Rubus idaeus Heritage transcripts v1.0 (Chile)

Analysis NameRubus idaeus Heritage transcripts v1.0 (Chile)
MethodTRINITY (de-novo assembly using TRINITY)
SourceIllumina HiSeq TM 2000 sequencing (100 bp double-end reads)
Date performed2017-01-01

The Rubus idaeus cv. Heritage (red raspberry) transcriptomic data hosted by the Genome Database for Rosaceae (GDR) was compiled and analyzed by Centro Regional de Estudios en Alimentos Saludables-CREAS and the Centro de Modelamiento Matemático (CMM) at Universidad de Chile. The goal of this project was to evaluate the molecular changes during raspberry ripening and isolate the differential expressed genes (DEGs) associated with the fruit development of this economically valuable crop. The specific objectives of the DEGs data generation were to:

1. Develop a sequence database for DEGs during Raspberry development;

2. Identify and characterize genes related to hormonal regulation and softening during raspberry ripening.

Using Illumina HiSeq TM 2000 sequencing platform (100 bp double-end reads), we performed transcriptome analysis of flower (F), green (G) and pink (P) fruit stages of red raspberry. Transcriptome was obtained by the de-novo assembly of 298 Million high-quality reads through Trinity assembler, out of the 41,650 high-quality transcripts, 18,171 coding sequences were successfully characterized using databases such as UniProtKB, NCBI Non-Redundant, KEGG, Gene Ontology, and InterProScan. A total of 2,409 transcripts were further identified as differentially expressed genes (DEGs) between the three libraries generated, and 253 DEGs was found between different fruit stages. Singular enrichment analysis of gene ontology (GO) detected an important group of DEGs over-expressed during fruit development; and associated with ethylene, auxin conjugation, abscisic acid response, brassinosteroids biosynthesis and signaling, and cell-wall disassembly process. Considering that raspberry is a non-climacteric fruit with an extremely short shelf-life (1-2 days) due to rapid softening and therefore, highly susceptible to damage during harvest and postharvest operations. Our transcriptome data provide valuable insights on genes involved in the ripening process of non-model fruit species such as Rubus fruit and may further help in developing these cultivars with improved fruit quality characteristics.

This project was supported by a 11110438 grant from the FONDECYT Program; R17A10001 grant from CONICYT-Regional GORE Valparaíso program and CIRIC INRIA-Chile, Powered@NLHPC(ECM-02) supercomputing infrastructure project.

Newbler Processing Summary
Number of reads available 372,829,426
Number of transcripts 41,650
Number of CDS 24,509
Number of Putative Unigenes 18,171
Average transcripts size (large transcripts) 1,168 bp
N50 2,046 bp

More information about the Transcriptomic data can be found in the publication:

Travisany D., Ayala-Raso A., Di-Genova A., Monsalve A., Bernales A., Martínez J.P., González-Agüero M., Defilippi B., Cherian S., Maass A., Fuentes L. "RNA-Seq analysis and transcriptome assembly of raspberry fruit (Rubus idaeus ¨Heritage¨) revealed several candidate genes involved in fruit development." Accepted in Scientia Horticulturae.

Bernales M., Monsalve L., Ayala-Raso A., Valdenegro M., Martínez J.P., Travisany D., Defilippi B., González-Agüero M., Cherian S., Fuentes L., Expression of two indole-3-acetic acid (IAA)-amido synthetases (GH3) genes during fruit development and ripening of raspberry (Rubus idaeus Heritage). Sci. Hort. 246, 2019, 168-175.

Fuentes L, Monsalve L, Morales-Quintana L, Valdenegro M, Martínez JP, Defilippi BG, González-Agüero M. Differential expression of ethylene biosynthesis genes in drupelets and receptacle of raspberry (Rubus idaeus). J. Plant Physiol. 2015 May 1; 179:100-5. doi: 10.1016/j.jplph.2015.02.005. 

 Available Files
 Rubus idaeus Heritage transcripts v1 Rubus_idaeus_heritage_sequences_GDr_20180225_1145-LFV.fasta