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

Plant species composition and product utility pattern of Garo homegardens in Meghalaya, India

Home garden is a traditional landuse system practiced by many rural households in the tropical region. The composition and management practices within homegardens are largely driven by cultural setup and ecological conditions. The present study characterized the plant species composition, utility patterns and management of  Garo homegardens in Dadenggre block, West Garo Hill district of Meghalaya, India. Fifty households from 5 villages were randomly selected and interviewed using a semi-structured questionnaire. The homegardens size ranged between 0.07 and 1.29ha, harbouring 132 plant species, out of which 74 species were trees, 19 shrubs and 39 herbs. Among the perennials, Areca catechu (areca nut) was the most common contributor to household earnings. When species were grouped into 9 utility classes (timber, medicinal, fruit, fuelwood, fodder, vegetables, ornamental, spice, and others), highest number was for fuelwood, followed by vegetables and fruits. The average household income was Rs. 318/100m2, the highest contribution from the sale of vegetables. Various home garden management activities were conducted, engaging family members and generating employment for others. Animal rearing is common in many households and the application of animal manure and household waste has helped maintain soil fertility of homegardens’ soils. Homegardens are integral to the Garo society, contributing significantly to household needs and activities.

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

The genome sequence and effector complement of the flax rust pathogen Melampsora lini

Rust fungi cause serious yield reductions on crops, including wheat, barley, soybean, coffee, and represent real threats to global food security. Of these fungi, the flax rust pathogen Melampsora lini has been developed most extensively over the past 80 years as a model to understand the molecular mechanisms that underpin pathogenesis. During infection, M. lini secretes virulence effectors to promote disease. The number of these effectors, their function and their degree of conservation across rust fungal species is unknown. To assess this, we sequenced and assembled de novo the genome of M. lini isolate CH5 into 21,130 scaffolds spanning 189 Mbp (scaffold N50 of 31 kbp). Global analysis of the DNA sequence revealed that repetitive elements, primarily retrotransposons, make up at least 45% of the genome. Using ab initio predictions, transcriptome data and homology searches, we identified 16,271 putative protein-coding genes. An analysis pipeline was then implemented to predict the effector complement of M. lini and compare it to that of the poplar rust, wheat stem rust and wheat stripe rust pathogens to identify conserved and species-specific effector candidates. Previous knowledge of four cloned M. lini avirulence effector proteins and two basidiomycete effectors was used to optimize parameters of the effector prediction pipeline. Markov clustering based on sequence similarity was performed to group effector candidates from all four rust pathogens. Clusters containing at least one member from M. lini were further analyzed and prioritized based on features including expression in isolated haustoria and infected leaf tissue and conservation across rust species. Herein, we describe 200 of 940 clusters that ranked highest on our priority list, representing 725 flax rust candidate effectors. Our findings on this important model rust species provide insight into how effectors of rust fungi are conserved across species and how they may act to promote infection on their hosts.This work was funded by a grant from the CSIRO Transformational Biology Capability Platform to Adnane Nemri. Claire Anderson was supported by an ARC Discovery Grant (DP120104044) awarded to David A. Jones and Peter N. Dodds

Transmission and Reflection of Strongly Nonlinear SolitaryWaves at Granular Interfaces

The interaction of a solitary wave with an interface formed by two strongly nonlinear noncohesive granular lattices displays rich behavior, characterized by the breakdown of continuum equations of motion in the vicinity of the interface. By treating the solitary wave as a quasiparticle with an effective mass, we construct an intuitive (energy- and linear-momentum-conserving) discrete model to predict the amplitudes of the transmitted solitary waves generated when an incident solitary-wave front, parallel to the interface, moves from a denser to a lighter granular hexagonal lattice. Our findings are corroborated with simulations. We then successfully extend this model to oblique interfaces, where we find that the angle of refraction and reflection of a solitary wave follows, below a critical value, an analogue of Snell?s law in which the solitary-wave speed replaces the speed of sound, which is zero in the sonic vacuum.Fil: Tichler, A. M.. Universiteit Leide. Instituut-Lorentz for Theoretical Physics; Holanda; Shell Global Solutions International; Holanda;Fil: Gomez, Leopoldo Raimundo. Universidad Nacional del Sur; Consejo Nacional de Invest Cientifícas y Tecnicas. Centro Cientifico Tecnológico - CONICET - Bahia Blanca. Instituto de Fisica del Sur; Argentina;Fil: Upadhyaya, N.. Universiteit Leide. Instituut-Lorentz for Theoretical Physics; Holanda;Fil: Campman, X. Shell Global Solutions International; Holanda;Fil: Nesterenko, V. F.. University of California. Jacobs School of Engineering; Estados Unidos de América;Fil: Vitelli, V.. Universiteit Leide. Instituut-Lorentz for Theoretical Physics; Holanda

Encapsulated somatic embryos of grape (Vitis vinifera L.): An efficient way for storage and propagation of pathogen-free plant material

Cotyledonary-stage somatic embryos (5-7 mm in length) originating from leaf explants of grape (Vitis vinifera L.) cv. Pusa seedless were encapsulated individually in 2 % alginate gel. The encapsulated somatic embryos (ESEs) germinated successfully on 0.7 % agar medium containing B5 macrosalts (half strength), MURASHIGE and SKOOG microsalts (full strength), 3 % sucrose and 2.9 μM gibberellic acid. The percentage of germination of ESEs was higher than that of nonencapsulated somatic embryos (NSEs) of the same size on the same medium. The percent germination of ESEs increased (69.2 ±2.8) on medium supplemented with quarter strength B5 macrosalts. Of the germinating ESEs, 36 % developed into plantlets. Abscisic acid at 0.004 and 0.02 μM had no significant influence on the frequency of germination and plantlet development, however resulted in a 4-week delay in germination. Transferring the embryos onto the full-strength B5 medium containing sucrose and ABA (0.04 μM) for 4-6 weeks prior to encapsulation resulted in extended storage of up to 90 d without loss of the germination potential and the capacity to regenerate into plantlets. Normally developed plantlets regenerated from ESEs were successfully adapted to soil.

Maternal, Fetal and Newborn Outcome with Respect to Anemic Status of Women Admitted in Maternity Ward of BPKIHS

Background: Anemia is a common problem in pregnancy particularly in developing countries. In Nepal, the prevalence of anemia in pregnancy is 48%. It is defined by WHO as hemoglobin level less than 11gm/dL in pregnancy. It leads to a number of threats to mother, fetus and newborn. Objectives: The objective of the study was to assess the maternal, fetal and newborn outcome with respect to anemic status of women admitted in maternity ward of BPKIHS, Dharan, Nepal. Methods: A descriptive cross-sectional study was conducted among the 20 to 35 years women admitted in maternity ward of BPKIHS. Total 193 respondents were included in the study by purposive sampling technique. Out of 193 respondents, 78 were anemic and 115 were non-anemic. Maternal, fetal and newborn outcome among all the respondents were assessed by interview and review of records. Pearson Chi-square test was used to find the association between two categorical variables. Results: Maternal outcomes such as preterm delivery, mode of delivery and fetal and newborn outcomes such as abnormal fetal heart rate, IUGR, LBW, low APGAR scores at 1 minute and at 5 minutes, need for resuscitation and need for admission in ward/nursery/NICU were significantly associated with anemic status of women at p value <0.05. The prevalence of anemia among the pregnant women was 40.5%. Conclusion: Maternal outcome such as preterm delivery, cesarean section were associated with anemia. Regarding the fetal and newborn outcome; abnormal fetal heart rate, IUGR, low birth weight, APGAR scores below 7, need for resuscitation, need for admission in ward/ nursery/NICU were associated with anemia

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

Genetic resources conservation and strategies for enhanced utilization in crop improvement

Global food production will need to double to feed the more than 9 billion people by 2050..