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Yang F.,Copenhagen University | Li W.,BGI Technology | Jorgensen H.J.L.,Copenhagen University
PLoS ONE | Year: 2013

The disease septoria leaf blotch of wheat, caused by fungal pathogen Septoria tritici, is of worldwide concern. The fungus exhibits a hemibiotrophic lifestyle, with a long symptomless, biotrophic phase followed by a sudden transition to necrotrophy associated with host necrosis. Little is known about the systematic interaction between fungal pathogenicity and host responses at specific growth stages and the factors triggering the transition. In order to gain some insights into global transcriptome alterations in both host and pathogen during the two phases of the compatible interaction, disease transition was monitored using pathogenesis-related gene markers and H2O 2 signature prior to RNA-Seq. Transcriptome analysis revealed that the slow symptomless growth was accompanied by minor metabolic responses and slightly suppressed defences in the host, whereas necrotrophic growth was associated with enhanced host responses involving energy metabolism, transport, signalling, defence and oxidative stress as well as a decrease in photosynthesis. The fungus expresses distinct classes of stage-specific genes encoding potential effectors, probably first suppressing plant defence responses/facilitating the symptomless growth and later triggering life style transition and inducing host necrosis/facilitating the necrotrophic growth. Transport, signalling, anti-oxidative stress mechanisms and apoplastic nutrient acquisition play important roles in the entire infection process of S. tritici. Our findings uncover systematic S. tritici -induced expression profiles of wheat related to specific fungal infection strategies and provide a transcriptome resource for studying both hosts and pathogens in plant-Dothideomycete interactions. © 2013 Yang et al. Source

Yang F.,Copenhagen University | Yin Q.,BGI Technology
Proteomics | Year: 2016

Zymoseptoria tritici causes Septoria tritici blotch disease of wheat. To obtain a comprehensive protein dataset of this fungal pathogen, proteomes of Z. tritici growing in nutrient-limiting and rich media and in vivo at a late stage of wheat infection were fractionated by 1D gel or strong cation exchange (SCX) chromatography and analyzed by LC-MS/MS. A total of 5731, 5376 and 3168 Z. tritici proteins were confidently identified from these conditions, respectively. Of these in vitro and in planta proteins, 9 and 11% were predicted to contain signal peptides, respectively. Functional classification analysis revealed the proteins were involved in the various cellular activities. Comparison of three distinct protein expression profiles demonstrates the elevated carbohydrate, lipid and secondary metabolisms, transport, protein processing and energy production specifically in the host environment, in contrast to the enhancement of signaling, defense, replication, transcription and cell division in vitro. The data provide useful targets towards a better understanding of the molecular basis of Z. tritici growth, development, stress response and pathogenicity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source

Dalal K.,Orebro University | Lin Z.,BGI Technology | Gifford M.,Orebro University | Svanstrom L.,University of Skovde
International Journal of Preventive Medicine | Year: 2013

Background: To estimate the economic loss due to road traffic injuries (RTIs) of the World Health Organization (WHO) member countries and to explore the relationship between the economic loss and relevant health system factors. Methods: Data from the World Bank and the WHO were applied to set up the databases. Disability-adjusted life year (DALY) and gross domestic product per capita were used to estimate the economic loss relating to RTIs. Regression analysis was used. Data were analyzed by IBM SPSS Statistics, Versions 20.0. Results: In 2005, the total economic loss of RTIs was estimated to be 167,752.4 million United States Dollars. High income countries (HIC) showed the greatest economic losses. The majority (96%) of the top 25 countries with the greatest DALY losses are low and middle income countries while 48% of the top 25 countries with the highest economic losses are HIC. The linear regression model indicates an inverse relationship between nurse density in the health system and economic loss due to RTI. Conclusions: RTIs cause enormous death and DALYs loss in low-middle income countries and enormous economic loss in HIC. More road traffic prevention programs should be promoted in these areas to reduce both incidence and economic burden of RTIs. Source

Homouz D.,Khalifa University | Chen G.,BGI Technology | Kudlicki A.S.,University of Texas Medical Branch
Scientific Reports | Year: 2015

We report and model a previously undescribed systematic error causing spurious excess correlations that depend on the distance between probes on Affymetrix® microarrays. The phenomenon affects pairs of features with large chip separations, up to over 100 probes apart. The effect may have a significant impact on analysis of correlations in large collections of expression data, where the systematic experimental errors are repeated in many data sets. Examples of such studies include analysis of functions and interactions in groups of genes, as well as global properties of genomes. We find that the average correlations between probes on Affymetrix microarrays are larger for smaller chip distances, which points out to a previously undescribed positional artifact. The magnitude of the artifact depends on the design of the chip, and we find it to be especially high for the yeast S98 microarray, where spurious excess correlations reach 0.1 at a distance of 50 probes. We have designed an algorithm to correct this bias and provide new data sets with the corrected expression values. This algorithm was successfully implemented to remove the positional artifact from the S98 chip data while preserving the integrity of the data. © 2015, Nature Publishing Group. All rights reserved. Source

Xie Y.,South China University of Technology | Xie Y.,Hong Kong University of Science and Technology | Wu G.,BGI Shenzhen | Tang J.,BGI Shenzhen | And 20 more authors.
Bioinformatics | Year: 2014

Motivation: Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining a large number of gene sequences from an organism with no reference genome. Owing to the rapid increase in throughputs and decrease in costs of next- generation sequencing, RNA-Seq in particular has become the method of choice. However, the very short reads (e.g. 2 × 90 bp paired ends) from next generation sequencing makes de novo assembly to recover complete or full-length transcript sequences an algorithmic challenge. Results: Here, we present SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse. Using as our benchmarks the known transcripts from these well-annotated genomes (sequenced a decade ago), we assessed how SOAPdenovo-Trans and two other popular transcriptome assemblers handled such practical issues as alternative splicing and variable expression levels. Our conclusion is that SOAPdenovo-Trans provides higher contiguity, lower redundancy and faster execution. © 2014 The Author. Published by Oxford University Press. All rights reserved. Source

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