Spatio-temporal expression patterns of Arabidopsis thaliana and Medicago truncatula defensin-like genes

Plant genomes contain several hundred defensin-like (DEFL) genes that encode short cysteine-rich proteins resembling defensins, which are well known antimicrobial polypeptides. Little is known about the expression patterns or functions of many DEFLs because most were discovered recently and hence are not well represented on standard microarrays. We designed a custom Affymetrix chip consisting of probe sets for 317 and 684 DEFLs from Arabidopsis thaliana and Medicago truncatula, respectively for cataloging DEFL expression in a variety of plant organs at different developmental stages and during symbiotic and pathogenic associations. The microarray analysis provided evidence for the transcription of 71% and 90% of the DEFLs identified in Arabidopsis and Medicago, respectively, including many of the recently annotated DEFL genes that previously lacked expression information. Both model plants contain a subset of DEFLs specifically expressed in seeds or fruits. A few DEFLs, including some plant defensins, were significantly up-regulated in Arabidopsis leaves inoculated with Alternaria brassicicola or Pseudomonas syringae pathogens. Among these, some were dependent on jasmonic acid signaling or were associated with specific types of immune responses. There were notable differences in DEFL gene expression patterns between Arabidopsis and Medicago, as the majority of Arabidopsis DEFLs were expressed in inflorescences, while only a few exhibited root-enhanced expression. By contrast, Medicago DEFLs were most prominently expressed in nitrogen-fixing root nodules. Thus, our data document salient differences in DEFL temporal and spatial expression between Arabidopsis and Medicago, suggesting distinct signaling routes and distinct roles for these proteins in the two plant species

Disentangling Population History and Character Evolution among Hybridizing Lineages.

Understanding the origin and maintenance of adaptive phenotypic novelty is a central goal of evolutionary biology. However, both hybridization and incomplete lineage sorting can lead to genealogical discordance between the regions of the genome underlying adaptive traits and the remainder of the genome, decoupling inferences about character evolution from population history. Here, to disentangle these effects, we investigated the evolutionary origins and maintenance of Batesian mimicry between North American admiral butterflies (Limenitis arthemis) and their chemically defended model (Battus philenor) using a combination of de novo genome sequencing, whole-genome resequencing, and statistical introgression mapping. Our results suggest that balancing selection, arising from geographic variation in the presence or absence of the unpalatable model, has maintained two deeply divergent color patterning haplotypes that have been repeatedly sieved among distinct mimetic and nonmimetic lineages of Limenitis via introgressive hybridization

Differentially expressed <i>NCR</i>s in nodules with different inoculations.

<p>^aTime point of nodule harvest.</p>b<p><i>S. meliloti</i> strain used for inoculation.</p><p>^cNumber of positively and negatively differentially expressed <i>NCR</i>s in comparison to mock-inoculated roots at 0 dpi. The <i>NCR</i>s with log₂ fold-change >1 and with false discovery rate adjusted P<0.05 are classified as differentially expressed.</p

Regulatory Patterns of a Large Family of Defensin-Like Genes Expressed in Nodules of <i>Medicago truncatula</i>

<div><p>Root nodules are the symbiotic organ of legumes that house nitrogen-fixing bacteria. Many genes are specifically induced in nodules during the interactions between the host plant and symbiotic rhizobia. Information regarding the regulation of expression for most of these genes is lacking. One of the largest gene families expressed in the nodules of the model legume <i>Medicago truncatula</i> is the nodule cysteine-rich (<i>NCR</i>) group of defensin-like (<i>DEFL</i>) genes. We used a custom Affymetrix microarray to catalog the expression changes of 566 <i>NCR</i>s at different stages of nodule development. Additionally, bacterial mutants were used to understand the importance of the rhizobial partners in induction of <i>NCR</i>s. Expression of early <i>NCR</i>s was detected during the initial infection of rhizobia in nodules and expression continued as nodules became mature. Late <i>NCR</i>s were induced concomitantly with bacteroid development in the nodules. The induction of early and late <i>NCR</i>s was correlated with the number and morphology of rhizobia in the nodule. Conserved 41 to 50 bp motifs identified in the upstream 1,000 bp promoter regions of <i>NCR</i>s were required for promoter activity. These <i>cis</i>-element motifs were found to be unique to the <i>NCR</i> family among all annotated genes in the <i>M. truncatula</i> genome, although they contain sub-regions with clear similarity to known regulatory motifs involved in nodule-specific expression and temporal gene regulation.</p> </div

Localization of expression of an <i>NCR</i> in Medicago nodules.

<p>A, GUS staining of a nodule section with the MtTC100321_s_at promoter:GUS construct. B, Detection of the antisense probe corresponding to MtTC100321_s_at in a 10-µm thick nodule section. C, Magnification of boxed area in B. Bars in A and B are 200 µm. Bar in C is 100 µm. I, meristematic zone; II, infection zone; II-III, intermediate zone; III, nitrogen fixation zone of the nodule. All nodules were harvested at 14 dpi with Sm1021.</p

The five conserved motifs found in the upstream regions of NCRs.

a<p>The motifs were identified using MEME, had the most significant E-values of all motifs identified and are represented in more than half of the input NCR sequences.</p>b<p>Number of promoters in which the motif was present in NCR genes.</p

The long-term maintenance of a resistance polymorphism through diffuse interactions

International audiencePlant resistance (R) genes are a crucial component in plant defence against pathogens. Although R genes often fail to provide durable resistance in an agricultural context, they frequently persist as long-lived balanced polymorphisms in nature. Standard theory explains the maintenance of such polymorphisms through a balance of the costs and benefits of resistance and virulence in a tightly coevolving host-pathogen pair. However, many plant-pathogen interactions lack such specificity. Whether, and how, balanced polymorphisms are maintained in diffusely interacting species is unknown. Here we identify a naturally interacting R gene and effector pair in Arabidopsis thaliana and its facultative plant pathogen, Pseudomonas syringae. The protein encoded by the R gene RPS5 recognizes an AvrPphB homologue (AvrPphB2) and exhibits a balanced polymorphism that has been maintained for over 2 million years (ref. 3). Consistent with the presence of an ancient balanced polymorphism, the R gene confers a benefit when plants are infected with P. syringae carrying avrPphB2 but also incurs a large cost in the absence of infection. RPS5 alleles are maintained at intermediate frequencies in populations globally, suggesting ubiquitous selection for resistance. However, the presence of P. syringae carrying avrPphB is probably insufficient to explain the RPS5 polymorphism. First, avrPphB homologues occur at very low frequencies in P. syringae populations on A. thaliana. Second, AvrPphB only rarely confers a virulence benefit to P. syringae on A. thaliana. Instead, we find evidence that selection for RPS5 involves multiple non-homologous effectors and multiple pathogen species. These results and an associated model suggest that the R gene polymorphism in A. thaliana may not be maintained through a tightly coupled interaction involving a single coevolved R gene and effector pair. More likely, the stable polymorphism is maintained through complex and diffuse community-wide interactions

Expression profiles of <i>NCR</i>s.

<p>Expression values are log₂-transformed intensity values. A, Hierarchical clustering (Euclidian average) of 571 NCR<i>s</i> and 14 treatments. Columns 1, 2, 3, 4, and 5 are data for mock-inoculated roots at 0, 4, 7, 14, and 40 dpi, respectively; columns 6, 7, 10, and 12 are roots inoculated with <i>S. meliloti</i> mutants <i>nodC</i>, <i>exoY</i>, <i>bacA</i> and <i>nifH</i> at 14 dpi, respectively; and columns 8, 9, 11, 13, and 14 are roots inoculated with Sm1021 at 3, 4, 7, 14, and 40 dpi, respectively. Color scales representing signal intensities are shown at the bottom. B, Expression profiles of 346 early <i>NCR</i>s. C, Expression profiles of 79 late <i>NCR</i>s. The box and whisker plots represent five different groups of intensity values, the minimum of which is the lowest whisker, the 25% quartile is represented by the bottom box, the 50% quartile is indicated by the median line, the 75% quartile is represented by the top box, the maximum value is the highest whisker, and the outliers are represented by x’s.</p

Correlation of <i>NCR</i> expression between nodules induced by Sm1021 and corresponding developmental time point mutants.

<p>All <i>NCR</i>s with “present” calls between the two treatments plotted were used to generate the scatter plots. Linear regression plots with a significant correlation (R²) are shown. A, Comparison between nodules induced by <i>exoY</i> at 14 dpi and Sm1021 at 3 dpi. B, Comparison between nodules induced by <i>bacA</i> at 14 dpi and Sm1021 at 7 dpi. C, Comparison between nodules induced by <i>nifH</i> at 14 dpi and Sm1021 at 14 dpi.</p