No abstract

Nucleotide binding site (NBS)-leucine-rich repeat (LRR) genes belong to the largest class of disease-resistance gene super groups in plants, and their intra- or interspecies nucleotide variations have been studied extensively to understand their evolution and function. However, little is known about the evolutionary patterns of their copy numbers in related species. Here, 129, 245, 239 and 508 NBSs were identified in maize, sorghum, brachypodium and rice, respectively, suggesting considerable variations of these genes. Based on phylogenetic relationships from a total of 496 ancestral branches of grass NBS families, three gene number variation patterns were categorized: conserved, sharing two or more species, and species-specific. Notably, the species-specific NBS branches are dominant (71.6%), while there is only a small percentage (3.83%) of conserved families. In contrast, the conserved families are dominant in 51 randomly selected house-keeping genes (96.1%). The opposite patterns between NBS and the other gene groups suggest that natural selection is responsible for the drastic number variation of NBS genes. The rapid expansion and/or contraction may be a fundamentally important strategy for a species to adapt to the quickly changing species-specific pathogen spectrum. In addition, the small proportion of conserved NBSs suggests that the loss of NBSs may be a general tendency in grass species.

Plant resistance (R) genes are a crucial component in plant defence against pathogens1. Although R genes often fail to provide durable resistance in an agricultural context, they frequently persist as long-lived balanced polymorphisms in nature2–4. 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 pair5,6. However, many plant–pathogen interactions lack such specificity7. Whether, and how, balanced polymorphisms are maintained in diffusely interacting species8 is unknown. Here we identify anaturally 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.

No abstract

A growing body of work addresses automated mining for biochemical information from digital repositories of scientific literature such as MEDLINE. Some of this work uses abstracts as the unit of text from which to extract facts. Other work uses sentences for this purpose, while still other work uses phrases. Here, we compare abstracts, sentences, and phrases in MEDLINE using the standard information retrieval performance measures of recall, precision, and effectiveness for the task of mining interactions among biochemical terms based on term cooccurrence. Results show statistically significant differences that can impact the choice of text unit, although no one of these three text units is unambiguously superior to the others.

Developing CRISPR/Cas9-mediated non-transgenic mutants in asexually propagated perennial crop plants is challenging but highly desirable. Here, we report a highly useful method using an Agrobacterium-mediated transient CRISPR/Cas9 gene expression system to create non-transgenic mutant plants without the need for sexual segregation. We have also developed a rapid, cost-effective, and high-throughput mutant screening protocol based on Illumina sequencing followed by high-resolution melting (HRM) analysis. Using tetraploid tobacco as a model species and the phytoene desaturase (PDS) gene as a target, we successfully created and expediently identified mutant plants, which were verified as tetra-allelic mutants. We produced pds mutant shoots at a rate of 47.5% from tobacco leaf explants, without the use of antibiotic selection. Among these pds plants, 17.2% were confirmed to be non-transgenic, for an overall non-transgenic mutation rate of 8.2%. Our method is reliable and effective in creating non-transgenic mutant plants without the need to segregate out transgenes through sexual reproduction. This method should be applicable to many economically important, heterozygous, perennial crop species that are more difficult to regenerate.

No abstract

The use of plant disease resistance (R) genes in breeding programs needs an understanding of their variation patterns. In our current study, we investigated the polymorphisms of 44 NBS-LRR class R-genes among 21 rice cultivars and 14 wild rice populations. Our data suggested that there were four basic types of variations: conserved, diversified, intermediate-diversified, and present/absent patterns. Common characteristics at a locus of conserved R-genes were: copy-number uniformity, clear divergence (long branches) with other paralogs, and highly identical alleles. On the other hand, copy-number variability, a nearly equal and non-zero branch lengths, and high levels of nucleotide diversity were observed at the loci of highly diversified R-genes. Research suggests that the ratio of diverse alleles to the total number of genes at a locus is one of the best criteria to characterize the variation pattern of an R-gene. Our data suggested that a significant genetic reduction was detected only in four present/absent R-genes, compared with the variation observed in wild rice. In general, no difference was detected between wild rice and cultivars, japonica and indica rice, or between lines from different geographic regions. Our results also suggested that R-genes were under strong selection, which shaped R-gene variation patterns.