Strategies for wheat stripe rust pathogenicity identified by transcriptome sequencing

Stripe rust caused by the fungus Puccinia striiformis f.sp. tritici (Pst) is a major constraint to wheat production worldwide. The molecular events that underlie Pst pathogenicity are largely unknown. Like all rusts, Pst creates a specialized cellular structure within host cells called the haustorium to obtain nutrients from wheat, and to secrete pathogenicity factors called effector proteins. We purified Pst haustoria and used next-generation sequencing platforms to assemble the haustorial transcriptome as well as the transcriptome of germinated spores. 12,282 transcripts were assembled from 454-pyrosequencing data and used as reference for digital gene expression analysis to compare the germinated uredinospores and haustoria transcriptomes based on Illumina RNAseq data. More than 400 genes encoding secreted proteins which constitute candidate effectors were identified from the haustorial transcriptome, with two thirds of these up-regulated in this tissue compared to germinated spores. RT-PCR analysis confirmed the expression patterns of 94 effector candidates. The analysis also revealed that spores rely mainly on stored energy reserves for growth and development, while haustoria take up host nutrients for massive energy production for biosynthetic pathways and the ultimate production of spores. Together, these studies substantially increase our knowledge of potential Pst effectors and provide new insights into the pathogenic strategies of this important organism.J.P.R. is an ARC Future Fellow (FT0992129). This project has been supported by Bioplatforms Australia through funding from the Commonwealth Government NCRIS and Education Investment Fund Super Science programs

The ins and outs of rust haustoria

Rust diseases caused by fungi of the order Pucciniales afflict a wide range of plants, including cereals, legumes, ornamentals, and fruit trees, and pose a serious threat to cropping systems and global food security. The obligate parasitic lifestyle of these fungi and their complex life cycles, often involving alternate hosts for the sexual and asexual stages, also make this group of pathogens of great biological interest. One of the most remarkable adaptations of rust fungi is the specialized infection structure that underpins the sustained biotrophic association with hosts; the haustorium.This work has been supported by grants from the TwoBlades corporation and the Australian research council

Geometry of River Networks II: Distributions of Component Size and Number

The structure of a river network may be seen as a discrete set of nested sub-networks built out of individual stream segments. These network components are assigned an integral stream order via a hierarchical and discrete ordering method. Exponential relationships, known as Horton's laws, between stream order and ensemble-averaged quantities pertaining to network components are observed. We extend these observations to incorporate fluctuations and all higher moments by developing functional relationships between distributions. The relationships determined are drawn from a combination of theoretical analysis, analysis of real river networks including the Mississippi, Amazon and Nile, and numerical simulations on a model of directed, random networks. Underlying distributions of stream segment lengths are identified as exponential. Combinations of these distributions form single-humped distributions with exponential tails, the sums of which are in turn shown to give power law distributions of stream lengths. Distributions of basin area and stream segment frequency are also addressed. The calculations identify a single length-scale as a measure of size fluctuations in network components. This article is the second in a series of three addressing the geometry of river networks.Comment: 16 pages, 13 figures, 4 tables, Revtex4, submitted to PR

Geometry of River Networks I: Scaling, Fluctuations, and Deviations

This article is the first in a series of three papers investigating the detailed geometry of river networks. Large-scale river networks mark an important class of two-dimensional branching networks, being not only of intrinsic interest but also a pervasive natural phenomenon. In the description of river network structure, scaling laws are uniformly observed. Reported values of scaling exponents vary suggesting that no unique set of scaling exponents exists. To improve this current understanding of scaling in river networks and to provide a fuller description of branching network structure, we report here a theoretical and empirical study of fluctuations about and deviations from scaling. We examine data for continent-scale river networks such as the Mississippi and the Amazon and draw inspiration from a simple model of directed, random networks. We center our investigations on the scaling of the length of sub-basin's dominant stream with its area, a characterization of basin shape known as Hack's law. We generalize this relationship to a joint probability density and show that fluctuations about scaling are substantial. We find strong deviations from scaling at small scales which can be explained by the existence of linear network structure. At intermediate scales, we find slow drifts in exponent values indicating that scaling is only approximately obeyed and that universality remains indeterminate. At large scales, we observe a breakdown in scaling due to decreasing sample space and correlations with overall basin shape. The extent of approximate scaling is significantly restricted by these deviations and will not be improved by increases in network resolution.Comment: 16 pages, 13 figures, Revtex4, submitted to PR

Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes

The wheat stem rust fungus Puccinia graminis f. sp. tritici (Pgt) is one of the most destructive pathogens of wheat. In this study, a draft genome was built for a founder Australian Pgt isolate of pathotype (pt.) 21-0 (collected in 1954) by next generation DNA sequencing. A combination of reference-based assembly using the genome of the previously sequenced American Pgt isolate CDL 75-36-700-3 (p7a) and de novo assembly were performed resulting in a 92 Mbp reference genome for Pgt isolate 21-0. Approximately 13 Mbp of de novo assembled sequence in this genome is not present in the p7a reference assembly. This novel sequence is not specific to 21-0 as it is also present in three other Pgt rust isolates of independent origin. The new reference genome was subsequently used to build a pan-genome based on five Australian Pgt isolates. Transcriptomes from germinated urediniospores and haustoria were separately assembled for pt. 21-0 and comparison of gene expression profiles showed differential expression in ∼10% of the genes each in germinated spores and haustoria. A total of 1,924 secreted proteins were predicted from the 21-0 transcriptome, of which 520 were classified as haustorial secreted proteins (HSPs). Comparison of 21-0 with two presumed clonal field derivatives of this lineage (collected in 1982 and 1984) that had evolved virulence on four additional resistance genes (Sr5, Sr11, Sr27, SrSatu) identified mutations in 25 HSP effector candidates. Some of these mutations could explain their novel virulence phenotypes.Authors wish to thank the Two Blades Foundation for financial support. Part of this work was supported through access to facilities managed by Bioplatforms Australia and funded by the Australian Government National Collaborative Research Infrastructure Strategy and Education Investment Fund Super Science Initiative

An analysis of Australia's carbon pollution reduction scheme

The authors review the decision-making since the Labour Government came into office (November 2007). The Australian Government’s ‘Carbon Pollution Reduction Scheme’ White Paper (15 December 2008) proposes that an Australian Emissions Trading Scheme (AETS) be implemented in mid-2010. Acknowledging that the scheme is comprehensive, the paper finds that in many cases, Australia will take a softer approach to climate change through the AETS than the European Union ETS(EUETS). The paper assesses key issues in the White Paper such as emissions reduction targets, GHG coverage, sectoral coverage, inclusion of unlimited quantities of offsets from Kyoto international markets and exclusion of deforestation activities

Exact Calculation of the Spatio-temporal Correlations in the Takayasu model and in the q-model of Force Fluctuations in Bead Packs

We calculate exactly the two point mass-mass correlations in arbitrary spatial dimensions in the aggregation model of Takayasu. In this model, masses diffuse on a lattice, coalesce upon contact and adsorb unit mass from outside at a constant rate. Our exact calculation of the variance of mass at a given site proves explicitly, without making any assumption of scaling, that the upper critical dimension of the model is 2. We also extend our method to calculate the spatio-temporal correlations in a generalized class of models with aggregation, fragmentation and injection which include, in particular, the $q$-model of force fluctuations in bead packs. We present explicit expressions for the spatio-temporal force-force correlation function in the $q$-model. These can be used to test the applicability of the $q$-model in experiments.Comment: 15 pages, RevTex, 2 figure