TY - JOUR
T1 - RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics
AU - Thole, Vera
AU - Bassard, Jean Etienne
AU - Ramírez-González, Ricardo
AU - Trick, Martin
AU - Ghasemi Afshar, Bijan
AU - Breitel, Dario
AU - Hill, Lionel
AU - Foito, Alexandre
AU - Shepherd, Louise
AU - Freitag, Sabine
AU - Nunes Dos Santos, Claúdia
AU - Menezes, Regina
AU - Banãdos, Pilar
AU - Naesby, Michael
AU - Wang, Liangsheng
AU - Sorokin, Artem
AU - Tikhonova, Olga
AU - Shelenga, Tatiana
AU - Stewart, Derek
AU - Vain, Philippe
AU - Martin, Cathie
N1 - This research was funded by the European Union Framework Program 7,
Project BacHBerry [FP7–613793]. The authors also acknowledge support from
the Institute Strategic Programmes ‘Designing Future Wheat’ (BB/P016855/1),
‘Understanding and Exploiting Plant and Microbial Secondary Metabolism’
(BB/J004596/1) and ‘Molecules from Nature’ (BB/P012523/1) from the UK
Biotechnology and Biological Sciences Research Council to the John Innes
Centre and the European funded COST ACTION FA1106 QualityFruit. VT, PV
and CM have also received funding from the European Union’s Horizon 2020
research and innovation programme through the TomGEM project under
grant agreement No. 679796. The funding bodies had no role in the design
of the study, collection, analysis and interpretation of data nor in writing the manuscript.
PY - 2019/12/19
Y1 - 2019/12/19
N2 - Background: Flavonoids 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. Results: To 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. Conclusions: We 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.
AB - Background: Flavonoids 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. Results: To 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. Conclusions: We 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.
KW - 13 berry fruit species
KW - Anthocyanin
KW - bHLH
KW - de novo assembly
KW - Fruit ripening
KW - Gene expression analysis
KW - MYB
KW - RNA-seq
KW - Transcription factors
KW - WDR
UR - http://www.scopus.com/inward/record.url?scp=85076990777&partnerID=8YFLogxK
U2 - 10.1186/s12864-019-6183-2
DO - 10.1186/s12864-019-6183-2
M3 - Article
C2 - 31856735
AN - SCOPUS:85076990777
SN - 1471-2164
VL - 20
JO - BMC Genomics
JF - BMC Genomics
IS - 1
M1 - 995
ER -