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International Journal of Genomics
Volume 2018, Article ID 8084032, 13 pages
Research Article

Transcriptomic Profiling of Fruit Development in Black Raspberry Rubus coreanus

1College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
2Science and Technology Management Division, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
3Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China

Correspondence should be addressed to Yan Wang; moc.361@yxwnaygnaw

Received 6 September 2017; Revised 9 February 2018; Accepted 20 February 2018; Published 1 April 2018

Academic Editor: Marco Gerdol

Copyright © 2018 Qing Chen et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


The wild Rubus species R. coreanus, which is widely distributed in southwest China, shows great promise as a genetic resource for breeding. One of its outstanding properties is adaptation to high temperature and humidity. To facilitate its use in selection and breeding programs, we assembled de novo 179,738,287 R. coreanus reads (125 bp in length) generated by RNA sequencing from fruits at three representative developmental stages. We also used the recently released draft genome of R. occidentalis to perform reference-guided assembly. We inferred a final 95,845-transcript reference for R. coreanus. Of these genetic resources, 66,597 (69.5%) were annotated. Based on these results, we carried out a comprehensive analysis of differentially expressed genes. Flavonoid biosynthesis, phenylpropanoid biosynthesis, plant hormone signal transduction, and cutin, suberin, and wax biosynthesis pathways were significantly enriched throughout the ripening process. We identified 23 transcripts involved in the flavonoid biosynthesis pathway whose expression perfectly paralleled changes in the metabolites. Additionally, we identified 119 nucleotide-binding site leucine-rich repeat (NBS-LRR) protein-coding genes, involved in pathogen resistance, of which 74 were in the completely conserved domain. These results provide, for the first time, genome-wide genetic information for understanding developmental regulation of R. coreanus fruits. They have the potential for use in breeding through functional genetic approaches in the near future.