Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP
2021
Аутори
Adams, Thomas M.Olsson, Tjelvar S. G.
Ramirez-Gonzalez, Ricardo H.
Bryant, Ruth
Bryson, Rosie
Campos, Pablo Eduardo
Fenwick, Paul
Feuerhelm, David
Hayes, Charlotte
Henriksson, Tina
Hubbard, Amelia
Jevtić, Radivoje
Judge, Christopher
Kerton, Matthew
Lage, Jacob
Lewis, Clare M.
Lilly, Christine
Meidan, Udi
Novoselović, Dario
Patrick, Colin
Wanyera, Ruth
Saunders, Diane G. O.
Чланак у часопису (Објављена верзија)
Метаподаци
Приказ свих података о документуАпстракт
BackgroundTranscriptomics 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.ResultsHere, 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.ConclusionsThe 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.
Кључне речи:
RNA-Seq / expVIP / Gene expression browser / Wheat yellow rust / Puccinia striiformis f / sp / tritici / Transcriptomics / Open scienceИзвор:
BMC Genomics, 2021, 22, 1Издавач:
- BMC, London
Финансирање / пројекти:
- RustWatch - A European early-warning system for wheat rust diseases (EU-H2020-773311)
- Industrial Partnership Award from the UK Biological Sciences Research Council (BBSRC) [BB/M025519/1]
- DeMMYR - Decoding the molecular mechanisms driving host adaptation of yellow rust on cereal crops and grasses (EU-H2020-715638)
- UK Research & Innovation (UKRI), Biotechnology and Biological Sciences Research Council (BBSRC) [BB/P016855/1, BB/P012574/1]
- John Innes Foundation
- Agriculture and Horticultural Development Board (AHDB)
- BASF Plc
- Limagrain UK Ltd.
- RAGT 2 N SAS.
- KWS UK Ltd.
- Syngenta UK Ltd.
- Masstock Arable (UK) Ltd.
DOI: 10.1186/s12864-021-07488-3
ISSN: 1471-2164
PubMed: 33750297
WoS: 000627892200003
Scopus: 2-s2.0-85102244628
Колекције
Институција/група
FiVeRTY - JOUR AU - Adams, Thomas M. AU - Olsson, Tjelvar S. G. AU - Ramirez-Gonzalez, Ricardo H. AU - Bryant, Ruth AU - Bryson, Rosie AU - Campos, Pablo Eduardo AU - Fenwick, Paul AU - Feuerhelm, David AU - Hayes, Charlotte AU - Henriksson, Tina AU - Hubbard, Amelia AU - Jevtić, Radivoje AU - Judge, Christopher AU - Kerton, Matthew AU - Lage, Jacob AU - Lewis, Clare M. AU - Lilly, Christine AU - Meidan, Udi AU - Novoselović, Dario AU - Patrick, Colin AU - Wanyera, Ruth AU - Saunders, Diane G. O. PY - 2021 UR - http://fiver.ifvcns.rs/handle/123456789/2077 AB - BackgroundTranscriptomics 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.ResultsHere, 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.ConclusionsThe 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. PB - BMC, London T2 - BMC Genomics T1 - Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP IS - 1 VL - 22 DO - 10.1186/s12864-021-07488-3 ER -
@article{ author = "Adams, Thomas M. and Olsson, Tjelvar S. G. and Ramirez-Gonzalez, Ricardo H. and Bryant, Ruth and Bryson, Rosie and Campos, Pablo Eduardo and Fenwick, Paul and Feuerhelm, David and Hayes, Charlotte and Henriksson, Tina and Hubbard, Amelia and Jevtić, Radivoje and Judge, Christopher and Kerton, Matthew and Lage, Jacob and Lewis, Clare M. and Lilly, Christine and Meidan, Udi and Novoselović, Dario and Patrick, Colin and Wanyera, Ruth and Saunders, Diane G. O.", year = "2021", abstract = "BackgroundTranscriptomics 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.ResultsHere, 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.ConclusionsThe 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.", publisher = "BMC, London", journal = "BMC Genomics", title = "Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP", number = "1", volume = "22", doi = "10.1186/s12864-021-07488-3" }
Adams, T. M., Olsson, T. S. G., Ramirez-Gonzalez, R. H., Bryant, R., Bryson, R., Campos, P. E., Fenwick, P., Feuerhelm, D., Hayes, C., Henriksson, T., Hubbard, A., Jevtić, R., Judge, C., Kerton, M., Lage, J., Lewis, C. M., Lilly, C., Meidan, U., Novoselović, D., Patrick, C., Wanyera, R.,& Saunders, D. G. O.. (2021). Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP. in BMC Genomics BMC, London., 22(1). https://doi.org/10.1186/s12864-021-07488-3
Adams TM, Olsson TSG, Ramirez-Gonzalez RH, Bryant R, Bryson R, Campos PE, Fenwick P, Feuerhelm D, Hayes C, Henriksson T, Hubbard A, Jevtić R, Judge C, Kerton M, Lage J, Lewis CM, Lilly C, Meidan U, Novoselović D, Patrick C, Wanyera R, Saunders DGO. Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP. in BMC Genomics. 2021;22(1). doi:10.1186/s12864-021-07488-3 .
Adams, Thomas M., Olsson, Tjelvar S. G., Ramirez-Gonzalez, Ricardo H., Bryant, Ruth, Bryson, Rosie, Campos, Pablo Eduardo, Fenwick, Paul, Feuerhelm, David, Hayes, Charlotte, Henriksson, Tina, Hubbard, Amelia, Jevtić, Radivoje, Judge, Christopher, Kerton, Matthew, Lage, Jacob, Lewis, Clare M., Lilly, Christine, Meidan, Udi, Novoselović, Dario, Patrick, Colin, Wanyera, Ruth, Saunders, Diane G. O., "Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP" in BMC Genomics, 22, no. 1 (2021), https://doi.org/10.1186/s12864-021-07488-3 . .