Progress 10/01/12 to 09/30/17
Outputs
Target Audience:Formal classroom teaching was delivered at UC Riverside where the target audience included graduate students in microbiology and undergraduate students in Biology / Bioinformatics. Material covered included descriptions of molecular ecology of microorganisms, microbiology and genetics, and Introduction to Bioinformatics. This covered a graduate Microbiology courses in Microbial Ecology, Bioinformatics and data analyses,and Microbial Pathogenesis. Undergraduate courses in Introductory Bioinformatics and Microbiology were presented. Scientific presentations at national and international meetings (Mycological Society of America, European Fungal Genetics Conference, Fungal Genetics, Gordon Research Conference, Canadian Institute for Advanced Research, Mexican Mycological Society, CISCE, Fungal Cell wall conference, FASEB Microbial Pathogenesis) and invited seminars at US and International universities. Changes/Problems:A focus on data analyses and computational research was emphasized over experimental and genetic work for this project due mainly to the availability of funds and personnel for these type of questions. The approach used was able to take advantage of centralized projects that generated genomic and transcriptomic data for fungi or fungal-plant interactions and mine these data to support our initial hypothesis generations for most efficient way to pursue intended research. This necessistated collaborations with multiple laboratories and institutions and strengthened the impact and scale of work that could be achieved. What opportunities for training and professional development has the project provided?Three graduatestudents have completed PhDs and one MS student in the period while an additional six students are current enrolled. All have focused on some aspect of comparative genomics, bioinformatics,mycology, fungal-fungalor fungal-bacteria interactions. Twentyundergraduate students have engaged in mentored research in the laboratory during this period and have gained laboratory skills and a perspective on mechanisms of scientific research. Eight postdoctoral scholars have received traning in the lab, with a majority focusing computational and comparative analyses. How have the results been disseminated to communities of interest?Presentations at international and national conferences have been made onthese findings and on the databases and tools developed for these products. The work has been disseminated in formal manuscripts, general overview reviews, and online blog posts. Teaching and mentoring of graduate students in the PI's lab as well as collaborating labs on bioinformatics and applications to plant-micro interactions also enabled dissemination of the information, theoretical and practical results of this work. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Objective 1: Goals to find genes in fungal cell wall and growth was supported by discovery of new cell wall gene families was explored as part of many genomic and comparative projects to study fungi. These include Melida et al 2014 which profiled cell walls in multiple types of fungi to experimentall compare the makeup. Many dozens of fungal genomes were sequenced in the course of this project period through efforts in collaboration with the Joint Genome Institute and the development of 1000 Fungal genomes dataset. The work has focused more on comparative genomics and eluciation of conservation of the genes. The work has also explored more on the breadth of the diversity of kindgom and need to better develop the understandingof phylogenetic relationships of the species. This has given new directions on importance of the gene complements. Objective 2: Efforts to focus on Fusarium genomics, phylogeny and identification focused around avocado disease. There are still unfinished aspects of this work which await a completion of the genomic resources of a larger collection of the Fusarium species but is underway as part of development of new software PHYling to support these analyes.A primary focus area has been on the avocado and tree disease caused by Fusarium vectored by shot hole borer beetles.Sevengenomes of Fusarium from the Ambrosia Fusarium Clade have been sequenced and are deposited in GenBank. The comparative analyses of these strains and species is still underway but the comparison of mating type prevalence has supported evidence that the populations of two specieswithin California have not interbred. Our work has developed methods for identification (Short et al 2017) of these species by PCR. In addition we have published a description of a new species,Fusarium kuroshium, which was introduced to San Diego county, characterized by morphological and molecular evidence (Na et al 2017). Ahigh level understanding of population genomics has been performedfrom ~30 strains of avocado dieback Fusarium isolated from Southern California and internationally to better pinpoint the origins of the introdiction into California byRADseq which has informed strain selection for additional whole genome sequencing.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Kirkland, T. N., Muszewska, A., and Stajich, J. E. 2018. Analysis of transposable elements in Coccidioides species. Journal of fungi (Basel, Switzerland) 4. doi:10.3390/jof4010013.
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Sinha, S., Flibotte, S., Neira, M., Formby, S., Plemenitas, A., Cimerman, N. G., Lenassi, M., Gostincar, C., Stajich, J. E., and Nislow, C. 2017. Insight into the recent genome duplication of the halophilic yeast Hortaea werneckii: combining an improved genome with gene expression and chromatin structure. G3: Genes|Genomes|Genetics 7(7):20152022. doi:10.1534/g3.117.040691.
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Chen, J., Wrightsman, T., Wessler, S. R., and Stajich, J. E. 2017. RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing. PeerJ 5:e2942. doi:10.7717/peerj.2942.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Spatafora, J. W., Chang, Y., Benny, G. L., Lazarus, K., Smith, M. E., Berbee, M. L., Bonito, G., Corradi, N., Grigoriev, I., Gryganskyi, A., James, T. Y., ODonnell, K., Roberson, R. W., Taylor, T. N., Uehling, J., Vilgalys, R., White, M. M., and Stajich, J. E. 2016. A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia 108:10281046. doi: 10.3852/16-042.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Short, D. P., ODonnell, K., Stajich, J. E., Hulcr, J., Kijimoto, T., Berger, M. C., Macias, A. M., Spahr, E. J., Bateman, C. C., Eskalen, A., et al. 2017. PCR multiplexes discriminate Fusarium symbionts of invasive Euwallacea ambrosia beetles that inflict damage on numerous tree species throughout the United States. Plant Disease 101(1):233240. doi:10.1094/PDIS-07-16-1046-RE.
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Coleine, C., Masonjones, S., Selbmann, L., Zucconi, L., Onofri, S., Pacelli, C., and Stajich, J. E. 2017. Draft genome sequences of the Antarctic endolithic fungi Rachicladosporium antarcticum CCFEE 5527 and Rachicladosporium sp. CCFEE 5018. Genome announcements 5. doi:10.1128/ genomeA.00397-17.
- Type:
Journal Articles
Status:
Accepted
Year Published:
2017
Citation:
Ahrendt, S. R., Medina, E. M., Chia-en, A. C., and Stajich, J. E. 2017. Exploring the binding prop- erties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling. PeerJ 5:e3206. doi:10.7717/peerj.3206.
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Aryal, S. K., Carter-House, D., Stajich, J. E., and Dillman, A. R. 2017. Microbial associates of the southern mole cricket (Scapteriscus borellii) are highly pathogenic. Journal of invertebrate pathology 150:5462. doi:10.1016/j.jip.2017.09.008.
|
Progress 10/01/15 to 09/30/16
Outputs
Target Audience:Formal classroom teaching was delivered at UC Riverside where the target audience included graduate students in microbiology and undergraduate students in Biology / Bioinformatics. Material covered included descriptions ofmolecular ecology of microorganisms, microbiology and genetics, and Introduction to Bioinformatics. This covered a graduate Microbiology course Microbial Ecology and undergraduate course in Introductory Bioinformatics. Scientific presentations at national and international meetings (Mycological Society of America, EuropeanFungal Genetics Conference, Gordon Research Conference, Canadian Institute for Advanced Research, Mexican Mycological Society) and invited seminars at US and International universities. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Graduate &undergraduate students and postdoctoral fellows were mentored and individual projects were developed. Students and postdocs in the laboratory have attended multiple conferences to present their work include Mycological Society of America, Biocrust conference, and Plant & Animal Genomes conference. How have the results been disseminated to communities of interest?New fungal genome resources have been deposited in public databases (e.g. Genbank, FungiDB, and JGI Mycocosm). Information about these resources, protocols for fungal growth and techniques, and molecular biology and DNA extraction are made available through websites I maintain including http://1000.fungalgenomes.org and http://zygolife.org. Additional public discourse on publications of interest to the plant pathology, mycological and fungal genetics communities are shared through twitter: @fungalgenomes and http://fungalgenomes.org/blog as well as public twitter channels @zygolife. We also have begun sharing images of zygomycetes through a public accounthttps://www.flickr.com/photos/zygolife/ which include important Scanning Electron Microscopy of zygomycetes. Our teams have also communicated fungal species descriptions on the Encylopedia of Life (EOL) pages http://eol.org developing a page for every zygomycete with genome sequencing. What do you plan to do during the next reporting period to accomplish the goals?For objective 1 will finalize the Fusarium phylogenomic analyses to demonstrate the utility of new phylogenomic work to resolve the relationships of these fung. We will also complete phylogeny and publications on a top level view of the kingdom and individual focused clades of the fungi that are resolved. Additional work on extremophile fungi (drought resistant) is being explored to understand their persistance and the multiple origins of these across the fungal phylogeny. For objective 2 we plan to sequence microbiomes of a panel of Avocado trees and fruits comparing how microbiome varies with region and variety and infection status. This will include methods for predictions or diagnostic testing as part of microbiome sequencing. For objective 3 we have multiple approaches to test the role of fungal-bacteria interactions including experiments with microscopy, transformation of several bacteria strains to see how they interact with Rhizopus, and comparative genomics of innate immune genes in zygomycete fungi.
Impacts
What was accomplished under these goals?
For objective 1 we have development of new phylogenomic tools to better understand the relationships of Fungi have been developed in this period. This includes publication of a new phylogeny of the zygomycete fungi and development of Phylogenomics tools and markers. This work has built up a resource of now more than 100 genomes of early diverging fungi in collaboration with the Joint Genome Institute. These datasets are publicly available and used for a variety of comparative questions. Additional refinementof fungal phylogenetic relationships has been generated from these data. For objective 2 we continue to work with Akif Eskalen at UCR on Fusarium dieback of avocado. We have sequenced and annotated genomes of the species found in Los Angeles and San Diego avocado groves. We also have resequenced genomes of these speces to evaluate population level variation among these. To better explore the role of bacterial and fungal microbiome in the severity of the disease we have initiated a project sequencing fungal (ITS) and bacteria (16S) markers to profile the community membership in healthy and infected trees. Initial work has also compared microbiome of the fruit, leaves, and woody tissue of avocado in order to better empirically evaluate the locations of the Fusarium infection. This work can lead to a diagnostic approach to compare infection severity and potentially identify inhibiting bacteria or fungi by contrasting healthy and diseased trees. Objective 3. We are now focusing on fungal-bacteria interactions in the strawberry mold and zygomycete fungus Rhizopus stoloniferand its associated bacteria. We have discovered bacteria associated with wild Rhizopus strains and in behavioral differences between infected and cured of the bacteria strains. Ourmetagenome sequencing has identified several lineages of bacteria found in these strains. We are comparing these patterns with those found in related zygomycete fungi the Mortirella, which haveobligate endohyphal symbiotic bacteria. This is a particularly important direction in developing an understanding of fungal-bacteria interactions and in host defenses that permit or exclude infecting bacteria.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
de Man TJ, Stajich JE, Kubicek CP, Teiling C, Chenthamara K, Atanasova L, Druzhinina IS, Levenkova N, Birnbaum SS, Barribeau SM, Bozick BA, Suen G, Currie CR, Gerardo NM. Small genome of the fungus Escovopsis weberi, a specialized disease agent of ant agriculture. Proc Natl Acad Sci U S A. 2016 Mar 29;113(13):3567-72. doi: 10.1073/pnas.1518501113.
- Type:
Journal Articles
Status:
Submitted
Year Published:
2016
Citation:
OH Cisse, JE Stajich. FGMP: assessing fungal genome completeness and gene content. BioRxiv. doi: https://doi.org/10.1101/049619
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
URen JM, Miadlikowska J, Zimmerman NB, Lutzoni F, Stajich JE, Arnold AE. Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota). Mol Phylogenet Evol. 2016 May;98:210-32. doi: 10.1016/j.ympev.2016.02.010.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Spatafora JW, Chang Y, Benny GL, Lazarus K, Smith ME, Berbee ML, Bonito G, Corradi N, Grigoriev I, Gryganskyi A, James TY, ODonnell K, Roberson RW, Taylor TN, Uehling J, Vilgalys R, White MM, Stajich JE. A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia. 2016 Sep;108(5):1028-1046.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Castanera R, L�pez-Varas L, Borgognone A, LaButti K, Lapidus A, Schmutz J, Grimwood J, P�rez G, Pisabarro AG, Grigoriev IV, Stajich JE, Ram�rez L. Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles. PLoS Genet. 2016 Jun 13;12(6):e1006108. doi: 10.1371/journal.pgen.1006108.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Dylan PG Short, Kerry ODonnell, Jason E Stajich, Jiri Hulcr, Teiya Kijimoto, Matthew C Berger, Angie M Macias, Ellie J Spahr, Craig C Bateman, Akif Eskalen, Shannon C Lynch, Anthony I Cognato, Miriam F Cooperband, Matthew T Kasson. PCR Multiplexes Discriminate Fusarium Symbionts of Invasive Euwallacea Ambrosia Beetles that Inflict Damage on Numerous Tree Species Throughout the United States. Plant Disease 101 (1), 233-240
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2015
Citation:
Ahrendt, Steven A. Investigating the evolution of environmental and biotic interactions in basal fungal lineages through comparative genomics
|
Progress 10/01/14 to 09/30/15
Outputs
Target Audience:Formal classroom teaching was delivered at UC Riverside where the target audience included graduate students in microbiology and undergraduate students. Material covered included descriptions of fungal diseases, molecular ecology of microorganisms, microbiology and genetics. This covered an upperlevel Microbiology course Pathogenic Microbiology, graduate coures Microbial pathogenesis, Microbial Ecology.Scientific presentations at national and international meetings(Mycological Society of America, Fungal Genetics Conference, Society for Molecular Biology and Evolution, International Conference on Mycorrhiza)and invited seminars at US and International universities. Changes/Problems:The projects will focus more on Fusarium than bacteria. We have funded projects on early diverging fungi (Zygomycetes) which will also take up more focus on the lab through those funded positions. We expect to focus some on agriculturally important zygomycetes that cause post-harvest disease rot and use a population genomics and comparative genomics framework. This work is just initiating but will synergize with other efforts to develop and use computational genomic methods to understand pathogen evolution and biology. What opportunities for training and professional development has the project provided?Graudate students were trained during this period through one-on-one mentoring on bioinformatics, software development, and genomic techniques. Postdocs in the labpresented their work at conferences and participated. One graduate student completed theirPhDthis period. Three postdocs completed their training in the lab this period and have moved on to either 2nd postdocs or other research opportunities. How have the results been disseminated to communities of interest?Work has been disseminated in the form of scientific publications, in online content at The Hyphal Tip blog (http://fungalgenoms.org/blog) and the 1000 Fungal Genomes project (http://1000.fungalgenomes.org). New work from the Zygolife project is also publicized through the project page http://zygolife.org and through twitter microblogging platform.The results from this work are also conveyed through presentations at scientific meetings and seminars. What do you plan to do during the next reporting period to accomplish the goals?We will primarily focus on completing the Fusarium research projects. This includes the phylogenomic analyses of the 150 genomes of Fusarium in order to demostratehow automated methods of phylogenetic marker extraction from unassembled or draft assembled genomes. In addition, analysis on the Fusarium dieback of avocado is being focused on to better understand the population biology, timing and sourceof introduction. We will continue to use genomics and comparative genomics to identify factors that may distinguish this species from other ambrosia fungi relatives.
Impacts
What was accomplished under these goals?
For Objective 1 - We completed and published work on early diverging Chytridiomycota on the CBM18 cell wall associated family (Liu et al, 2015) also revealed ways in which some chitin binding gene families can protect cells from chitinases as potential defense mechanism. This also provides new ideas about the role of protective proteins in evolution of pathogenesis. We are exploring the evolution of fungal gene families related to cell walls as part of the ongoing 1000 Fungal Genomes project I am co-leading. The first analyses of the phylogeny are completed and the comparison of gene contents, and patterns of cell wall synthesis and degradation pathways is being explored. One graduate student Steven Ahrent completed his PhD summer 2015 and his thesis work covered evolution of early branching Chytrid fungi, their response to light and ability to sense the environment. This work also produced resources for new genomes of chytrid fungi that we are in the process of analyzing and completing publications. Objective 2. We have focused on a recently emerged pathogen of avocado in southern california caused by a Fusarium species that is vectored by the polyphagus shot hole borer beetle. We have sequenced several strains of the fungus from isolates made by Akif Eskalen at UCR, and in collaboration withNCAUR USDA facility in Peoria, Ill viaTodd Ward and Kerry O'Donnell. We have sequenced more than 8 strains of the fungus, and are comparing these whole genome datasets to understand about introgression between populations. We are buildling on initial work that used RADseq and multilocus sequencing to characterize the isolates. In addition, a large 150 species phylogeny of Fusarium based on whole genome sequences is nearly complete which I have completed using data provided bt the NCAUR collaborators.We have also developed new software and protocols (PHYling) for using low coverage genome sequencing to extract genes for phylogenetic analyses of Fusarium species in order to establish methods for using this approach for classification of species/strains using this highthroughput approach. Objective 3. We previously published one paper (Sachs et al. 2014). This objective is mostly completed at this time, thoughpublication of the bacterial genome genome sets is still in process to explore the degradation of an island of symbiosis related genes in the genome across a collection of strains of cheaters and cooperating Bradyrhizobium bacteria.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Liu, P., Stajich, J.E. Characterization of the Carbohydrate Binding Module 18 gene family in the amphibian pathogen Batrachochytrium dendrobatidis. Fungal Genetics & Biology; 77:31-9
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Wang Y, Smith KM, Taylor JW, Freitag M, Stajich JE. Endogenous Small RNA Mediates Meiotic Silencing of a Novel DNA Transposon. G3; 5(10):1949-60
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Pieuchot L, Lai J, Loh RA, Leong FY, Chiam KH, Stajich J, Jedd G. Cellular Subcompartments through Cytoplasmic Streaming. Dev Cell; 34(4):410-20
|
Progress 10/01/13 to 09/30/14
Outputs
Target Audience: Formal classroom teaching was delivered at UC Riverside where the target audience included primarily minority undergraduate students. Material covered included descriptions of important fungal diseasesand genetics. This was done through a freshman interactive laboratory classcalledDynamic Genomes, and an upperlevel Microbiology course Pathogenic Microbiology. Workshop training on genome tools was performed at the Marine Biological Lab, Woods Hole, MA as part of the Molecular Mycology course. Scientific presentations at international (International Mycological Congress, European Fungal Genetics, CBS-KNAWL Symposium and national (Mycological Society of America, Neurospora Genetics Confrerence) and invited seminars at US and International universities. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? Graudate students were trained during this period through one-on-one mentoring on bioinformatics, software development, and genomic techniques. One student presented his work at a national meeting (Mycological Society of America). How have the results been disseminated to communities of interest? Work has been disseminated in the form of scientific publications, in online content at The Hyphal Tip blog (http://fungalgenoms.org/blog) and the 1000 Fungal Genomes project (http://1000.fungalgenomes.org). The results from this work are also conveyed through presentations at scientific meetings and seminars. Any actionable data regarding population structure, interbreeding of strains of Fusarium which can inform growers is disseminated through Dr Akif Eskalen, a CE specialist at UCR and through the California Avocado Commission. What do you plan to do during the next reporting period to accomplish the goals? Objective 1 - further work to release additional versions of the FungiDB database in collaboration with developers in the EuPathDB team which now has the NIH supported role to provide the FungiDB database. Work in the Stajich lab will focus on community liason and setting of priorities for datatypes and datasets to load into the system. Objective 2 - Software and testing of the phylogenomics via light coverage sequencing will be tested further and a full software package released for general use. The collaborative efforts on population and genomic studies of Fusarium and the avocado dieback disease will continue with manuscripts describing the RADseq population data and the whole genome sequence. Additional sampling of strains in the emerging infestations will be performed through collaboration with Dr Akif Eskalen and farm advisors in the Southern California region. Objective 3 - This objective is expected to be completed in this next year with genome publications for the strains and comparisons between them to be finalized to test for correlations in gene content and symbioses potential or loss.
Impacts
What was accomplished under these goals?
For Objective 1 - we have completed manuscripts (Sain et al, in preparation; Melida et al. Env Microbiology 2014) on cell wall profiling in Neurospora and early diverging fungi. We have learned how cell wall changes evolutionary among a few sampled fungi. In addition, work on early diverging Chytridiomycota on the CBM18 cell wall associated family (Liu et al, in revision) also revealed ways in which some chitin binding gene families can protect cells from chitinases as potential defense mechanism. This also provides new ideas about the role of protective proteins in evolution of pathogenesis. Objective 2. We have focused on a recently emerged pathogen of avocado in southern california caused by a Fusarium species that is vectored by a beetle. My lab has completed a population genomics survey of 60+ strains in collaboration with Akif Eskalen's lab at UCR using RADSeq. We have also annotated the genome of the pathogen using an assembly produced by the NCAUR USDA facility in Peoria, Ill in collaboration with Todd Ward and Kerry O'Donnell. We are continuing to analyze the genome and new transcriptome data from growth on sawdust vs rich media to understand how and what are differently expressed genes which may be important for colonization. We have also developed new software and protocols (PHYling) for using low coverage genome sequencing to extract genes for phylogenetic analyses of Fusairum species in order to establish methods for using this approach for classification of species/strains using this highthroughput approach. Objective 3. We have published one paper (Sachs et al. 2014) on the role of transitions in lifestyles between mutualistic symbionts and pathogens in bacteria. Additional ongoing work is nearing completion of genome sequences and comparisons of strains with different lifestyles to see how genomic content correlates with behavior.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
anbon, G., Ormerod, K.L., Paulet, D., Byrnes III, E.J., Chatterjee, G., Yadav, V., Hon, C., Billmyre, R.B., Brunel, F., Bahn, Y., Chen, W., Chen, Y., Chow, E.W., Copp�e, J., Floyd-Averette, A., Gaillardin, C., Gerik, K.J., Goebels, C., Goldberg, J., Gonzalez-Hilarion, S., Gujja, S., Hamlin, J.L., Hsueh, Y., Ianiri, G., Jones, S., Kodira, C.D., Lam, W., Marra, M.A., Mesner, L.D., Mieczkowski, P.A., Moyrand, F., Nielsen, K., Rossignol, T., Schein, J.E., Shun, S., Wood, I.A., Zeng, Q., Neuv�glise, C., Newlon, C., Perfect, J.R., Lodge, J.K., Idnurm, A., Stajich, J.E., Kronstad, J.W., Sanyal, K., Heitman, J., Fraser, J.A., Cuomo, C.A., Dietrich, F.S. Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation. PLoS Genetics. Vol. 10: 4 p.e1004261. 26p
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Inglis, D.O., Skrzypek, M.S., Liaw, E., Moktali, V., Sherlock, G., Stajich, J.E. Literature-based gene curation and a proposed genetic nomenclature for Cryptococcus. Eukaryotic Cell. Vol. 13: 7 p.878-883.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Treseder, K.K., Maltz, M.R., Hawkins, B.A., Fierer, N., Stajich, J.E., McGuire, K.L. 2014. Evolutionary histories of fungi are reflected in their continental-scale biogeography. Ecology Letters. Vol. 17: 9 p.1086-93.
- Type:
Journal Articles
Status:
Accepted
Year Published:
2014
Citation:
Melida, H., Sain, D., Stajich, J.E., Bulone, V. 2014. Deciphering the uniqueness of mucormycete cell walls by combining biochemical and phylogenomic approaches. Environmental Microbiology. 14p. doi: 10.1111/1462-2920.12601.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Teixeira, M.M., de Almeida, L.G., Kubitschek-Barreira, P., Alves, F.L., Kioshima, �.S., Abadio, A.K., Fernandes, L., Derengowski, L.S., Ferreira, K.S., Souza, R.C., Ruiz, J.C., de Andrade, N.C., Paes, H.C., Nicola, A.M., Albuquerque, P., Gerber, A.L., Martins, V.P., Peconick, L.D., Neto, A.V., Chaucanez, C.B., Silva, P.A., Cunha, O.L., de Oliveira, F.F., dos Santos, T.C., Barros, A.L., Soares, M.A., de Oliveira, L.M., Marini, M.M., Villalobos-Duno, H., Cunha, M.M., de Hoog, S., da Silveira, J.F., Henrissat, B., Ni�o-Vega, G.A., Cisalpino, P.S., Mora-Montes, H.M., Almeida, S.R., Stajich, J.E., Lopes-Bezerra, L.M., Vasconcelos, A.T., Felipe, M.S. Comparative genomics of the major agents of human and animal Sporotrichosis: Sporothrix schenckii and Sporothrix brasiliensis. BMC Genomics. 2014; 15:943. doi: 10.1186/1471-2164-15-943.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Ouyang, S., Park, G., Atamian, H.S., Han, C.S., Stajich, J.E., Kaloshian, I., Borkovich, K.A. Regulation of Innate Immunity to the Fungal Pathogen Fusarium oxysporum by MicroRNAs in Tomato. PLoS Pathogens. Vol. 10(10):e1004464
- Type:
Journal Articles
Status:
Accepted
Year Published:
2015
Citation:
Collins, R.A., Stajich, J.E., Field, D.J., Olive, J.E., DeAbreu, D. The intrinsically low fidelity of nuclear pre-mRNA splicing in Neurospora: implications for the origin of introns and spliceosomes. RNA
- Type:
Journal Articles
Status:
Under Review
Year Published:
2015
Citation:
Liu, P., Stajich, J.E. Characterization of the Carbohydrate Binding Module 18 gene family in the amphibian pathogen Batrachochytrium dendrobatidis. Fungal Genetics & Biology
- Type:
Book Chapters
Status:
Published
Year Published:
2015
Citation:
Stajich, J.E. Phylogenomics enabling Genomic based Mycology. The Mycota VII. Editors: David McLaughlin. Springer. Vol. B.
- Type:
Other
Status:
Published
Year Published:
2015
Citation:
Kennedy P, Stajich J. Twenty-first century mycology: a diverse, collaborative, and highly relevant science. New Phytol. 2015;205(1):23-6. doi: 10.1111/nph.13165.
- Type:
Websites
Status:
Published
Year Published:
2014
Citation:
http://fungidb.org - Fungal Genome Database
- Type:
Websites
Status:
Published
Year Published:
2014
Citation:
http://zygolife.org - Zygomycetes Genealogy of Life Project website
|
Progress 01/01/13 to 09/30/13
Outputs
Target Audience: Target audience. As part of teaching and outreach I participate in co-instruction for the Dynamic Genomes course. Students in the UC Riverside Dynamic Genomes course, a class for first year students. Undergraduate students learn in this calss about transposable elements and their role in maize and rice. My projects also develop bioinformatics tools for fungal genomes. The community of fungal researchers who use the FungiDB database include scientists, students, and postdoctoral researchers working in agriculture, medical, and model systems work on fungi. Efforts.Most of the undergraduate students in the course are from underrepresented minority groups and the UCR campus is a MInority Serving Institute. The fungal genetics scientists who use these tools constitute a broad collection of small and large universities. Changes/Problems: At this stage, no specific funding has been acquired for Fusarium research in the laboratory. However, we are exploring a population genomic study of Fusarium causing disease of avocado at the present time using RAD-Seq. This work will lead to better understanding of the F. euwallacae causing disease currently in Southern California. What opportunities for training and professional development has the project provided? The project has trained four postdoctoral fellows interacting on bioinformatics and experimental biology research. Their research questions span Rice and mosquito transposable elements and cell wall genes in fungi. Graduate students have performed research projects on genotype to phenotype exploration of potential cell wall genes, roles of small RNAs. One on one training was performed with all members of the project team. In addition several postdocs and students have participated in the Cold Spring Harbor course - Programming for Biologists - which is co-taught by one postdoc from the group (S Robb). The resulting training from this course also has assisted in training students and postdocs back in the lab at UCR. How have the results been disseminated to communities of interest? FungiDB has been presented to the audience of scientists who use the tool through outreach and training at multiple conferences and workshops. This includes the Fungal Genetics conference, the Medical Mycology course, and seminars and lectures presented by PI Stajich. A short article was written by PI Stajich for the Nautilus magazine on the importance of fungal symbioses (http://nautil.us/issue/10/mergers--acquisitions/top-5-real-wolves-of-wall-street ). What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Objective 1. Work to discover new cell wall genes was performed in Sain 2013 dissertation and 2 manuscripts in preparation or submission. This includes several dozen genes in Neurospora crassa linked to potential roles in cell wall biology. Two manuscripts in preparation or submitted include data from the Sain (2013) thesis and report cell wall composition differences among the early diverging lineages of Fungi with the Dikarya. This finding is also linked to genomic comparisons which highlight how genome changes can be associated with phenotypic changes. Objective 2. One release of FungiDB was made during the period and additional updated release is expected in mid-2014. The number of genomes has grown to more than 50 supported by FungiDB and the next release will have more than 60 and multiple functional genomics datasets. Objective 3. A study (Sachs et al 2013) was published demonstrated how symbioses evolved among Gamma proteobacteria. Additional work on the genomics of rhizobia bacteria is in preparation but shows how gene content has changed among populations of bacteria that are associated with plants.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Gioti A, Stajich JE, Johannesson H. Neurospora and the dead-end hypothesis: genomic consequences of selfing in the model genus. Evolution. 2013 Dec;67(12):3600-16. doi: 10.1111/evo.12206.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Sachs JL, Skophammer RG, Bansal N, Stajich JE. Evolutionary origins and diversification of proteobacterial mutualists. Proc Biol Sci. 2013 Nov 27;281(1775):20132146. doi: 10.1098/rspb.2013.2146.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Traeger S, Altegoer F, Freitag M, Gabaldon T, Kempken F, Kumar A, Marcet-Houben M, P�ggeler S, Stajich JE, Nowrousian M. The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution. PLoS Genet. 2013;9(9):e1003820. doi: 10.1371/journal.pgen.1003820.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Gryganskyi AP, Humber RA, Stajich JE, Mullens B, Anishchenko IM, Vilgalys R. Sequential utilization of hosts from different fly families by genetically distinct, sympatric populations within the Entomophthora muscae species complex. PLoS One. 2013 Aug 8;8(8):e71168. doi: 10.1371/journal.pone.0071168.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
James TY, Pelin A, Bonen L, Ahrendt S, Sain D, Corradi N, Stajich JE. Shared signatures of parasitism and phylogenomics unite cryptomycota and microsporidia. Curr Biol. 2013 Aug 19;23(16):1548-53. doi: 10.1016/j.cub.2013.06.057
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Hibbett DS, Stajich JE, Spatafora JW. Toward genome-enabled mycology.
Mycologia. 2013 Nov-Dec;105(6):1339-49. doi: 10.3852/13-196.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Rosenblum EB, James TY, Zamudio KR, Poorten TJ, Ilut D, Rodriguez D, Eastman JM, Richards-Hrdlicka K, Joneson S, Jenkinson TS, Longcore JE, Parra Olea G, Toledo LF, Arellano ML, Medina EM, Restrepo S, Flechas SV, Berger L, Briggs CJ, Stajich JE. Complex history of the amphibian-killing chytrid fungus revealed with genome resequencing data. Proc Natl Acad Sci U S A. 2013 Jun 4;110(23):9385-90. doi: 10.1073/pnas.1300130110.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Robb SM, Lu L, Valencia E, Burnette JM 3rd, Okumoto Y, Wessler SR, Stajich JE. The use of RelocaTE and unassembled short reads to produce high-resolution snapshots of transposable element generated diversity in rice. G3 (Bethesda). 2013 Jun 21;3(6):949-57. doi: 10.1534/g3.112.005348.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Jamieson K, Rountree MR, Lewis ZA, Stajich JE, Selker EU. Regional control of histone H3 lysine 27 methylation in Neurospora. Proc Natl Acad Sci U S A. 2013 Apr 9;110(15):6027-32. doi: 10.1073/pnas.1303750110
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Cheng CK, Au CH, Wilke SK, Stajich JE, Zolan ME, Pukkila PJ, Kwan HS. 5'-Serial Analysis of Gene Expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea. BMC Genomics. 2013 Mar 20;14:195. doi: 10.1186/1471-2164-14-195.
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2013
Citation:
D. Sain. Discovery of Fungal Cell Wall Components Using Evolutionary and Functional
Genomics 2013 PhD Dissertation, University of California, Riverside.
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Progress 01/01/12 to 12/31/12
Outputs
OUTPUTS: Presentations were made at national scientific meetings (American Phyotopathological Society, Mycological Society of America) and international meetings (International Society for Human and Animal Mycosis) described the population and functional genomics work that relate to the lab's development of tools for fungal genomics resources. The chitin binding module evolution and gene family evolution in fungi was presented in the form of posters and talks at these meetings. Training modules on use of FungiDB were presented at summer courses for Molecular Mycology and posters presented at conferences. Two new releases of FungiDB in the period were deployed that include more than 50 genomes currently. These resources provide new tools for researchers studying fungal genomes, evolution, and identifying potential genes involved in pathogenicity and analysis of their own data in the context of genome comparisons. Additional presentations on the metagenomics and development of fungal identification with molecular markers was presented at national conference. J. Stajich co-organized a workshop in Fall 2012 to support community involvement in marker development for molecular identification of fungi with next generation sequencing technologies. PARTICIPANTS: Peng Liu, postdoctoral researcher, Stajich Laboratory, University of California, Riverside Partners/Collaborators on FungiDB David Roos, Univ of Pennsylvania Brett Tyler, Oregon State University Collaborators on CBM18 project Ioannis Stergiopoulos, UC Davis The project provided training and professional development in the form of new tutorials and lectures delivered at fungal-specific courses on genomics. Students were also training on an individual basis through campus training at UC Riverside with other plant pathogen focus labs, from Oomycetes to filamentous fungi. TARGET AUDIENCES: Training workshops on fungal genomics have been delivered at conferences and fungal-specific training workshops over the past year. These will improve the genomics literacy of these scientists (students and postdocs). As Oomycetes are also included in the FungiDB database, this training also include delivery of the message to Oomycete researchers in the form of workshops at their annual meetings and at a Oomycete specific workshop held every summer. PROJECT MODIFICATIONS: As previously applied for USDA funding for Fusarium work has not been awarded we have expanded our focus on fungal cell work including Neurospora crassa as a model for discovery of fungal cell wall functions and the amphibian pathogen Batrachochytrium dendrobatidis which contains an expanded gene families of Chitin Binding proteins important in cell walls and interacting with hosts. Experiments to tag and express the proteins in yeast and test their localization and binding affinity will improve our understanding of how the Chitin binding genes can allow a pathogen to escape detection. We are focusing on development of techniques for studying chitin-binding module containing genes through in vivo expression and in vitro testing of binding affinities. This will be coupled with parallel experiments in collaborator's labs on LysM and the GH18 family which also binds chitin, to understand their role in evading plant defense systems. Additional grants have been sought in the area of other plant pathogens such as Sclerotinia and may direct the genomics tool development depending on their success.
Impacts
Current outcomes include the discovery of expanded copy number of chitin binding proteins in some early lineages of Fungi. Comparison of these copies shows rapid evolution indicating potential importance of the family for pathogenesis. The results of this analysis provide insight into the potential adaptations since there are only metabolism and these cell wall protein expansions identified when the genome is compared to non-pathogenic relatives. We are seeking to understand if this is linked to the rise of pathogenicity since these proteins may prevent hosts from recognizing the chitin in the fungal cell wall. This approach is a model for other examples of expanded families and also in testing predictions about host-pathogen interactions. The discoveries made include several predicted secreted proteins have been GFP tagged and shown to localize to outer membranes in Saccharomyces cerevisiae expression system. Purification of the protein has succeeded but binding specificity assays are still underway. In addition the lab is supporting research for many Fungal research systems through the continued development of the FungiDB database and the fungal genomics tools it provides. Two releases (versions 2.0, 2.1) were made in this period. New tools were developed for population genomics analysis to begin to provide researchers who are not informatics specialists the tools to build diagnostic markers from genome sequences. Focus on loading plant pathogenic fungi was undertaken in order to support more direct comparison of these fungal genomes and give researchers the chance to generate hypotheses about genes or processes that distinguish pathogens. Resources include an updated website at http://fungidb.org , downloadable systematic datasets, integrated results from many bioinformatics analysis in a format that allows querying for data mining, and new interfaces for uploading users own datasets to link locations in the genome with their own data and observations. The system also allows for user comments and gene page curation which can permit more functional data to flow from the community into FungiDB and become a nexus point for functional annotation aggregation.
Publications
- Abramyan J, Stajich JE. 2012. Species-specific chitin-binding module 18 expansion in the amphibian pathogen Batrachochytrium dendrobatidis. MBio. 3(3):e00150-12.
- Stajich JE, Harris T, Brunk BP, Brestelli J, Fischer S, Harb OS, Kissinger JC, Li W, Nayak V, Pinney DF, Stoeckert CJ Jr, Roos DS. 2012. FungiDB: an integrated functional genomics database for fungi. Nucleic Acids Res. 40 (Database issue):D675-81.
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