RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics
文献类型：期刊论文
| 作者 | Thole, Vera; Bassard, Jean-Etienne; Ramirez-Gonzalez, Ricardo; Trick, Martin12; Afshar, Bijan Ghasemi13; Breitel, Dario11; Hill, Lionel; Foito, Alexandre10; Shepherd, Louise10; Freitag, Sabine10 |
| 刊名 | BMC GENOMICS
 |
| 出版日期 | 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 |
| WOS记录号 | WOS:000508020900003 |
| 出版者 | BMC |
| 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] |
| 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.Heriot Watt Univ, Sch Engn & Phys Sci, Inst Mech Proc & Energy Engn, Edinburgh, Midlothian, Scotland 3.NI Vavilov Res Inst Plant Ind, Fruit Crops Genet Resources Dept, B Morskaya St 42-44, St Petersburg 190000, Russia 4.Chinese Acad Sci, Inst Bot, 20 Nanxincun, Beijing 100093, Peoples R China 5.Evolva, Duggingerstr 23, CH-4153 Reinach, Switzerland 6.Pontificia Univ Catolica Chile, Fac Agron & Ingn Forestal, Av Vicuna Mackenna Ote 4860, Macul, Chile 7.Univ Nova Lisboa, Fac Ciencias Med, NOVA Med Sch, CEDOC, Rua Camara Pestana 6, P-1150082 Lisbon, Portugal 8.Inst Biol Expt & Tecnol, Av Republ, P-2780157 Oeiras, Portugal 9.James Hutton Inst, Dundee DD2 5DA, Scotland 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). |
入库方式： OAI收割
来源：植物研究所
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