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Long AGO1 transcripts were not detected in the A. thaliana siliques after wounding and accumulation of MAMP-modified H3 was localized in the cytoplasm ( S1 Fig ). Long AGO1 transcripts were also not detected in N. benthamiana leaves after infection with P. syringae pv. tomato strain DC3000 ( S1 Fig ).
In order to investigate MAMP variation in the MAMP families, we first defined primary and secondary MAMP families. Primary MAMP families are those that contain only one MAMP variant (one allele). Secondary MAMP families contain both primary MAMP families and additional MAMP variants that harbor the same primary MAMP variant but differ from the primary MAMP variant at one or more positions. We defined the A. thaliana MAMP families at three different levels of resolution: family at the allele level, family at the peptide level, and family at the genus level. We estimated the number of primary and secondary MAMP families at each resolution level by filtering for family size of four or more peptides. For all three resolutions, P. syringae harbored more families than P. savastanoi ( S4 Text ). Pseudomonas in general harbor more MAMP families than Ralstonia ( S4 Text ).
To investigate MAMP variation between species and genera, we counted each MAMP variant at each resolution level (allele, peptide, genus) and then counted each unique MAMP allele at each resolution level. We then summed these totals for all MAMP families at each resolution level. The distribution of MAMP families across the levels of resolution (allele, peptide, genus) provides an estimate of the number of MAMP families in the A. thaliana and P. savastanoi genomes. Variation in MAMP families was highest at the peptide and allele levels (S5 Text), while genera showed less variation (Fig 3).
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Exploring the evolution of the association of distinct MAMP signals to genes involved in immunity at both the population and QTL levels is necessary to understand how microbes succeed in infection. Along these lines, the current study suggested loci that have evolved in plant populations to recognize different variants of flagellin and EF-Tu. With the exception of the single flagellin variant flg22-ABA, these plant populations are exquisitely specific for their cognate MAMPs [ 8, 9, 10 ]. It is curious to note that the variation at two loci in particular, one on chromosome 2 associated with elf18 variants, and a second on chromosome 4 associated with both elf18 and flg22, appeared to affect the plant’s response to both MAMPs. This finding suggests that these loci are both necessary and sufficient for triggering plant immunity to elf18 and flg22. This is not the first example of a plant allele that elicits the same response to both elf18 and flg22. For example, the ubiquitous flg22 allele flg22-HA elicits the same response to both elf18 and flg22 in Arabidopsis [ 5, 9 ] as well as in other Brassicaceae species [ 3, 4, 7, 9 ]. This MAMP independent phenotype suggests that the plant may recognize elf18 and flg22 as functionally equivalent.
One major goal of our studies has been to identify the genetic variants underlying the phenotypic variation we observe. We employ a combination of GWAS and transgressive segregants to identify these genetic variants. This combination of approaches will rapidly identify candidate genes for any given phenotype. GWAS in this study successfully identified strong candidate genes for flg22 variants on chromosomes 1, 2, 3, and 6. While the other haplotypes associated with SGI did not reach genome-wide significance, the coding regions of the genes identified were enriched for predicted functional polymorphism. In this study we hypothesize that the identification of genetic variants associated with SGI reveal regions where natural variation in plant immunity has evolved to confer broad specificity to MAMP recognition.
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Seedlings growth inhibition (SGI) was estimated for 186 genotypes of A. thaliana that were part of the panel in Atwell et al. [ 21 ]. Plants grown in the absence (control) or presence of 100nM MAMP (treatment) were grown in pairs and cultivated in sterile conditions as described in Vetter et al. [ 3 ]. Seedling growth inhibition was calculated as relative reduction of fresh mass in percent by [(CFMTFM) / CFM] * 100, where CFM stands for control fresh mass and TFM for treatment fresh mass.
Previously, we reported that responses to elf18 and flg22 were correlated with variation at the loci for the receptor and co-receptor, FLS2 and EFR, respectively [ 21 ]. Here, we provide the genetic data supporting this finding. We also investigated the potential for feedback between the perception of a MAMP and signaling, as would be expected in the scenario of a two-receptor system [ 4 ].
MAMP PRO 5.0.5.3998 is a plugin for managing MAMP files. MAMP PRO Patched Version manages both MAMP files in MAMP PRO and local MAMP files on your computer. Importantly, MAMP PRO can be installed without MAMP PRO itself being installed on your computer. All you need to do is to clone the repository to your computer. You will also need to create your own MAMP PRO Settings File, which will enable you to access all of MAMP PRO’s features and options.
A full description of the procedure and methodology used for MAMP variant discovery can be found in MAMP-DB 1.0, which is available at http://mamp.cbi.pku.edu.cn/mampdb/. The tools for variant discovery are now available as parts of the MAMP PRO 5.0.5.3998 software package at http://mamp.cbi.pku.edu.cn/pro. The full MAMP database comprises approximately 98,000 prokaryotic sequences from sequenced bacterial genomes and approximately 5000 sequences from the published eukaryotic MAMP database containing sequences from infected plants. MAMP variant discovery requires the input of a sequence file, which can be obtained from the MAMP-DB website. This file will be used as the ‘query’ sequence and aligned with sequences from the MAMP database. All alignments are subsequently converted to the FASTA format. The program then identifies exact matches, while the program ‘snpstat’ provides frequency calculations for each position of the query sequence. Finally, MAMP variants are identified by looking for positions in the query sequence that differ from those present in the MAMP database. To locate the point at which the MAMP variants starts and ends, the program ‘FindNA’ is used. A MAMP variant can be defined by the following properties: length, start and end position and composition of the variant. Both categories, counts of nucleotides (A, T, C, G) and counts of amino acids (Ala, Arg, Asn, Asp, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, Val) were used to infer variants. To classify MAMP variants, the program ‘mamPhyla’ was used. For each MAMP variant, corresponding annotations, such as genome ID, taxonomic description, functional description and accession number are reported. Furthermore, the program ‘mamPredict’ computes the p-values according to the Mann and Whitney test. The program ‘mamPlot’ summarizes and illustrates these results. MAMP variants are represented by means of p-value color coding, whereby red denotes high and blue low p-values. The intensity of the color is proportional to the absolute p-value. Variants are graphically annotated with one or more of the following: number of occurrences, accession number, taxonomy ID, functional description, definition of the MAMP variant (whether it is a truncation, a frameshift, etc.) or the MIC-value of the MAMP variant (proportion of the time a MAMP variant is detected). In addition, the p-values of the Mann and Whitney test are displayed next to each variant. The program ‘mamSearch’ supports the quick search of a selected gene or MAMP variant among the complete list of annotated MAMP variants. Validated MAMP variants can be exported in a variety of formats, e.g. in plain text, tabular form or comma separated values. MAMP PRO 5.0.5.3998 includes an updated list of annotation and validation data, including MIC values for sixteen MAMP variants with p-values from the Mann and Whitney test less than 0.05. The MAMP PRO 5.0.5.
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MAMP PRO 5.0.5.3998 System Requirements
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- Processor: Intel Core 2 Duo 2GHz or faster
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