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

	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 4; Afshar, Bijan Ghasemi 3; Breitel, Dario 5; Hill, Lionel ; Foito, Alexandre 6; Shepherd, Louise 6; Freitag, Sabine 6; dos Santos, Claudia Nunes 7,8,9; Menezes, Regina 7,8,9; Banados, Pilar 10; Naesby, Michael 11; Wang, Liangsheng12 ; Sorokin, Artem 13; Tikhonova, Olga 13; Shelenga, Tatiana 13; Stewart, Derek 6,14; Vain, Philippe ; Martin, Cathie
	2019
发表期刊	BMC GENOMICS
ISSN	1471-2164
卷号	20 期号:1
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.
关键词	13 berry fruit species RNA-seq de novo assembly Anthocyanin Gene expression analysis Fruit ripening Transcription factors MYB bHLH WDR
学科领域	Biotechnology & Applied Microbiology ; Genetics & Heredity
DOI	10.1186/s12864-019-6183-2
收录类别	SCI
语种	英语
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
WOS记录号	WOS:000508020900003
出版者	BMC
文献子类	Article
出版地	LONDON
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]
作者邮箱	vera.thole@jic.ac.uk
作品OA属性	Green Published, gold
引用统计	被引频次：34[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	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.Norwich Res Pk, John Innes Ctr, Dept Metab Biol, Norwich NR4 7UH, Norfolk, England 2.Univ Copenhagen, Dept Plant & Environm Sci, DK-1871 Frederiksberg, Denmark 3.Univ Strasbourg, CNRS, Inst Plant Mol Biol, 12 Rue Gen Zimmer, F-67084 Strasbourg, France 4.Norwich Res Pk, John Innes Ctr, Dept Crop Genet, Norwich NR4 7UH, Norfolk, England 5.Norwich Res Pk, John Innes Ctr, Dept Computat & Syst Biol, Norwich NR4 7UH, Norfolk, England 6.Norwich Res Pk, Trop Biosci UK LTD, Norwich NR4 7UG, Norfolk, England 7.James Hutton Inst, Dundee DD2 5DA, Scotland 8.Inst Biol Expt & Tecnol, Av Republ, P-2780157 Oeiras, Portugal 9.Univ Nova Lisboa, Fac Ciencias Med, NOVA Med Sch, CEDOC, Rua Camara Pestana 6, P-1150082 Lisbon, Portugal 10.Univ Nova Lisboa, Inst Tecnol Quim & Biol Antonio Xavier, Av Republ, P-2780157 Oeiras, Portugal 11.Pontificia Univ Catolica Chile, Fac Agron & Ingn Forestal, Av Vicuna Mackenna Ote 4860, Macul, Chile 12.Evolva, Duggingerstr 23, CH-4153 Reinach, Switzerland 13.Chinese Acad Sci, Inst Bot, 20 Nanxincun, Beijing 100093, Peoples R China 14.NI Vavilov Res Inst Plant Ind, Fruit Crops Genet Resources Dept, B Morskaya St 42-44, St Petersburg 190000, Russia 15.Heriot Watt Univ, Sch Engn & Phys Sci, Inst Mech Proc & Energy Engn, Edinburgh, Midlothian, Scotland
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).

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