Transcriptomic Profiling of Fruit Development in Black Raspberry Rubus coreanus

Abstract

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.

WITHDRAWN: Combined Transcriptomic and Metabolic Analysis Reveals the Potential Mechanism for Fruit Development and Quality Control of Rubus chingii Hu

“…It is in agreement with the ndings in R. ellipticus that the concentrations of polyphenolic compounds reached maximum in unripened stages S-1 and S-2, and then decreased signi cantly as the fruits proceeding towards maturation [58]. The phenols are produced by plants for defensive purposes as "natural pesticides" and then would be oxidized and switch to anthocyanins biosynthesis for fruits maturation [32,35,38]. Similarity, in R. coreanus, degradation of aromatic compounds, and starch and sucrose metabolism were enriched in the two early stages, while polycyclic aromatic hydrocarbon degradation and bisphenol degradation were detected specially in the later stages, leading to the formation of special aroma and avor of ripening Rubus fruits [32].…”

“…Another obvious sign of ripe and soft fruits is the degradation of cell wall components and cuticular/wax layer. So DEGs for cutin, suberin and wax biosynthesis were signi cantly enriched across R. coreanus fruit ripening [32], and this case was also found in R. chingii fruit in our study. Altogether, these results will be bene cial for de ning the syntheses and conversions of metabolites for fruit qualities and provide the basic data for modi able led managements for R. chingii.…”

“…The phenols are produced by plants for defensive purposes as "natural pesticides" and then would be oxidized and switch to anthocyanins biosynthesis for fruits maturation [32,35,38]. Similarity, in R. coreanus, degradation of aromatic compounds, and starch and sucrose metabolism were enriched in the two early stages, while polycyclic aromatic hydrocarbon degradation and bisphenol degradation were detected specially in the later stages, leading to the formation of special aroma and avor of ripening Rubus fruits [32]. Another obvious sign of ripe and soft fruits is the degradation of cell wall components and cuticular/wax layer.…”

Identification of novel anthocyanins synthesis pathway from fungus, Aspergillus sydowii H-1

“…Although most studies have identified lncRNAs in anthocyanins-producing plants, among which only Yuanxiu Lin et al found that lncRNAs in strawberry may regulate anthocyanins synthesis by competitively binding miRNA [50]. The others have not linked lncRNAs to target genes involved in the anthocyanins synthesis pathway [51][52][53]. We predicted three lncRNAs involved in the regulation of anthocyanins-related genes, as one of the other possible mechanisms for the production of anthocyanins in fungi, which providing a possible direction for exploring the mechanism of anthocyanins production.…”

Genetic and genomic resources for Rubus breeding: a roadmap for the future

“…A type I chalcone Isomerase, RcMCHI2 (Unigene 18325), from R. coreanus complemented an Arabidopsis testa 5–1 mutant and restored its ability to produce anthocyanin pigments in the cotyledon and hypocotyl and to accumulate delphinidin 3-O-rutinoside and cyaniding 3-O-rutinoside. Recently, differential expression was evaluated in fruit transcripts of R. coreanus from China across three developmental stages 105 . They identified 23 transcripts in the flavonoid biosynthesis pathways whose expression corresponded to metabolite accumulation during ripening.…”