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

doi:10.1186/s12864-019-6183-2

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	RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics
	Thole, Vera ; Bassard, Jean-Etienne ; Ramirez-Gonzalez, Ricardo ; Trick, Martin 8; Afshar, Bijan Ghasemi 7; Breitel, Dario 9; Hill, Lionel ; Foito, Alexandre 10; Shepherd, Louise 10; Freitag, Sabine 10
刊名	BMC GENOMICS
	2019
卷号	20 期号:1
关键词	13 berry fruit species RNA-seq de novo assembly Anthocyanin Gene expression analysis Fruit ripening Transcription factors MYB bHLH WDR
ISSN号	1471-2164
DOI	10.1186/s12864-019-6183-2
文献子类	Article
英文摘要	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.
学科主题	Biotechnology & Applied Microbiology ; Genetics & Heredity
出版地	LONDON
WOS关键词	CHILENSIS MOL. STUNTZ ; ARISTOTELIA-CHILENSIS ; GENOME SEQUENCE ; ANTHOCYANIN BIOSYNTHESIS ; BLUEBERRY TRANSCRIPTOME ; MYB ; ARABIDOPSIS ; ANTIOXIDANT ; PROTEIN ; QUANTIFICATION
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
语种	英语
出版者	BMC
WOS记录号	WOS:000508020900003
资助机构	European Union Framework Program 7, Project BacHBerry [FP7] [613793] ; UK Biotechnology and Biological Sciences Research CouncilUK Research & Innovation (UKRI)Biotechnology and Biological Sciences Research Council (BBSRC) [BB/P016855/1, BB/J004596/1, BB/P012523/1] ; European funded COST ACTION [FA1106] ; European Union's Horizon 2020 research and innovation programme through the TomGEM project [679796]
内容类型	期刊论文
源URL	[http://ir.ibcas.ac.cn/handle/2S10CLM1/19808]
专题	中科院北方资源植物重点实验室
作者单位	1.Univ Nova Lisboa, Inst Tecnol Quim & Biol Antonio Xavier, Av Republ, P-2780157 Oeiras, Portugal 2.Univ Nova Lisboa, Fac Ciencias Med, NOVA Med Sch, CEDOC, Rua Camara Pestana 6, P-1150082 Lisbon, Portugal 3.Inst Biol Expt & Tecnol, Av Republ, P-2780157 Oeiras, Portugal 4.James Hutton Inst, Dundee DD2 5DA, Scotland 5.Norwich Res Pk, John Innes Ctr, Dept Metab Biol, Norwich NR4 7UH, Norfolk, England 6.Univ Copenhagen, Dept Plant & Environm Sci, DK-1871 Frederiksberg, Denmark 7.Univ Strasbourg, CNRS, Inst Plant Mol Biol, 12 Rue Gen Zimmer, F-67084 Strasbourg, France 8.Norwich Res Pk, John Innes Ctr, Dept Crop Genet, Norwich NR4 7UH, Norfolk, England 9.Norwich Res Pk, John Innes Ctr, Dept Computat & Syst Biol, Norwich NR4 7UH, Norfolk, England 10.Norwich Res Pk, Trop Biosci UK LTD, Norwich NR4 7UG, Norfolk, England
推荐引用方式 GB/T 7714	Thole, Vera,Bassard, Jean-Etienne,Ramirez-Gonzalez, Ricardo,et al. RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics[J]. BMC GENOMICS,2019,20(1).
APA	Thole, Vera.,Bassard, Jean-Etienne.,Ramirez-Gonzalez, Ricardo.,Trick, Martin.,Afshar, Bijan Ghasemi.,...&Martin, Cathie.(2019).RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics.BMC GENOMICS,20(1).
MLA	Thole, Vera,et al."RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics".BMC GENOMICS 20.1(2019).