Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP.
Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP.
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DOI：
10.1186/s12864-021-07488-3
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发表时间：
2021-03-09
期刊：
影响因子：
4.4
通讯作者：
Saunders DGO
中科院分区：
文献类型：
--
作者：
Adams TM;Olsson TSG;Ramírez-González 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
转录组学正越来越多地应用于对植物及其病原体之间的相互作用产生新的见解。对小麦条锈菌（Puccinia striiformis f.基于RNA的测序（RNA-Seq）已经证明是特别有价值的，克服了与其专性生物营养性质相关的障碍。这包括应用RNA-Seq方法来研究Pst和小麦基因随时间的表达动态，以及通过使用称为“田间病原体组学”的基于RNA-Seq的新型监测方法来研究Pst群体组成。作为一种双重RNA-Seq方法，田间病原体组学技术还提供了来自宿主的基因表达数据，为宿主反应提供了新的见解。然而，这为审讯创造了丰富的数据。在这里，我们使用田间病原体组学方法从Pst感染的田间小麦样品中生成了538个新的RNA-Seq数据集，使这一重要病理系统的转录组学数据量增加了一倍。然后，我们分析了这些数据集，以及来自4个Pst感染时间过程的66个RNA-Seq数据集和420个Pst感染的植物田间和实验室样品。为这1024个RNA-Seq数据集中的每一个生成Pst和小麦的基因表达值的数据库，并将其并入锈菌表达浏览器（http：//www.example.com）的开发中。www.rust-expression.com这使得第一次能够同时“点击”访问Pst及其小麦宿主的基因表达谱，并代表了三种小麦锈菌病原体中任何一种的最大的经处理的RNA-Seq数据集数据库。我们还证明了浏览器的效用，通过调查的表达推定的Pst毒力基因随着时间的推移，并检查了寄主植物对Pst感染的反应。rust expression浏览器为更广泛的社区提供了巨大的价值，促进了数据共享和透明度，随着更多数据集的公开，底层数据库可以不断扩展。在线版本包含补充材料，可通过10.1186/s12864-021-07488-3获得。
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. 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. 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. The online version contains supplementary material available at 10.1186/s12864-021-07488-3.
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