دورية أكاديمية
Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP.
| العنوان: | Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP. |
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| المؤلفون: | Adams TM; John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK., Olsson TSG; John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK., Ramírez-González RH; John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK., Bryant R; RAGT Seeds Ltd, Grange Road, Ickleton, Essex, CB10 1TA, UK., Bryson R; BASF SE, Agricultural Centre, Limburgerhof, Germany., Campos PE; INTA EEA Bordenave, Bordenave, 8187, Buenos Aires, Argentina., Fenwick P; Limagrain UK Ltd, Woolpit, IP30 9UP, UK., Feuerhelm D; Syngenta Seeds Ltd, Hill Farm Road, Cambridgeshire, CB22 4QT, UK., Hayes C; Elsoms Wheat Ltd, Spalding, Lincolnshire, PE11 1QG, UK., Henriksson T; Lantmännen Lantbruk, Svalöv, Sweden., Hubbard A; NIAB, Cambridge, CB3 0LE, UK., Jevtić R; Institute of Field and Vegetable Crops, Novi Sad, Serbia., Judge C; NIAB, Cambridge, CB3 0LE, UK., Kerton M; DSV United Kingdom Ltd, Banbury, Oxfordshire, OX17 1FE, UK., Lage J; KWS UK Limited, Hertfordshire, SG8 7RE, UK., Lewis CM; John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK., Lilly C; Frontier Agriculture, Witham St Hughs, Lincolnshire, LN6 9TN, UK., Meidan U; Hazera Seeds Ltd., Berurim M.P Shikmim, 7983700, Tel Aviv-Yafo, Israel., Novoselović D; Agricultural Institute Osijek, Osijek, Croatia., Patrick C; Masstock Arable (UK) Ltd. (trading as Agrii), Andoversford, Gloucestershire, GL54 4LZ, UK., Wanyera R; Kenya Agricultural and Livestock Research Organization, Njoro, Nakuru, Kenya., Saunders DGO; John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK. Diane.Saunders@jic.ac.uk. |
| المصدر: | BMC genomics [BMC Genomics] 2021 Mar 09; Vol. 22 (1), pp. 166. Date of Electronic Publication: 2021 Mar 09. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: London : BioMed Central, [2000- |
| مواضيع طبية MeSH: | Basidiomycota*/genetics , Transcriptome*, Plant Diseases/genetics ; Triticum/genetics ; Virulence |
| مستخلص: | Background: Transcriptomics is being increasingly applied to generate new insight into the interactions between plants and their pathogens. For the wheat yellow (stripe) rust pathogen (Puccinia striiformis f. sp. tritici, Pst) RNA-based sequencing (RNA-Seq) has proved particularly valuable, overcoming the barriers associated with its obligate biotrophic nature. This includes the application of RNA-Seq approaches to study Pst and wheat gene expression dynamics over time and the Pst population composition through the use of a novel RNA-Seq based surveillance approach called "field pathogenomics". As a dual RNA-Seq approach, the field pathogenomics technique also provides gene expression data from the host, giving new insight into host responses. However, this has created a wealth of data for interrogation. Results: Here, we used the field pathogenomics approach to generate 538 new RNA-Seq datasets from Pst-infected field wheat samples, doubling the amount of transcriptomics data available for this important pathosystem. We then analysed these datasets alongside 66 RNA-Seq datasets from four Pst infection time-courses and 420 Pst-infected plant field and laboratory samples that were publicly available. A database of gene expression values for Pst and wheat was generated for each of these 1024 RNA-Seq datasets and incorporated into the development of the rust expression browser ( http://www.rust-expression.com ). This enables for the first time simultaneous 'point-and-click' access to gene expression profiles for Pst and its wheat host and represents the largest database of processed RNA-Seq datasets available for any of the three Puccinia wheat rust pathogens. We also demonstrated the utility of the browser through investigation of expression of putative Pst virulence genes over time and examined the host plants response to Pst infection. Conclusions: The rust expression browser offers immense value to the wider community, facilitating data sharing and transparency and the underlying database can be continually expanded as more datasets become publicly available. |
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| معلومات مُعتمدة: | 773311 H2020 European Research Council; BB/M025519/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; BB/P016855/1 and BB/P012574/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; 715638 European Research Council () |
| فهرسة مساهمة: | Keywords: Gene expression browser; Open science; Puccinia striiformis f. sp. tritici; RNA-Seq; Transcriptomics; Wheat yellow rust; expVIP |
| تواريخ الأحداث: | Date Created: 20210322 Date Completed: 20210514 Latest Revision: 20210514 |
| رمز التحديث: | 20240628 |
| مُعرف محوري في PubMed: | PMC7941908 |
| DOI: | 10.1186/s12864-021-07488-3 |
| PMID: | 33750297 |
| قاعدة البيانات: | MEDLINE |
Find this article in full text from Springer Verlag. 
Full Text Finder | تدمد: | 1471-2164 |
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| DOI: | 10.1186/s12864-021-07488-3 |