Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP
Abstract 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,...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2021-03-01
|
| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-021-07488-3 |
| _version_ | 1818557907539591168 |
|---|---|
| author | Thomas M. Adams Tjelvar S. G. Olsson Ricardo H. Ramírez-González Ruth Bryant Rosie Bryson Pablo Eduardo Campos Paul Fenwick David Feuerhelm Charlotte Hayes Tina Henriksson Amelia Hubbard Radivoje Jevtić Christopher Judge Matthew Kerton Jacob Lage Clare M. Lewis Christine Lilly Udi Meidan Dario Novoselović Colin Patrick Ruth Wanyera Diane G. O. Saunders |
| author_facet | Thomas M. Adams Tjelvar S. G. Olsson Ricardo H. Ramírez-González Ruth Bryant Rosie Bryson Pablo Eduardo Campos Paul Fenwick David Feuerhelm Charlotte Hayes Tina Henriksson Amelia Hubbard Radivoje Jevtić Christopher Judge Matthew Kerton Jacob Lage Clare M. Lewis Christine Lilly Udi Meidan Dario Novoselović Colin Patrick Ruth Wanyera Diane G. O. Saunders |
| author_sort | Thomas M. Adams |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-14T00:05:51Z |
| format | Article |
| id | doaj.art-f1c246df504f44cc9b988ee9d7198c11 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-14T00:05:51Z |
| publishDate | 2021-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-f1c246df504f44cc9b988ee9d7198c112022-12-21T23:26:03ZengBMCBMC Genomics1471-21642021-03-0122111010.1186/s12864-021-07488-3Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIPThomas M. Adams0Tjelvar S. G. Olsson1Ricardo H. Ramírez-González2Ruth Bryant3Rosie Bryson4Pablo Eduardo Campos5Paul Fenwick6David Feuerhelm7Charlotte Hayes8Tina Henriksson9Amelia Hubbard10Radivoje Jevtić11Christopher Judge12Matthew Kerton13Jacob Lage14Clare M. Lewis15Christine Lilly16Udi Meidan17Dario Novoselović18Colin Patrick19Ruth Wanyera20Diane G. O. Saunders21John Innes Centre, Norwich Research ParkJohn Innes Centre, Norwich Research ParkJohn Innes Centre, Norwich Research ParkRAGT Seeds LtdBASF SE, Agricultural CentreINTA EEA BordenaveLimagrain UK LtdSyngenta Seeds LtdElsoms Wheat LtdLantmännen LantbrukNIABInstitute of Field and Vegetable CropsNIABDSV United Kingdom LtdKWS UK LimitedJohn Innes Centre, Norwich Research ParkFrontier AgricultureHazera Seeds Ltd.Agricultural Institute OsijekMasstock Arable (UK) Ltd. (trading as Agrii)Kenya Agricultural and Livestock Research OrganizationJohn Innes Centre, Norwich Research ParkAbstract 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.https://doi.org/10.1186/s12864-021-07488-3RNA-SeqexpVIPGene expression browserWheat yellow rustPuccinia striiformis f. sp. triticiTranscriptomics |
| spellingShingle | Thomas M. Adams Tjelvar S. G. Olsson Ricardo H. Ramírez-González Ruth Bryant Rosie Bryson Pablo Eduardo Campos Paul Fenwick David Feuerhelm Charlotte Hayes Tina Henriksson Amelia Hubbard Radivoje Jevtić Christopher Judge Matthew Kerton Jacob Lage Clare M. Lewis Christine Lilly Udi Meidan Dario Novoselović Colin Patrick Ruth Wanyera Diane G. O. Saunders Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP BMC Genomics RNA-Seq expVIP Gene expression browser Wheat yellow rust Puccinia striiformis f. sp. tritici Transcriptomics |
| title | Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP |
| title_full | Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP |
| title_fullStr | Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP |
| title_full_unstemmed | Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP |
| title_short | Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP |
| title_sort | rust expression browser an open source database for simultaneous analysis of host and pathogen gene expression profiles with expvip |
| topic | RNA-Seq expVIP Gene expression browser Wheat yellow rust Puccinia striiformis f. sp. tritici Transcriptomics |
| url | https://doi.org/10.1186/s12864-021-07488-3 |
| work_keys_str_mv | AT thomasmadams rustexpressionbrowseranopensourcedatabaseforsimultaneousanalysisofhostandpathogengeneexpressionprofileswithexpvip AT tjelvarsgolsson rustexpressionbrowseranopensourcedatabaseforsimultaneousanalysisofhostandpathogengeneexpressionprofileswithexpvip AT ricardohramirezgonzalez rustexpressionbrowseranopensourcedatabaseforsimultaneousanalysisofhostandpathogengeneexpressionprofileswithexpvip AT ruthbryant rustexpressionbrowseranopensourcedatabaseforsimultaneousanalysisofhostandpathogengeneexpressionprofileswithexpvip AT rosiebryson rustexpressionbrowseranopensourcedatabaseforsimultaneousanalysisofhostandpathogengeneexpressionprofileswithexpvip AT pabloeduardocampos rustexpressionbrowseranopensourcedatabaseforsimultaneousanalysisofhostandpathogengeneexpressionprofileswithexpvip AT paulfenwick rustexpressionbrowseranopensourcedatabaseforsimultaneousanalysisofhostandpathogengeneexpressionprofileswithexpvip AT davidfeuerhelm rustexpressionbrowseranopensourcedatabaseforsimultaneousanalysisofhostandpathogengeneexpressionprofileswithexpvip AT charlottehayes rustexpressionbrowseranopensourcedatabaseforsimultaneousanalysisofhostandpathogengeneexpressionprofileswithexpvip AT tinahenriksson rustexpressionbrowseranopensourcedatabaseforsimultaneousanalysisofhostandpathogengeneexpressionprofileswithexpvip AT ameliahubbard rustexpressionbrowseranopensourcedatabaseforsimultaneousanalysisofhostandpathogengeneexpressionprofileswithexpvip AT radivojejevtic rustexpressionbrowseranopensourcedatabaseforsimultaneousanalysisofhostandpathogengeneexpressionprofileswithexpvip AT christopherjudge rustexpressionbrowseranopensourcedatabaseforsimultaneousanalysisofhostandpathogengeneexpressionprofileswithexpvip AT matthewkerton rustexpressionbrowseranopensourcedatabaseforsimultaneousanalysisofhostandpathogengeneexpressionprofileswithexpvip AT jacoblage rustexpressionbrowseranopensourcedatabaseforsimultaneousanalysisofhostandpathogengeneexpressionprofileswithexpvip AT claremlewis rustexpressionbrowseranopensourcedatabaseforsimultaneousanalysisofhostandpathogengeneexpressionprofileswithexpvip AT christinelilly rustexpressionbrowseranopensourcedatabaseforsimultaneousanalysisofhostandpathogengeneexpressionprofileswithexpvip AT udimeidan rustexpressionbrowseranopensourcedatabaseforsimultaneousanalysisofhostandpathogengeneexpressionprofileswithexpvip AT darionovoselovic rustexpressionbrowseranopensourcedatabaseforsimultaneousanalysisofhostandpathogengeneexpressionprofileswithexpvip AT colinpatrick rustexpressionbrowseranopensourcedatabaseforsimultaneousanalysisofhostandpathogengeneexpressionprofileswithexpvip AT ruthwanyera rustexpressionbrowseranopensourcedatabaseforsimultaneousanalysisofhostandpathogengeneexpressionprofileswithexpvip AT dianegosaunders rustexpressionbrowseranopensourcedatabaseforsimultaneousanalysisofhostandpathogengeneexpressionprofileswithexpvip |