RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics

Abstract

BackgroundFlavonoids are produced in all flowering plants in a wide range of tissues including in berry fruits. These compounds are of considerable interest for their biological activities, health benefits and potential pharmacological applications. However, transcriptomic and genomic resources for wild and cultivated berry fruit species are often limited, despite their value in underpinning the in-depth study of metabolic pathways, fruit ripening as well as in the identification of genotypes rich in bioactive compounds.ResultsTo access the genetic diversity of wild and cultivated berry fruit species that accumulate high levels of phenolic compounds in their fleshy berry(-like) fruits, we selected 13 species from Europe, South America and Asia representing eight genera, seven families and seven orders within three clades of the kingdom Plantae. RNA from either ripe fruits (ten species) or three ripening stages (two species) as well as leaf RNA (one species) were used to construct, assemble and analyse de novo transcriptomes. The transcriptome sequences are deposited in the BacHBerryGEN database (http://jicbio.nbi.ac.uk/berries) and were used, as a proof of concept, via its BLAST portal (http://jicbio.nbi.ac.uk/berries/blast.html) to identify candidate genes involved in the biosynthesis of phenylpropanoid compounds. Genes encoding regulatory proteins of the anthocyanin biosynthetic pathway (MYB and basic helix-loop-helix (bHLH) transcription factors and WD40 repeat proteins) were isolated using the transcriptomic resources of wild blackberry (Rubus genevieri) and cultivated red raspberry (Rubus idaeus cv. Prestige) and were shown to activate anthocyanin synthesis in Nicotiana benthamiana. Expression patterns of candidate flavonoid gene transcripts were also studied across three fruit developmental stages via the BacHBerryEXP gene expression browser (http://www.bachberryexp.com) in R. genevieri and R. idaeus cv. Prestige.ConclusionsWe report a transcriptome resource that includes data for a wide range of berry(-like) fruit species that has been developed for gene identification and functional analysis to assist in berry fruit improvement. These resources will enable investigations of metabolic processes in berries beyond the phenylpropanoid biosynthetic pathway analysed in this study. The RNA-seq data will be useful for studies of berry fruit development and to select wild plant species useful for plant breeding purposes.

Metabolic elicitors of Pseudomonas fluorescens N 21.4 elicit flavonoid metabolism in blackberry fruit

“…In that study it is also said that Ru MYB 5 interacts with other transcription factors ( RuTTG1 and RubHLH1 ) related to proanthocyanidins synthesis, showing decreasing transcript levels during ripening. Despite not having seen differential gene expression of RuMYB5 in our work, the tendency discussed in Thole et al 42 . work has been seen, with a higher concentration of catechin and epicatechin in red fruit and a lower concentration in black fruit.…”

“…However, in our study, RuMYB 5 did not exceed the control differential expression. In the work of Thole et al ., 42 it is said that RuMYB5 from cultivated blackberry has a peak of expression at the early intermediate ripening fruit stage, which could be related to a higher concentration of catechin and epicatechin in green‐red fruit stages. In that study it is also said that Ru MYB 5 interacts with other transcription factors ( RuTTG1 and RubHLH1 ) related to proanthocyanidins synthesis, showing decreasing transcript levels during ripening.…”

Discrete bHLH transcription factors play functionally overlapping roles in pigmentation patterning in flowers of Antirrhinum majus

“…Of course, the effects of the MBW complex on anthocyanin production reflect the net responses of all anthocyanin biosynthetic genes and the relative changes in enzyme and transporter activity on anthocyanin accumulation. To investigate the net effect of the MBW components on the regulation of anthocyanin production in N. benthamiana , we tested different combinations of regulatory proteins for induction of anthocyanins in the leaves of N. benthamiana ‘Northern Territory’ which does not suffer from reported problems with induction of anthocyanins in leaves of the more commonly used laboratory strain (Bally et al ., 2015; Thole et al ., 2019). Anthocyanin levels were significantly induced by Ros 1 on its own (>25 fold) and these were further elevated by inclusion of a vector expressing Del in the transient assay (>45 fold) (Fig.…”

De Novo Transcriptome Analysis of R. nigrum cv. Aldoniai in Response to Blackcurrant Reversion Virus Infection

“…Hence, it is necessary to attain a comprehensive understanding of the molecular mechanisms of resistance to BRV in Ribes for novel blackcurrant breeding programs and acceleration of the selection process. Recently, RNA-sequencing (RNA-Seq) technology and digital gene expression analysis have provided new and rapid approaches for detecting differences in the transcriptomes of non-model plants [ 17 , 18 , 19 ]. Global investigation of gene expression during BRV infection will help to elucidate the mechanisms of BRV resistance in Ribes plants.…”