Plants are ubiquitous and important in ecosystems and are an essential source of food and products for humans. One of the most important factors affecting the survival, growth and development of plants is pests and diseases. Nearly 40% of the world's crop production is lost due to pests and diseases. However, researchers have found that some plants are naturally resistant to diseases and this ability is closely related to its genes. Therefore, great efforts have been made to explore the genes involved in plant disease resistance mechanisms——Plant Resistance Gene (R gene).
Plants do not have the same immune system immune cells as animals, so how do plants fight against pathogens? This is when it comes to the immune mechanism of plants in response to pathogenic bacteria. Plants mainly have two stages of defense mechanisms:
Broad-spectrum defense PTI (PAMP-triggered immunity)
Specific defense ETI (effector triggered immunity).
The first stage of broad-spectrum defense PTI: When pathogens invade plants, the pathogen/microbe associated molecular pattern (PAMP/MAMP) associated with pathogens is recognized by the corresponding template recognition receptors (pattern recognition receptors, PRR) of the plant The identification triggers a broad-spectrum defense response and inhibits the initial infection of pathogenic bacteria. Among them, plant immune receptors PRRs are located on the cell membrane and belong to the receptor kinase family.
—Fig . 1 PRRs and PTI of plants —
Phase II Specific Defense ETI: Evolved ability of plants to recognize potential pathogens and predators and activate defense mechanisms against them. The activation of these mechanisms is based on the recognition of effector proteins by so-called resistance genes (R genes), which trigger the plant's own hypersensitivity response, leading to plant cell apoptosis and preventing further spread of the pathogen. This step is called effector triggered immunity (ETI).
The article "Pattern-recognition receptors are required for NLR-mediated plant immunity" of the Center for Excellence in Molecular Plant Science, Chinese Academy of Sciences shows that ETI will strongly up-regulate the transcription and protein of some important signal components of PTI (including BAK1, BIK1 and RBOHD, etc.) level, revealing the synergistic interaction mode between PTI and ETI immune system.
— Figure 2 PTI is a model of a key component of ETI —
Plant R genes play a key role in ETI. R genes generally have several specific structural domains, and different types of R genes can have different combinations of structural domains. The common structure of R gene: it is composed of leucine-rich repeat region (leucine-rich repeat, LRR), nucleotide-binding region (nucleotide-binding, NB) and TIR (Toll/interleukin-1-receptor).
Here is a database for searching R genes:
Plant Resistance Gene database (Plant Resistance Gene database, PRGdb), http://prgdb.crg.eu/wiki/Main_Page, you can search for the reported R genes according to species name and R gene type name.
In January 2022, a research paper entitled PRGdb 4.0: an updated database dedicated to genes involved in plant disease resistance process was published in Nucleic Acids Research, making the Plant Resistance Gene Database (PRGdb; http://prgdb.org /prgdb4/) has been greatly expanded, keeping pace with the growing body of knowledge and data available (sequenced proteomes, cloned genes, public analysis data, etc.).
PRGdb provides two methods for searching R genes: searching according to the type of R gene and searching according to the structural domain contained in the R gene. At the same time, if you need to know whether there is an R gene in unigene, it also supports local and online BLAST comparison. There are 10 domains in PRGdb, including MLO, PRW8, GNK2, CC, TIR, NBS, LRR, Receptor-Like Kinase, Ser-Thr Kinase, others.
The database website has added an updated prediction tool, more data and contains plant resistance transcriptome experiments, providing more easily accessible experimental information, PRGdb provides 199 reference resistance genes from 182 sequenced proteomes and 586652 a putative drug resistance gene. Compared with the previous version, PRGdb 4.0 increased the number of reference drug resistance genes from 153 to 199, and the number of putative drug resistance genes increased from 177K for 76 proteomes to 586K for 182 sequenced proteomes.
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In addition to the plant resistance gene database PRGdb, there are some general databases for botanical research:
01. Genome in NCBI, directly download the genome file on NCBI:
ftp://ftp.ncbi.nlm.nih.gov/genomes/
02. Plant genome database (contains about 30 plants, check for details:):
Correspondence list download of about 30 plant genomes
http://www.plantgdb.org/prj/GenomeBrowser/
03. Contains genome data of multiple species (such as: about 100 citrus, cucumber, eucalyptus, crabapple, etc.):
About 100 corresponding list of plant genomes to download
https://phytozome.jgi.doe.gov/pz/portal.html#
04. Ensembl database (plants):
Correspondence list download of about 70 plant genomes
http://plants.ensembl.org/species.html
05. Arabidopsis database:
https://www.arabidopsis.org/index.jsp
06. Another comprehensive (including tomato, potato, tobacco, eggplant, etc.) database:
https://solgenomics.net/
More database content can be obtained by replying to the background "Plant Disease Resistance Gene Database".
Arguably, NGS has accelerated tuberculosis research by enabling more detailed and comprehensive analyzes of bacteria and their interactions with their hosts.
references:
Yuan M,Jiang Z,Bi G, et al. Pattern-recognition receptors are required for NLR-mediated plant immunity. Nature. 2021;592 (7852):105-109. doi:10.1038/s41586-021-03316-6