases including NCBI non-redundant, Cluster of Orthologous Groups and Gene ontology database, suggesting that our transcriptome dataset provides a valuable resource for investigating metabolic processes in red raspberry. To analyze the relationship between several novel transcripts and the amounts of metabolites such as γ-aminobutyric acid and anthocyanins, real-time PCR and target metabolite analysis were performed on two different ripening stages of Nova. This is the first attempt using Illumina sequencing platform for RNA sequencing and de novo assembly of Nova fruit without reference genome. Our data provide the most comprehensive transcriptome resource available for Rubus fruits, and will be useful for understanding the ripening process and for breeding R. idaeus cultivars with improved fruit quality.

Properties
Additional details for this publication include:
Property NameValue
Publication ModelPrint-Electronic
ISSN1432-203X
eISSN1432-203X
Publication Date2014 Jul 15
Journal AbbreviationPlant Cell Rep.
LanguageEnglish
Language AbbrENG
Publication TypeJournal Article
Cross References
This publication is also available in the following databases:
DatabaseAccession
PMID: PubMedPMID:25023872
AGL: USDA National Agricultural LibraryAGL:4896653