Author
Stuart G. Gordon
Other affiliations: Ohio State University, Ohio Agricultural Research and Development Center, College of Wooster
Bio: Stuart G. Gordon is an academic researcher from Presbyterian College. The author has contributed to research in topics: Phytophthora sojae & Population. The author has an hindex of 13, co-authored 19 publications receiving 1486 citations. Previous affiliations of Stuart G. Gordon include Ohio State University & Ohio Agricultural Research and Development Center.
Papers
More filters
••
Virginia Tech1, Lawrence Berkeley National Laboratory2, Joint Genome Institute3, Wageningen University and Research Centre4, University of Warwick5, Imperial College London6, University of California, Berkeley7, Cornell University8, Ohio Agricultural Research and Development Center9, Agriculture and Agri-Food Canada10, Agricultural Research Service11, Lawrence Livermore National Laboratory12, North Carolina State University13, University of Tennessee14, Oak Ridge National Laboratory15, University of California, Merced16, University of Queensland17, Wilkes University18, Bowling Green State University19, Hokkaido University20
TL;DR: Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oömycete avirulence genes.
Abstract: Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oomycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oomycete avirulence genes.
1,016 citations
••
University of St. Thomas (Minnesota)1, St. Cloud State University2, Hiram College3, University of Missouri4, University of Nebraska–Lincoln5, Michigan State University6, Presbyterian College7, University of Southern Mississippi8, Austin College9, Bowling Green State University10, University of California, Los Angeles11, Joint Genome Institute12, Northern Illinois University13, University of South Florida14, University of California, Berkeley15
TL;DR: The use of bioinformatic tools and databases changed the way scientists investigate problems, it must change how scientists teach to create new opportunities for students to gain experiences reflecting the influence of genomics, proteomics, and bioinformatics on modern life sciences research.
Abstract: Community Page Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum Jayna L. Ditty 1 , Christopher A. Kvaal 2 , Brad Goodner 3 , Sharyn K. Freyermuth 4 , Cheryl Bailey 5 , Robert A. Britton 6 , Stuart G. Gordon 7 , Sabine Heinhorst 8 , Kelynne Reed 9 , Zhaohui Xu 10 , Erin R. Sanders-Lorenz 11 , Seth Axen 12 , Edwin Kim 12 , Mitrick Johns 13 , Kathleen Scott 14 , Cheryl A. Kerfeld 12,15 * 1 Department of Biology, University of St. Thomas, St. Paul, Minnesota, United States of America, 2 Department of Biological Sciences, St. Cloud State University, St. Cloud, Minnesota, United States of America, 3 Department of Biology, Hiram College, Hiram, Ohio, United States of America, 4 Biochemistry Department, University of Missouri- Columbia, Columbia, Missouri, United States of America, 5 Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America, 6 Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America, 7 Department of Biology, Presbyterian College, Clinton, South Carolina, United States of America, 8 Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, Mississippi, United States of America, 9 Biology Department, Austin College, Sherman, Texas, United States of America, 10 Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America, 11 Department of Microbiology, Immunology and Molecular Genetics, University of California – Los Angeles, Los Angeles, California, United States of America, 12 Department of Energy-Joint Genome Institute, Walnut Creek, California, United States of America, 13 Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, United States of America, 14 Department of Integrative Biology, University of South Florida, Tampa, Florida, United States of America, 15 Department of Plant and Microbial Biology, University of California Berkley, Berkeley, California, United States of America Introduction Undergraduate life sciences education needs an overhaul, as clearly described in the National Research Council of the National Academies’ publication BIO 2010: Transforming Undergraduate Education for Future Research Biologists. Among BIO 2010’s top recommendations is the need to involve students in working with real data and tools that reflect the nature of life sciences research in the 21st century [1]. Education research studies support the importance of utilizing primary literature, designing and implementing experiments, and analyzing results in the context of a bona fide scientific question [1–12] in cultivating the analytical skills necessary to become a scientist. Incorporating these basic scientific methodologies in under- graduate education leads to increased undergraduate and post-graduate reten- tion in the sciences [13–16]. Toward this end, many undergraduate teaching orga- nizations offer training and suggestions for faculty to update and improve their teaching approaches to help students learn as scientists, through design and discovery (e.g., Council of Undergraduate Research [www.cur.org] and Project Kaleidoscope [ www.pkal.org]). With the advent of genome sequencing and bioinformatics, many scientists now formulate biological questions and inter- pret research results in the context of genomic information. Just as the use of bioinformatic tools and databases changed the way scientists investigate problems, it must change how scientists teach to create new opportunities for students to gain experiences reflecting the influence of genomics, proteomics, and bioinformatics on modern life sciences research [17–41]. Educators have responded by incorpo- rating bioinformatics into diverse life science curricula [42–44]. While these published exercises in, and guidelines for, bioinformatics curricula are helpful and inspirational, faculty new to the area of bioinformatics inevitably need training in the theoretical underpinnings of the algo- rithms [45]. Moreover, effectively inte- grating bioinformatics into courses or independent research projects requires infrastructure for organizing and assessing student work. Here, we present a new platform for faculty to keep current with the rapidly changing field of bioinfor- matics, the Integrated Microbial Genomes Annotation Collaboration Toolkit (IMG- ACT) (Figure 1). It was developed by instructors from both research-intensive and predominately undergraduate institu- tions in collaboration with the Department of Energy-Joint Genome Institute (DOE- JGI) as a means to innovate and update undergraduate education and faculty de- velopment. The IMG-ACT program pro- vides a cadre of tools, including access to a clearinghouse of genome sequences, bioin- formatics databases, data storage, instruc- tor course management, and student notebooks for organizing the results of their bioinformatic investigations. In the process, IMG-ACT makes it feasible to provide undergraduate research opportu- nities to a greater number and diversity of students, in contrast to the traditional mentor-to-student apprenticeship model for undergraduate research, which can be too expensive and time-consuming to provide for every undergraduate. The IMG-ACT serves as the hub for the network of faculty and students that use the system for microbial genome analysis. Open access of the IMG-ACT infrastructure to participating schools en- sures that all types of higher education institutions can utilize it. With the infra- structure in place, faculty can focus their efforts on the pedagogy of bioinformatics, involvement of students in research, and use of this tool for their own research agenda. What the original faculty mem- bers of the IMG-ACT development team present here is an overview of how the IMG-ACT program has affected our Citation: Ditty JL, Kvaal CA, Goodner B, Freyermuth SK, Bailey C, et al. (2010) Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum. PLoS Biol 8(8): e1000448. doi:10.1371/journal.pbio.1000448 Published August 10, 2010 Copyright: s 2010 Ditty et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: No specific funding was received for this work. The Community Page is a forum for organizations and societies to highlight their efforts to enhance the dissemination and value of scientific knowledge. Competing Interests: The authors have declared that no competing interests exist. Abbreviations: IMG-ACT; Integrated Microbial Genomes Annotation Collaboration Toolkit * E-mail: ckerfeld@lbl.gov PLoS Biology | www.plosbiology.org August 2010 | Volume 8 | Issue 8 | e1000448
118 citations
••
TL;DR: This region of the soybean genome contains numerous other resistance gene loci as well as pathogen and pest resistance QTL, confirming that Rps8 segregated as a single dominant gene in this population.
Abstract: Phytophthora root and stem rot caused by Phytophthora sojae MJ. Kaufmann & J.W. Gerdemann is a serious disease of soybean [Glycine max (L.) Merr.] worldwide. Recently, a new locus for resistance to P. sojae, Rps8, was identified and mapped in two small soybean populations. The objective of this study was to verify the genomic location of Rps8 in a larger population. One hundred thirty-eight F 2:3 families from a cross between 'Williams' (rps8/rps8) x PI 399073 (Rps8/Rps9) were genotyped by simple sequence repeat (SSR) and restriction fragment length polymorphism (RFLP) markers. From this set of families, 138 and 69 were phenotyped with P. sojae races 1 and 25, respectively. The segregation ratio for each race fit a 3:1 resistant:susceptible, confirming that Rps8 segregated as a single dominant gene. On the basis of linkage analysis with SSR and RFLP markers, Rps8 was located on molecular linkage group F in this population. This region of the soybean genome contains numerous other resistance gene loci as well as pathogen and pest resistance QTL.
71 citations
••
56 citations
••
TL;DR: Seventeen regions on LGs E, F, M, and O were significantly associated with the disease resistance in both populations, and a QTL on LG M near marker Satt463 (50.1 cM) is unique to PI 391589A and B.
Abstract: Soybean [Glycine max (L.) Merr.] PI 391589B, a selection from PI 391589A was recently identified as a new source of resistance to Sclerotinia sclerotiorum (Lib.) deBary, which causes Sclerotinia stem rot. The objective of this study was to identify the quantitative trait loci (QTLs) associated with resistance to S. sclerotiorum in Pls 391589A and 391589B. BC 1 F 4:5 and BC 1 F 4:6 populations from a cross of 'Kottman'(2) x PI 391589A and a population of F 2 -derived lines from a cross of PI 391589B x IA2053 were evaluated for resistance to S. sclerotiorum in the field and in the greenhouse from 2003 to 2005 and genotyped with simple sequence repeat markers. Single factor analysis identified 18 markers on nine linkage groups (LGs) significantly (P < 0.05) associated with resistance to S. sclerotiorum in the two populations. Four regions on LGs E, F, M, and O were significantly associated with the disease resistance in both populations. The four regions are between Satt411 (12.9 cM) and Satt369 (56.2 cM) on LG E, between Satt269 (11.4 cM) and AW186493 (21.0 cM) on LG F, between Satt463 (50.1 cM) and Satt323 (60.1 cM) on LG M, and between Satt581 (106.0 cM) and Satt153 (118.14 cM) on LG O on the soybean composite map developed by Song and others in 2004. Composite interval mapping identified seven QTLs (P < 0.10), each explaining 6.0 to 15.7% of the phenotypic variance. A QTL on LG M near marker Satt463 (50.1 cM) is unique to PI 391589A and B. Therefore, Pls 391589A and 391589B offer breeders a new allele for resistance to the disease.
56 citations
Cited by
More filters
••
École Normale Supérieure1, J. Craig Venter Institute2, Joint Genome Institute3, Alfred Wegener Institute for Polar and Marine Research4, University of Konstanz5, University of Wisconsin–Milwaukee6, University of Melbourne7, University of Washington8, University of Nantes9, University of Wisconsin-Madison10, Ghent University11, University of Rhode Island12, Sewanee: The University of the South13, University of Arizona14, Hebrew University of Jerusalem15, Georgia Institute of Technology16, Leibniz Institute for Neurobiology17, Stazione Zoologica Anton Dohrn18, University of British Columbia19, Stanford University20, Scottish Association for Marine Science21, University of North Carolina at Wilmington22
TL;DR: Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms, and documents the presence of hundreds of genes from bacteria, likely to provide novel possibilities for metabolite management and for perception of environmental signals.
Abstract: Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one- fifth of the primary productivity on Earth(1,2). The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology(3-5). Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (similar to 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.
1,500 citations
••
Broad Institute1, Sainsbury Laboratory2, Ohio Agricultural Research and Development Center3, Uppsala University4, Wageningen University and Research Centre5, Virginia Bioinformatics Institute6, University of California, Riverside7, University of Aberdeen8, Scottish Crop Research Institute9, University of Warwick10, Agricultural Research Service11, Royal Institute of Technology12, Cornell University13, Oregon State University14, Lafayette College15, University of Glasgow16, Harvard University17, Delaware Biotechnology Institute18, North Carolina State University19, University of Delaware20, University of Tennessee21, University of Maryland, Baltimore22, Vanderbilt University23, College of Wooster24, Bowling Green State University25, Edinburgh Cancer Research Centre26, J. Craig Venter Institute27, Tel Aviv University28, University of Wisconsin-Madison29, University of Hohenheim30, University of Dundee31
TL;DR: The sequence of the P. infestans genome is reported, which at ∼240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates and probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.
Abstract: Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement(1). To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world's population(1). Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion(2). Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars(3,4). Here we report the sequence of the P. infestans genome, which at similar to 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for similar to 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.
1,341 citations
••
TL;DR: The number of well-supported cases of transfer from both prokaryotes and eukaryotes, many with significant functional implications, is now expanding rapidly and major recent trends include the important role of HGT in adaptation to certain specialized niches and the highly variable impact of H GT in different lineages.
Abstract: Horizontal gene transfer (HGT; also known as lateral gene transfer) has had an important role in eukaryotic genome evolution, but its importance is often overshadowed by the greater prevalence and our more advanced understanding of gene transfer in prokaryotes. Recurrent endosymbioses and the generally poor sampling of most nuclear genes from diverse lineages have also complicated the search for transferred genes. Nevertheless, the number of well-supported cases of transfer from both prokaryotes and eukaryotes, many with significant functional implications, is now expanding rapidly. Major recent trends include the important role of HGT in adaptation to certain specialized niches and the highly variable impact of HGT in different lineages.
1,185 citations
••
TL;DR: Functional analyses of two motifs, RXLR and EER, present in translocated oomycete effectors are reported, showing that RXLR-EER-encoding genes are transcriptionally upregulated during infection and 425 potential genes encoding secreted RXLR/EER class proteins in the P. infestans genome are identified.
Abstract: Bacterial, oomycete and fungal plant pathogens establish disease by translocation of effector proteins into host cells, where they may directly manipulate host innate immunity. In bacteria, translocation is through the type III secretion system, but analogous processes for effector delivery are uncharacterized in fungi and oomycetes. Here we report functional analyses of two motifs, RXLR and EER, present in translocated oomycete effectors. We use the Phytophthora infestans RXLR-EER-containing protein Avr3a as a reporter for translocation because it triggers RXLR-EER-independent hypersensitive cell death following recognition within plant cells that contain the R3a resistance protein. We show that Avr3a, with or without RXLR-EER motifs, is secreted from P. infestans biotrophic structures called haustoria, demonstrating that these motifs are not required for targeting to haustoria or for secretion. However, following replacement of Avr3a RXLR-EER motifs with alanine residues, singly or in combination, or with residues KMIK-DDK--representing a change that conserves physicochemical properties of the protein--P. infestans fails to deliver Avr3a or an Avr3a-GUS fusion protein into plant cells, demonstrating that these motifs are required for translocation. We show that RXLR-EER-encoding genes are transcriptionally upregulated during infection. Bioinformatic analysis identifies 425 potential genes encoding secreted RXLR-EER class proteins in the P. infestans genome. Identification of this class of proteins provides unparalleled opportunities to determine how oomycetes manipulate hosts to establish infection.
758 citations
••
TL;DR: Significant research progress is revealing mechanisms of MAMP perception, the host defense processes and specific host proteins that pathogen effectors target, the mechanisms of R protein activation, and the ways in which pathogenic effector suites and R genes evolve.
Abstract: The plant basal immune system can detect broadly present microbe-associated molecular patterns (MAMPs, also called PAMPs) and induce defenses, but adapted microbes express a suite of effector proteins that often act to suppress these defenses. Plants have evolved other receptors (R proteins) that detect these pathogen effectors and activate strong defenses. Pathogens can subsequently alter or delete their recognized effectors to avoid defense elicitation, at risk of a fitness cost associated with loss of those effectors. Significant research progress is revealing, among other things, mechanisms of MAMP perception, the host defense processes and specific host proteins that pathogen effectors target, the mechanisms of R protein activation, and the ways in which pathogen effector suites and R genes evolve. These findings carry practical ramifications for resistance durability and for future resistance engineering. The present review uses numerous questions to help clarify what we know and to identify areas that are ripe for further investigation.
749 citations