James’ research encompasses genome analysis of agriculturally important fungal pathogens and host crop species, and bioinformatic investigation of their evolution and underlying biology of their interactions during infection. His research has described the first analysis of the genomes of several species of agricultural and economic importance. They have defined a broad genetic basis for the biological activities of these organisms and formed a major foundational resource that has facilitated numerous subsequent studies by enabling high-throughput reverse genetics approaches in the study of these species.
James Hane
Project Leader / Senior Research Fellow
Biography
Related Resources & Publications
Oliver, R., Hane, J., Mair, W., & Lopez-Ruiz, F. (2024). "The 2023 update of target site mutations associated with resistance to fungicides and a web-tool to assist label designations." Journal of Plant Diseases and Protection, 131, 1265-1270. DOI: https://doi.org/10.1007/s41348-024-00872-7
Rozano, L., Hane, J.K., Mancera, R.L (2023). "The Molecular Docking of MAX Fungal Effectors with Plant HMA Domain-Binding Proteins." International Journal of Molecular Sciences. DOI: https://doi.org/10.3390/ijms242015239
Jones D, Fornarelli R, Derbyshire M, Gibberd M, Barker K, Hane J. (2023). "The pursuit of genetic gain in agricultural crops through the application of machine-learning to genomic prediction" Front. Genet. DOI: https://doi.org/10.3389/fgene.2023.1186782
Rozano, L., Jones, D. A. B., Hane, J. K., & Mancera, R. L. (2023). "Template-Based Modelling of the Structure of Fungal Effector Proteins." Molecular Biotechnology. DOI: https://doi.org/10.1007/s12033-023-00703-4
Rozano, L., Mukuka, Y. M., Hane, J. K., & Mancera, R. L. (2023). "Ab Initio Modelling of the Structure of ToxA-like and MAX Fungal Effector Proteins." International Journal of Molecular Sciences. DOI: https://doi.org/10.3390/ijms24076262
Severn-Ellis, A.A., Schoeman, M.H., Bayer, P.E., Hane, J.K., Rees, D.J.G., Edwards, D., Batley, J. (2022) "Genome Analysis of the Broad Host Range Necrotroph Nalanthamala psidii Highlights Genes Associated With Virulence" Frontiers in Plant Science. DOI: doi.org/10.3389/fpls.2022.811152
Jones, D.A.B., Moolhuijzen, P.M., Hane, J.K. (2021) "Remote homology clustering identifies lowly conserved families of effector proteins in plant-pathogenic fungi" Mircobial Genomics. DOI: https://doi.org/10.1099/mgen.0.000637
Bertazzoni, S., Jones, D., Phan, H.T., Tan, K.C., Hane, J. (2021) "Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome." BMC Genomics DOI: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07699-8
Jones, D.A.B., Rozano, L., Debler, J.W. Mancera, R.L., Moolhuijzen, P.M., Hane, J.K. (2021) "An automated and combinative method for the predictive ranking of candidate effector proteins of fungal plant pathogens" Scientific Reports DOI: https://doi.org/10.1038/s41598-021-99363-0
Andronis, C.E., Hane, J.K., Bringans, S., Hardy, G.E.S.J., Jacques, S., Lipscombe, R., Tan, K.C. (2021) "Gene Validation and Remodelling Using Proteogenomics of Phytophthora cinnamomi, the Causal Agent of Dieback" Frontiers in Microbiology. DOI: https://doi.org/10.3389/fmicb.2021.665396
Andronis, C.E., Hane, J., Bringans, S., Hardy, G., Jacques, S., Lipscombe, R., Tan, K-C. (2021). "Gene validation and remodelling using proteogenomics of Phytophthora cinnamomi, the causal agent of Dieback." Frontiers Microbiol. DOI: http://dx.doi.org/10.3389/fmicb.2021.665396
Michael, P.J., Jones, D., White, N., Hane, J.K., Bunce, M., Gibberd, M. (2020) "Crop-zone weed Mycobiomes of the South-Western Australian grain belt." Frontiers in Microbiology DOI: https://doi.org/10.3389/fmicb.2020.581592
Shah R.M., Williams A.H., Hane J, Lawrence J., Farfan-Caceres L.M., Debler J., Oliver R.P., Lee R. (2020) "Reference Genome Assembly for Australian Ascochyta rabiei Isolate ArME14" Genetics GSA G3 DOI: https://doi.org/10.1534/g3.120.401265
Hane, J.K., Paxman, J., Jones D.A.B., Oliver, R.P., De Wit, P.J.G.M. (2019) "Catastrophy”, a genome-informed trophic classification of filamentous plant pathogens – How many different types of filamentous plant pathogens are there?" Frontiers in Microbiology DOI: https://doi.org/10.3389/fmicb.2019.03088
Derbyshire, M.C., Denton-Giles, M., Hane, J.K., Chang, S., Mousavi-Derazmmahelleh, M., Raffaele, S., Buchwaldt, L., Kamphuis, L.G. (2019) "A whole genome scan of SNP data suggests a lack of abundant hard selective sweeps in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum" PLOS One DOI: https://doi.org/10.1371/journal.pone.0214201
Mousavi-Derazmahalleh, M., Chang, S., Thomas, G., Derbyshire, M., Bayer, P.E., Edwards, D., Nelson, M.N., Erskine, W., Lopez-Ruiz, F.J., Clements, J., and Hane, J.K. (2019) "Prediction of pathogenicity genes involved in adaptation to a lupin host in the fungal pathogens Botrytis cinerea and Sclerotinia sclerotiorum via comparative genomics" BMC Genomics DOI: https://doi.org/10.1186/s12864-019-5774-2
Bertazzoni, S., Williams, A.H., Jones, D.A., Syme, R.A., Tan, K.C., Hane, J.K. (2018) "Accessories make the outfit: Accessory Chromosomes and other dispensable DNA regions in plant-pathogenic Fungi." Molecular Plant-Microbe Interactions DOI: https://pubmed.ncbi.nlm.nih.gov/29664319/
Jones, D.A.B., Bertazzoni, S., Turo, C.J., Syme, R. A., Hane, J.K. (2018) "Bioinformatic prediction of plant–pathogenicity effector proteins of fungi" Current Opinion in Microbiology. doi/org/10.1016/j.mb.2018.01.017 DOI: https://pubmed.ncbi.nlm.nih.gov/29462764/
Mousavi-Derazmahalleh, M., Bayer, P., Nevado, B., Hurgobin, B., Filatov, D., Kilian, A., Kamphuis, L.G., Singh, K.B., Hane, J., Edwards, D., Erskine, W. and Nelson, M.N. (2018) "Migration and adaptation of wild narrow-leafed lupin" Theoretical and Applied Genetics DOI: https://link.springer.com/article/10.1007/s00122-017-3045-7
Mousavi-Derazmahalleh, M., Bayer, P.E., Hane, J.K., Babu, V., Nguyen, H.T., Nelson, M.N., Erskine, W., Varshney, R.K., Papa, R., Edwards, D (2018) "Adapting legume crops to climate change using genomic approaches" Plant, Cell & Environment DOI: https://pubmed.ncbi.nlm.nih.gov/29603775/
Mousavi-Derazmahalleh, M., Bayer, P.E., Nevado, B., Hurgobin, B., Filatov, D., Kilian, A., Kamphuis, L.G., Singh, K.B., Berger, J.D., Hane, J.K., Edwards, D., Erskine, W., Nelson, M.N (2018) "Exploring the genetic and adaptive diversity of a pan-Mediterranean crop wild relative: Narrow-leafed lupin" Theoretical & Applied Genetics DOI: https://doi.org/10.1007/s00122-017-3045-7
Moolhuijzen, P., Theen See, P., Hane, J.K., Shi, G., Liu, Z., Oliver, R.P., Moffat, C.S. (2018) "Comparative genomics of the wheat fungal pathogen Pyrenophora tritici-repentis reveals chromosomal variations and genome plasticity" BMC Genomics DOI: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4680-3
Syme, R.A., Tan, K., Ryback, K., Friesen, T.L., McDonald, B.A., Oliver, R.P., Hane, J.K. (2018) "Pan-Parastagonospora Comparative Genome Analysis – effector prediction and genome evolution." Genome Biology and Evolution DOI: https://doi.org/10.1093/gbe/evy192
Anderson, J.P., Sperschneider, J., Win, J., Kidd, B., Yoshida, K., Hane, J., Saunders, D.G.O, Singh, K.B. (2017) "Comparative secretome analysis of Rhizoctonia solani isolates with different host ranges reveals unique secretomes and cell death inducing effectors." Scientific Reports. DOI: https://doi.org/10.1038/s41598-017-10405-y
Hane, J.K., Ming, Y., Kamphuis, L.G., Nelson, M.N., Garg, G., Atkins, C.A., Bayer, P.E., Bravo, A., Bringans, S., Cannon, S., Edwards, D., Foley, R., Gao, L., Harrison, M.J., Huang, W., Hurgobin, B., Li, S., Liu, C., McGrath, A., Morahan, G., Murray, J., Weller, J., Jian, J., Singh, K.B. (2016) "A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plant–microbe interactions and legume evolution" Plant Biotechnology Journal DOI: doi.org/10.1111/pbi.12615
Anderson, J.P., Hane, J.K., Stoll, T., Pain, N., Hastie, M.L., Kaur, P., Hoogland, C., Gorman, J.J., Singh, K.B. (2016) "Proteomic Analysis of Rhizoctonia solani Identifies Infection-specific, Redox Associated Proteins and Insight into Adaptation to Different Plant Hosts" Molecular & Cellular Proteomics DOI: 10.1074/mcp.M115.054502
Anderson, J.P., Hane, J.K., Stoll, T., Pain, N., Hastie, M.L., Parwinder, K., Hoogland, C., Gorman, J.J., Singh, K.B. (2016) "Mass-spectrometry data for Rhizoctonia solani proteins produced during infection of wheat and vegetative growth" Data in Brief DOI: doi.org/10.1016/j.dib.2016.05.042
Foley, R.C., Kidd, B.N., Hane, J.K., Anderson, J.P., Singh, K.B. (2016) "Reactive Oxygen Species Play a Role in the Infection of the Necrotrophic Fungi, Rhizoctonia solani in Wheat" PLoS ONE DOI: doi.org/10.1371/journal.pone.0152548
McDonald, M.C., McGinness, L., Hane J.K., Williams, A.H., Milgate, A., Solomon, P.S (2016) "Utilizing Gene Tree Variation to Identify Candidate Effector Genes in Zymoseptoria tritici" G3 Genes | Genomes | Genetics DOI: doi.org/10.1534/g3.115.025197
Syme, R.A., Tan, K.C., Hane, J.K., Dodhia, K., Stoll, T., Hastie, M., Furuki, E., Ellwood, S.R., Williams, A.H., Tan, Y., Testa, A.C., Gorman, J.J., Oliver, R.P. (2016) "Comprehensive Annotation of the Parastagonospora nodorum Reference Genome Using Next-Generation Genomics, Transcriptomics and Proteogenomics" PLoS ONE DOI: doi.org/10.1371/journal.pone.0147221
Testa, A.C., Oliver, R.P., Hane, J.K. (2016) "OcculterCut: A Comprehensive Survey of AT-Rich Regions in Fungal Genomes" Genome Biology and Evolution DOI: doi.org/10.1093/gbe/evw121
Williams. A.H., Sharma, M., Thatcher, L.F., Azam, S., Hane, J.K., Sperschneider, J., Kidd, B.N., Anderson, J.P., Ghosh, R., Lichtenzveig, J., Corby Kistler, H., Shea, T., Young, S., Buck, S.A., Kamphuis, L.G., Saxena, R., Pande, S., Ma, L., Varshney, R.K., Singh, K.B (2016) "Comparative genomics and prediction of conditionally dispensable sequences in legume–infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors" BMC Genomics DOI: 10.1186/s12864-016-2486-8
Foley, R.C., Jimenez-Lopez, J.C., Kamphuis, L.G., Hane, J.K., Melser, S., Singh, K.B. (2015) "Analysis of conglutin seed storage proteins across lupin species using transcriptomic, protein and comparative genomic approaches" BMC Plant Biology DOI: doi.org/10.1186/s12870-015-0485-6
McDonald, M.C., Williams, A.H., Milgate, A., Pattemore, J.A., Solomon, P.S., Hane, J.K. (2015) "Next-generation re-sequencing as a tool for rapid bioinformatic screening of presence and absence of genes and accessory chromosomes across isolates of Zymoseptoria tritici" Fungal Genetics and Biology DOI: doi.org/10.1016/j.fgb.2015.04.012
Testa, A., Oliver, R.P., Hane, J.K (2015) "Overview of genomic and bioinformatic resources for Zymoseptoria tritici" Fungal Genetics and Biology DOI: doi.org/10.1016/j.fgb.2015.04.011
Testa, A.C., Hane, J.K., Ellwood, S.R., Oliver, R.P. (2015) "CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts" BMC Genomics DOI: doi.org/10.1186/s12864-015-1344-4
Thatcher, L.F., Kamphuis, L.G., Hane, J.K., Oñate-Sánchez, L., Singh, K.B. (2015) "The Arabidopsis KH-Domain RNA-Binding Protein ESR1 Functions in Components of Jasmonate Signalling, Unlinking Growth Restraint and Resistance to Stress" PLOS ONE DOI: doi.org/10.1371/journal.pone.0126978
Kamphuis, L.G., Hane, J.K., Nelson, M.N., Gao, L., Atkins, C.A., Singh, K.B. (2014) "Transcriptome sequencing of different narrow-leafed lupin tissue types provides a comprehensive uni-gene assembly and extensive gene-based molecular markers" Plant Biotechnology Journal DOI: doi.org/10.1111/pbi.12229
Pattemore, J.A., Hane, J.K., Williams, A.H., Wilson, B.A.L., Stodart, B.J., Ash, G.J. (2014) "The genome sequence of the biocontrol fungus Metarhizium anisopliae and comparative genomics of Metarhizium species" BMC Genomics DOI: 10.1186/1471-2164-15-660
Hane, J.K., Anderson, J.P., Williams, A.H., Sperschneider, J., Singh, K.B. (2014) "Genome Sequencing and Comparative Genomics of the Broad Host-Range Pathogen Rhizoctonia solani AG8" PLOS Genetics DOI: doi.org/10.1371/journal.pgen.1004281