David Hughes

Name	David Hughes
Job title	Scientific Specialist -Bioinformatics Scientist
Email address	david.hughes@rothamsted.ac.uk
Department	Intelligent Data Ecosystems
Research cluster	CAS: Genomics and Bioinformatics
ORCID	https://orcid.org/0000-0003-1439-5421
Preferred citation	Hughes, D. J.
Office	Harpenden

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Research outputs

The mechanisms behind the contrasting responses to waterlogging in black-grass (Alopecurus myosuroides) and wheat (Triticum aestivum)

Harrison, C., Noleto-Dias, C., Ruvo, G., Hughes, D. J., Smith, D., Mead, A., Ward, J. L., Heuer, S. and Macgregor, D. 2024. The mechanisms behind the contrasting responses to waterlogging in black-grass (Alopecurus myosuroides) and wheat (Triticum aestivum). Functional Plant Biology. 51, p. FP23193. https://doi.org/10.1071/FP23193

The complete genome assemblies of 19 insect pests of worldwide importance to agriculture

King, R., Buer, B., Davies, T. G. E., Ganko, E., Guest, M., Hassani-Pak, K., Hughes, D. J., Raming, K., Rawlings, C. J., Williamson, M. S., Crossthwaite, A., Nauen, R. and Field, L. M. 2023. The complete genome assemblies of 19 insect pests of worldwide importance to agriculture. Pesticide Biochemistry and Physiology. 191, p. 105339. https://doi.org/10.1016/j.pestbp.2023.105339

Novel molecules and target genes for vegetative heat tolerance in wheat

Rose, T., Wilkinson, M. D., Lowe, C., Xu, J., Hughes, D. J., Hassall, K. L., Hassani-Pak, K., Amberkar, S., Noleto-Dias, C., Ward, J. L. and Heuer, S. 2022. Novel molecules and target genes for vegetative heat tolerance in wheat. Plant Environmental Interactions. 3 (6), pp. 264-289. https://doi.org/10.1002/pei3.10096

Arable soil nitrogen dynamics reflect organic inputs via the extended composite phenotype

Neal, A. L., Barrat, H., Bacq-Lebreuil, A., Qin, Y., Zhang, X., Takahashi, T., Rubio, V., Hughes, D. J., Clark, I. M., Cardenas, L. M., Gardiner, L., Krishna, R., Glendining, M. J., Ritz, K., Mooney, S. and Crawford, J. W. 2023. Arable soil nitrogen dynamics reflect organic inputs via the extended composite phenotype. Nature Food. 4, pp. 51-60. https://doi.org/10.1038/s43016-022-00671-z

Genetic diversity in nitrogen fertilizer responses and N gas emission in modern wheat

Oszvald, M., Hassall, K. L., Hughes, D. J., Torres-Ballesteros, A., Clark, I. M., Riche, A. B. and Heuer, S. 2022. Genetic diversity in nitrogen fertilizer responses and N gas emission in modern wheat. Frontiers in Plant Science. 13, p. 816475. https://doi.org/10.3389/fpls.2022.816475

A Near-Chromosome Level Genome Assembly of the European Hoverfly, Sphaerophoria Rueppellii (Diptera: Syrphidae), and a Comparative Analysis of Insecticide Resistance-Related Gene Families in Hemipteran Crop Pests and Pollinators

Bailey, E., Field, L. M., Rawlings, C. J., King, R., Mohareb, F., Hassani-Pak, K., Hughes, D. J., Williamson, M. S., Ganko, E., Buer, B. and Nauen, R. 2022. A Near-Chromosome Level Genome Assembly of the European Hoverfly, Sphaerophoria Rueppellii (Diptera: Syrphidae), and a Comparative Analysis of Insecticide Resistance-Related Gene Families in Hemipteran Crop Pests and Pollinators. BMC Genomics. 23 (1), p. 198. https://doi.org/10.1186/s12864-022-08436-5

A scaffold-level genome assembly of a minute pirate bug, Orius laevigatus, and a comparative analysis of insecticide resistance-related gene families with hemipteran crop pests

Bailey, E., Field, L. M., Rawlings, C. J., King, R., Mahareb, F., Hassani-Pak, K., Hughes, D. J., Williamson, M. S., Ganko, E., Buer, B. and Nauen, R. 2022. A scaffold-level genome assembly of a minute pirate bug, Orius laevigatus, and a comparative analysis of insecticide resistance-related gene families with hemipteran crop pests. BMC Genomics. 23, p. 45. https://doi.org/10.1186/s12864-021-08249-y

Land management legacy affects abundance and function of the acdS gene in wheat root associated pseudomonads

Ruscoe, H., Taketani, R., Clark, I. M., Lund, G., Hughes, D. J., Dodd, I., Hirsch, P. R. and Mauchline, T. H. 2021. Land management legacy affects abundance and function of the acdS gene in wheat root associated pseudomonads. Frontiers in Microbiology. 12, p. 611339. https://doi.org/10.3389/fmicb.2021.611339

Investigating the origins and evolution of a glyphosate-resistant weed invasion in South America

Gaines, T., Slavov, G., Hughes, D. J., Kupper, A., Sparks, C., Oliva, J., Vila-Aiub, M., Alejandro Garcia, M., Aldo Merotto Jr and Neve, P. 2021. Investigating the origins and evolution of a glyphosate-resistant weed invasion in South America. Molecular Ecology. 30 (21), pp. 5360-5372. https://doi.org/10.1111/mec.16221

Metagenomic approaches reveal differences in genetic diversity and relative abundance of nitrifying bacteria and archaea in contrasting soils

Clark, I. M., Hughes, D. J., Fu, Q., Abadie, M. and Hirsch, P. R. 2021. Metagenomic approaches reveal differences in genetic diversity and relative abundance of nitrifying bacteria and archaea in contrasting soils . Scientific Reports. 11, p. 15905. https://doi.org/10.1038/s41598-021-95100-9

Microbiome Aggregated Traits and Assembly are More Sensitive to Soil Management than Diversity

Neal, A. L., Hughes, D. J., Clark, I. M., Jansson, J. K. and Hirsch, P. R. 2021. Microbiome Aggregated Traits and Assembly are More Sensitive to Soil Management than Diversity. mSystems. 6 (3), pp. e01056-20. https://doi.org/10.1128/mSystems.01056-20

Crop Type Exerts Greater Influence Upon Rhizosphere Phosphohydrolase Gene Abundance and Phylogenetic Diversity than Phosphorus Fertilization.

Neal, A. L., McLaren, T., Campolino, M. L., Hughes, D. J., Coelho, A. M., De Paula Lana, U. G., Gomes, E. A. and De Sousa, S. M. 2020. Crop Type Exerts Greater Influence Upon Rhizosphere Phosphohydrolase Gene Abundance and Phylogenetic Diversity than Phosphorus Fertilization. FEMS Microbiology Ecology. 97 (4), p. fiab033. https://doi.org/10.1093/femsec/fiab033

Wheat dwarfing influences selection of the rhizosphere microbiome

Kavamura, V. N., Robinson, R. J., Hughes, D., Clark, I. M., Rossmann, M., De Melo, I.S., Hirsch, P. R., Mendes, R. and Mauchline, T. H. 2020. Wheat dwarfing influences selection of the rhizosphere microbiome. Scientific Reports. 10, p. 1452. https://doi.org/10.1038/s41598-020-58402-y

Land management and microbial seed load effect on rhizosphere and endosphere bacterial community assembly in wheat

Kavamura, V. N., Robinson, R. J., Hayat, R., Clark, I. M., Hughes, D. J., Rossmann, M., Hirsch, P. R., Mendes, R. and Mauchline, T. H. 2019. Land management and microbial seed load effect on rhizosphere and endosphere bacterial community assembly in wheat. Frontiers in Microbiology. 10 (2625). https://doi.org/10.3389/fmicb.2019.02625

Basic LEUCINE ZIPPER TRANSCRIPTION FACTOR 67 transactivates DELAY OF GERMINATION 1 to establish primary seed dormancy in Arabidopsis

Bryant, F. M., Hughes, D. J., Hassani-Pak, K. and Eastmond, P. J. 2019. Basic LEUCINE ZIPPER TRANSCRIPTION FACTOR 67 transactivates DELAY OF GERMINATION 1 to establish primary seed dormancy in Arabidopsis. The Plant Cell. https://doi.org/10.1105/tpc.18.00892

Transcriptome changes induced by arbuscular mycorrhizal fungi in sunflower (Helianthus annuus L.) roots

Vangelisti, A., Natali, L., Bernardi, R., Sbrana, C., Turrini, A., Hassani-Pak, K., Hughes, D. J., Cavallini, A., Giovannetti, M. and Giordani, T. 2018. Transcriptome changes induced by arbuscular mycorrhizal fungi in sunflower (Helianthus annuus L.) roots. Scientific Reports. 8 (4), pp. 1-14. https://doi.org/10.1038/s41598-017-18445-0

Insecticide resistance mediated by an exon skipping event.

Berger, M., Puinean, A. M., Randall, E., Zimmer, C. T., Silva, W. M., Bielza, P., Field, L. M., Hughes, D. J., Mellor, I., Hassani-Pak, K., Siqueira, H. A. A., Williamson, M. S. and Bass, C. 2016. Insecticide resistance mediated by an exon skipping event. Molecular Ecology. 25 (22), pp. 5692-5704. https://doi.org/10.1111/mec.13882

Comparative genomics to explore phylogenetic relationship, cryptic sexual potential and host specificity of Rhynchosporium species on grasses

Penselin, D., Munsterkotter, M., Kirsten, S., Felder, M., Taudien, S., Plazer, M., Ashelford, K., Paskiewicz, K. H., Harrsion, R. J., Hughes, D. J., Wolf, T., Shelest, E., Graap, J., Hoffmann, J., Wenzel, C., Woltje, N., King, K. M., Fitt, B. D. L., Guldener, U., Avrova, A. and Knogge, W. 2016. Comparative genomics to explore phylogenetic relationship, cryptic sexual potential and host specificity of Rhynchosporium species on grasses. BMC Genomics. 17, pp. 953 (1-32p). https://doi.org/10.1186/s12864-016-3299-5

Control of arable crop pathogens: climate change mitigation, impacts and adaptation

Fitt, B. D. L., Hughes, D. J. and Stotz, H. U. 2016. Control of arable crop pathogens: climate change mitigation, impacts and adaptation. in: Edwards, D. and Batley, J. (ed.) Plant genomics and climate change Springer, New York. pp. 49-66

Climate change increases risk of fusarium wheat ear blight on wheat in central China

Zhang, X., Halder, J., White, Robin P., Hughes, D. J., Ye, Z., Wang, C., Xu, R., Gan, B. and Fitt, B. D. L. 2014. Climate change increases risk of fusarium wheat ear blight on wheat in central China. Annals of Applied Biology - AAB. 164 (3), pp. 384-395. https://doi.org/10.1111/aab.12107

Arable crop disease control, climate change and food security

Fitt, B. D. L., Evans, N., Gladders, P., Hughes, D. J. and West, J. S. 2013. Arable crop disease control, climate change and food security.

Climate change and arable crop disease control: mitigation and adaptation

Fitt, B. D. L., Evans, N., Gladders, P., Hughes, D. J., Madgwick, J. W., Jeger, M. J., Townsend, J. A., Turner, J. A. and West, J. S. 2011. Climate change and arable crop disease control: mitigation and adaptation. Deising, H. B., Lyr, H., Russell, P. E., Kuck, K. H., Gisi, U. and Dehne, H. W. (ed.) Modern Fungicides and Antifungal Compounds VI: Proceedings 16th Reinhardsbrunn Symposium, Friedrichroda, 25-29 April 2010 . Deutsche Phytomedizinische Gesellschaft, Braunschweig. pp. 17-26

Disease control on UK winter oilseed rape contributes to climate change mitigation

Mahmuti, M., West, J. S., Watts, J., Gladders, P., Hughes, D. J. and Fitt, B. D. L. 2011. Disease control on UK winter oilseed rape contributes to climate change mitigation. Abstracts 13th International Rapeseed Congress, Prague, 5-9 June 2011 . pp. 1330-1333

Effects of disease control by fungicides on greenhouse gas emissions by UK arable crop production

Hughes, D. J., West, J. S., Atkins, S. D., Gladders, P., Jeger, M. J. and Fitt, B. D. L. 2011. Effects of disease control by fungicides on greenhouse gas emissions by UK arable crop production. Pest Management Science. 67 (9), pp. 1082-1092. https://doi.org/10.1002/ps.2151

Resistance to Pyrenopeziza brassicae (light leaf spot) in Brassica napus (oilseed rape) stops asexual but not sexual sporulation

Boys, E. F., Roques, S., West, J. S., Werner, C. P., King, G. J., Dyer, P. S., Hughes, D. J. and Fitt, B. D. L. 2011. Resistance to Pyrenopeziza brassicae (light leaf spot) in Brassica napus (oilseed rape) stops asexual but not sexual sporulation. Abstracts 13th International Rapeseed Congress, Prague, 5-9 June 2011 .

Arable crop disease control, climate change and food security

Fitt, B. D. L., Evans, N., Gladders, P., Hughes, D. J., Jeger, M. J., Turner, J. A. and West, J. S. 2011. Arable crop disease control, climate change and food security. Crop protection in Southern Britain. Aspects of Applied Biology 106 . pp. 161-169

Climate change and arable crop disease control: mitigation and adaptation

Fitt, B. D. L., Evans, N., Gladders, P., Hughes, D. J., Madgwick, J. W., Jeger, J., Townsend, J. A., Turner, J. A. and West, J. S. 2010. Climate change and arable crop disease control: mitigation and adaptation. Abstracts 16th International Reinhardsbrunn Symposium: Modern Fungicides and Antifungal Compounds, Friedrichroda, 25-29 April 2010 . pp. 18