The rpg4/Rpg5 stem rust resistance locus in barley; resistance genes and cytoskeleton dynamics

Two closely linked resistance genes, rpg4 and Rpg5, conferring resistance to several races of Puccinia graminis, were cloned and characterized. The Rpg5 gene confers resistance to an isolate of Puccinia graminis f. sp. secalis (Pgs), while rpg4 confers resistance to Puccinia graminis f. sp. tritici (Pgt). Rpg5 is a novel gene containing nucleotide binding site-leucine rich repeat domains in combination with a serine threonine protein kinase domain. High-resolution mapping plus allele and recombinant sequencing identified the rpg4 gene, which encodes an actin depolymerizing factor-like protein (ADF2). Resistance against the Pgt races QCCJ, MCCF, TTKSK (aka Ug99) and RCRS requires both Rpg5 and rpg4, while Rpg5 alone confers resistance to Pgs isolate 92-MN-90. The dependency on the actin modifying protein ADF2 indicates cytoskeleton reorganization or redirection plays a role in pathogen-host interactions. Rpg5 may interact with ADF2 to activate or deactivate its function in the resistance response. Alternatively, Rpg5 could initiate signal transduction leading to resistance in response to detecting ADF2 protein modification. Pgt may redirect the actin cytoskeleton by inducing modifications of ADF2. The redirection of actin could possibly enable the pathogen to develop a haustoria-plant cell cytoskeleton interface for acquisition of nutrients

Unraveling the genomic reorganization of polygalacturonase-inhibiting proteins in chickpea

Polygalacturonase-inhibiting proteins (PGIPs) are cell wall proteins that inhibit pathogen polygalacturonases (PGs). PGIPs, like other defense-related proteins, contain extracellular leucine-rich repeats (eLRRs), which are required for pathogen PG recognition. The importance of these PGIPs in plant defense has been well documented. This study focuses on chickpea (Cicer arietinum) PGIPs (CaPGIPs) owing to the limited information available on this important crop. This study identified two novel CaPGIPs (CaPGIP3 and CaPGIP4) and computationally characterized all four CaPGIPs in the gene family, including the previously reported CaPGIP1 and CaPGIP2. The findings suggest that CaPGIP1, CaPGIP3, and CaPGIP4 proteins possess N-terminal signal peptides, ten LRRs, theoretical molecular mass, and isoelectric points comparable to other legume PGIPs. Phylogenetic analysis and multiple sequence alignment revealed that the CaPGIP1, CaPGIP3, and CaPGIP4 amino acid sequences are similar to the other PGIPs reported in legumes. In addition, several cis-acting elements that are typical of pathogen response, tissue-specific activity, hormone response, and abiotic stress-related are present in the promoters of CaPGIP1, CaPGIP3, and CaPGIP4 genes. Localization experiments showed that CaPGIP1, CaPGIP3, and CaPGIP4 are located in the cell wall or membrane. Transcript levels of CaPGIP1, CaPGIP3, and CaPGIP4 genes analyzed at untreated conditions show varied expression patterns analogous to other defense-related gene families. Interestingly, CaPGIP2 lacked a signal peptide, more than half of the LRRs, and other characteristics of a typical PGIP and subcellular localization indicated it is not located in the cell wall or membrane. The study’s findings demonstrate CaPGIP1, CaPGIP3, and CaPGIP4’s similarity to other legume PGIPs and suggest they might possess the potential to combat chickpea pathogens

Barley stem rust resistance genes: structure and function

Rusts are biotrophic pathogens that attack many plant species but are particularly destructive on cereal crops. The stem rusts (caused by Puccinia graminis) have historically caused severe crop losses and continue to threaten production today. Barley (Hordeum vulgare L.) breeders have controlled major stem rust epidemics since the 1940s with a single durable resistance gene Rpg1. As new epidemics have threatened, additional resistance genes were identified to counter new rust races, such as the rpg4/Rpg5 complex locus against races QCCJ and TTKSK. To understand how these genes work, we initiated research to clone and characterize them. The Rpg1 gene encodes a unique protein kinase with dual kinase domains, an active kinase, and a pseudokinase. Function of both domains is essential to confer resistance. The rpg4 and Rpg5 genes are closely linked and function coordinately to confer resistance to several wheat (Triticum aestivum L.) stem rust races, including the race TTKSK (also called Ug99) that threatens the world's barley and wheat crops. The Rpg5 gene encodes typical resistance gene domains NBS, LRR, and protein kinase but is unique in that all three domains reside in a single gene, a previously unknown structure among plant disease resistance genes. The rpg4 gene encodes an actin depolymerizing factor that functions in cytoskeleton rearrangement

In-scene LWIR downwelling radiance estimation

Effective hyperspectral thermal infrared imaging requires accurate atmospheric compensation to convert the measured at-sensor radiance to the ground radiance. The ground radiance consists of the thermal emission of the material and the reflected downwelling radiance. An accurate estimate of the downwelling radiance is required for temperature-emissivity separation (TES) to remove the spectrally sharp reflected atmospheric effects and retrieve a smooth and accurate material emissivity to use for detection. Determination of the downwelling radiance is difficult due to the fact that a down-looking sensor has no knowledge of the atmospheric properties above its line of sight. As the sensor altitude increases and more of the atmospheric emitters are below the sensor, a relationship forms between the upwelling and downwelling radiances. This relationship comes at the expense of increased pixel size, which increases the likelihood of mixed pixels and nonlinear spectral mixing. In this paper improvements to methods used to estimate the downwelling radiance of low altitude collections are proposed. The ground radiances of reflective pixels are used to estimate the atmosphere above the sensor. The reflective pixels are identified from their sharp atmospheric spectral features. Using the assumption that emissivity spectra are smooth across the narrow reflected atmospheric downwelling radiance features, the temperatures and emissivities are then separated for the reflective pixels using a look-up-table of downwelling radiances. The downwelling radiance that provides the best overall fit for the reflective pixels is then chosen as the scene downwelling radiance.United States. Air Force Research Laboratory (Air Force Contract #FA8721-05-C-0002

The global meningitis genome partnership.

Genomic surveillance of bacterial meningitis pathogens is essential for effective disease control globally, enabling identification of emerging and expanding strains and consequent public health interventions. While there has been a rise in the use of whole genome sequencing, this has been driven predominately by a subset of countries with adequate capacity and resources. Global capacity to participate in surveillance needs to be expanded, particularly in low and middle-income countries with high disease burdens. In light of this, the WHO-led collaboration, Defeating Meningitis by 2030 Global Roadmap, has called for the establishment of a Global Meningitis Genome Partnership that links resources for: N. meningitidis (Nm), S. pneumoniae (Sp), H. influenzae (Hi) and S. agalactiae (Sa) to improve worldwide co-ordination of strain identification and tracking. Existing platforms containing relevant genomes include: PubMLST: Nm (31,622), Sp (15,132), Hi (1935), Sa (9026); The Wellcome Sanger Institute: Nm (13,711), Sp (> 24,000), Sa (6200), Hi (1738); and BMGAP: Nm (8785), Hi (2030). A steering group is being established to coordinate the initiative and encourage high-quality data curation. Next steps include: developing guidelines on open-access sharing of genomic data; defining a core set of metadata; and facilitating development of user-friendly interfaces that represent publicly available data

Investigation of Puccinia graminis resistance genes in barley

The barley stem rust resistance gene Rpg1 was cloned and characterized by a map-based approach. It was shown to have a novel R-gene structure containing tandem kinase domains. To determine the origin of Rpg1 we analyzed alleles from several barley land races (Hordeum vulgare) and wild barley (H. vulgare subsp. spontaneum) accessions. Our allele analysis determined that the functional Rpg1 gene is rare among the landraces and was absent from the wild accessions examined. During the 1990s two new races of Puccinia graminis f. sp. tritici (Pgt) designated QCCJ and TTKSK, virulent on Rpg1, emerged in North America and Eastern Africa, respectively. Analysis of barley accessions for QCCJ and TTKSK reaction identified the barley line Q21861 as the best resistance source and was designated the rpg4 gene. Q21861 also contains resistance against Puccinia graminis f. sp. secalis (Pgs) designated the Rpg5 gene. The two resistance genes initially co-segragated to a region on barley chromosome 5H(7). In an attempt to quickly identify an rpg4/Rpg5 candidate gene, five Rpg1 gene family members were identified and mapped. One was tightly linked to the rpg4/Rpg5 locus but segregated away in a high-resolution mapping population. Recombinant analysis of the high-resolution population revealed that rpg4 and Rpg5 were distinct genes. We cloned and partially characterized a 70 kbp genomic region from barley containing the rpg4 and Rpg5 genes. An Rpg5 candidate gene was identified and confirmed by allele sequencing. The predicted RPG5 protein from the resistant line Q21861 contains a Nucleotide-Binding-Site, Leucine-Rich-Repeat region and a protein kinase domain. A reverse genetics approach, Virus Induced Gene Silencing was used to confirm the Rpg5 gene. A gene encoding an actin depolymerizing factor-like protein (ADF2) was identified as rpg4. The Adf2 gene (rpg4), in combination with Rpg5, appears to be essential for resistance against the Pgt races, but not for the Pgs isolate. One possible hypothesis for the Adf2 gene function is that it might be activated or inactivated by RPG5 upon pathogen recognition. Thus making the ADF2 protein inaccessible for the fungus to redirect actin networks to establish a haustoria-plant interface to obtain nutrients from the plant