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Kang H.,Chinese Academy of Agricultural Sciences | Zhu D.,Chinese Academy of Agricultural Sciences | Zhu D.,Hunan Agricultural University | Lin R.,Chinese Academy of Sciences | And 5 more authors.
DNA Research | Year: 2016

Identification of polymorphic transposable elements (TEs) is important because TE polymorphism creates genetic diversity and influences the function of genes in the host genome. However, de novo scanning of polymorphic TEs remains a challenge. Here, we report a novel computational method, called PTEMD (polymorphic TEs and their movement detection), for de novo discovery of genome-wide polymorphic TEs. PTEMD searches highly identical sequences using reads supported breakpoint evidences. Using PTEMD, we identified 14 polymorphic TE families (905 sequences) in rice blast fungus Magnaporthe oryzae, and 68 (10,618 sequences) in maize. We validated one polymorphic TE family experimentally, MoTE-1; all MoTE-1 family members are located in different genomic loci in the three tested isolates. We found that 57.1% (8 of 14) of the PTEMD-detected polymorphic TE families in M. oryzae are active. Furthermore, our data indicate that there are more polymorphic DNA transposons in maize than their counterparts of retrotransposons despite the fact that retrotransposons occupy largest fraction of genomic mass. We demonstrated that PTEMD is an effective tool for identifying polymorphic TEs in M. oryzae and maize genomes. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. Source


Whitehill J.G.A.,Ohio State University | Whitehill J.G.A.,University of British Columbia | Opiyo S.O.,Molecular and Cellular Imaging Center Columbus | Koch J.L.,U.S. Department of Agriculture | And 3 more authors.
Journal of Chemical Ecology | Year: 2012

The emerald ash borer (Agrilus planipennis, EAB) is an invasive wood-borer indigenous to Asia and is responsible for widespread ash (Fraxinus spp.) mortality in the U. S. and Canada. Resistance and susceptibility to EAB varies among Fraxinus spp., which is a result of their co-evolutionary history with the pest. We characterized constitutive phenolic profiles and lignin levels in the phloem of green, white, black, blue, European, and Manchurian ash. Phloem was sampled twice during the growing season, coinciding with phenology of early and late instar EAB. We identified 66 metabolites that displayed a pattern of variation, which corresponded strongly with phylogeny. Previously identified lignans and lignan derivatives were confirmed to be unique to Manchurian ash, and may contribute to its high level of resistance to EAB. Other compounds that had been considered unique to Manchurian ash, including hydroxycoumarins and the phenylethanoids calceolarioside A and B, were detected in closely related, but susceptible species, and thus are unlikely to contribute to EAB resistance of Manchurian ash. The distinct phenolic profile of blue ash may contribute to its relatively high resistance to EAB. © 2012 Springer Science+Business Media, LLC. Source


Asselin J.A.E.,Ohio Agricultural Research and Development Center | Asselin J.A.E.,Cornell University | Lin J.,Ohio Agricultural Research and Development Center | Lin J.,Molecular and Cellular Imaging Center Columbus | And 13 more authors.
Plant Physiology | Year: 2015

AvrE family type III effector proteins share the ability to suppress host defenses, induce disease-associated cell death, and promote bacterial growth. However, despite widespread contributions to numerous bacterial diseases in agriculturally important plants, the mode of action of these effectors remains largely unknown. WtsE is an AvrE family member required for the ability of Pantoea stewartii ssp. stewartii (Pnss) to proliferate efficiently and cause wilt and leaf blight symptoms in maize (Zea mays) plants. Notably, when WtsE is delivered by a heterologous system into the leaf cells of susceptible maize seedlings, it alone produces water-soaked disease symptoms reminiscent of those produced by Pnss. Thus, WtsE is a pathogenicity and virulence factor in maize, and an Escherichia coli heterologous delivery system can be used to study the activity of WtsE in isolation from other factors produced by Pnss. Transcriptional profiling of maize revealed the effects of WtsE, including induction of genes involved in secondary metabolism and suppression of genes involved in photosynthesis. Targeted metabolite quantification revealed that WtsE perturbs maize metabolism, including the induction of coumaroyl tyramine. The ability of mutant WtsE derivatives to elicit transcriptional and metabolic changes in susceptible maize seedlings correlated with their ability to promote disease. Furthermore, chemical inhibitors that block metabolic flux into the phenylpropanoid pathways targeted by WtsE also disrupted the pathogenicity and virulence activity of WtsE. While numerous metabolites produced downstream of the shikimate pathway are known to promote plant defense, our results indicate that misregulated induction of phenylpropanoid metabolism also can be used to promote pathogen virulence. © 2015 American Society of Plant Biologists. All rights reserved. Source

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