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The John Innes Centre magazine Summer 2017 027/ 12 06 14 THE EARTH UNDER OUR FEET Investigating how soil microbes can benefi t crop growth BOTANICAL BOUDICAS Dr Patricia Fara’s 2017 Innes Lecture RETAINING THE ASHES? Recent research into the spread of ash dieback disease 10 06 Cover__John Innes Advances 1 06/07/2017 16:52 IN THIS ISSUE Contents Summer 2017 03 Welcome to Advances JIC Director Professor Dale Sanders introduces the third issue of the new-look magazine 04 Four new Institute Strategic Programmes ‘Molecules from Nature’, ‘Genes in the Environment’, ‘Plant Health’ and ‘Designing Future Wheat’ 06 Science Research Spotlight The latest research, including a new antibiotic from ant bacteria and solving a colourful mystery 08 The earth under our feet Dr Jacob Malone investigates how the microbial 16 battles in soil can be utilised to benefit crops 10 Fifty years of research 12 Brilliant brassicas at the John Innes Centre With Brassica research at JIC thriving, advances may mean some brassica crops could be grown To celebrate 50 years in Norwich, Dr Sarah year-round in a controlled climate Wilmot looks back over five decades of research 14 From Arusha with love John Innes Centre PhD scientists reflect on the two-week AfriPlantSci summer school in Arusha 15 Botanical Boudicas Dr Patricia Fara’s 2017 Innes Lecture looks at 06 the struggles of women in science over the years 16 Retaining the ashes? Research into the spread of ash dieback disease continues; the survival of this iconic species is still in the balance 18 Awards and achievements Recognising John Innes Centre scientists for their contributions to science 19 Alumnus profile 04 15 Professor Sir David Hopwood, one of JIC’s most eminent scientists, reflects on his career Cover images clockwise from top left: Brassica oleracea, anthocyanic vacuolar inclusions in delphinium, AfriPlantSci summer school in Arusha, domatia of the acacia tree, scientists at John Innes Institute circa 1976 Advances | Summer 2017 Contents__John Innes Advances 2 06/07/2017 17:03 INTRODUCTION Welcome to Advances Professor Dale Sanders, Director of the John Innes Centre introduces the third issue of the new-look Advances magazine his edition, we are pleased to most eminent scientists from the last 50 years, school earlier in the year at the Nelson Mandela introduce four new strategic Professor Sir David Hopwood, for some African Institute of Science & Technology research programmes (p4) funded fascinating career insights and how the institute in Arusha, Tanzania (p14). Our continued by the UK Biotechnology and has changed since he first arrived in 1968. collaboration with the Biosciences eastern TBiological Sciences Research Council and central Africa-International Livestock (BBSRC). These new strategic programmes In The earth under our feet (p8) we take you into Research Institute (BecA-ILRI) hub and our represent a significant investment in the the world of the soil bacteria Pseudomonas support of key events, such as the AfriPlantSci future of the John Innes Centre and its which fights microscopic battles in the soil, summer school, is part of our wider international world-leading scientists. defending plants against pathogens by endeavours to maximise the translation of our producing a suite of antibiotic compounds. research, to help build capacity and to promote Through these new programmes the John Innes Meanwhile, new breakthroughs in Brassica collaborations in Africa and worldwide. Centre will deliver fundamental insights into research (p12) have led to the development of plant and microbial life and address high-profile a new line of fast-growing sprouting broccoli. This year we’re celebrating 50 years in Norwich national and international challenges in with anniversary events throughout the year. agriculture, the environment and human health. Through analysing the diversity of the ash We’re delighted to invite you to join us at our Research at the John Innes Centre spans dieback fungus, our scientists are investigating Open Day on September 16 – it’s free to attend, diverse scientific disciplines from exploring what the future holds for the iconic ash tree, with a range of family-friendly activities to enjoy. how plants and bacteria produce valuable and how we can prevent further spread of You can find out more complex molecules, to developing more the disease (p16). about this event and resilient and nutritious crops. some milestones Three John Innes Centre PhD students share the from the John Innes For this edition’s alumnus interview (p19) we lessons they learned and challenges they faced Centre’s last five catch up with one of the John Innes Centre’s during the two-week AfriPlantSci summer decades on p10. About the John Innes Centre The John Innes Centre is a world-leading research centre based on the Norwich visit: www.jic.ac.uk Research Park. Our mission is to generate knowledge of plants and microbes through innovative research, to train scientists for the future and apply our email: [email protected] knowledge to benefit agriculture, health and well-being and the environment. for more information or follow us John Innes Centre Advances Editorial & Content Team @JohnInnesCentre Oliver Heaton, Adrian Galvin, Sarah Wilmot, Felicity Perry, Andrew Lawn, Edward Allen, Anne Edwards /JohnInnesCentre Photography Andrew Davis Subscribe to the Advances This magazine has been produced in conjunction with: Newhall Publishing Ltd New Hall Lane, Hoylake, Wirral CH47 4BQ e-zine for free at: 0844 545 8102 [email protected] www.newhallpublishing.com www.jic.ac.uk/advances-magazine John Innes Centre Welcome to Advances__John Innes Advances 3 06/07/2017 17:05 JIC NEWS Four new Institute Strategic Programmes Our core research areas are funde d by the UK Biotechnology and Biological Sciences Research Council (BBSRC) and directly address food security, human health and industrial biotechnology. To meet those objectives our research is organised into four Institute Strategic Programmes (ISPs) Plant Health Genes in the Led by Professor Richard Morris, the Plant Health ISP will investigate the processes and Environment mechanisms that promote plant health and crop The Genes in the Environment ISP, led by resilience, focusing on advancing understanding Professor Lars Østergaard, aims to develop of plant interactions with symbionts that benefit a wider and deeper understanding of how the nutrient uptake and crop productivity, and pests environment influences plant growth and and pathogens that limit crop yields. The Plant development. This research will provide Health ISP brings together leading researchers a deeper knowledge of pathways that enable from the John Innes Centre and The Sainsbury Laboratory to unravel the plants to adapt – over both short and longer evolutionary timescales molecular dialogue between plants and microbes, the establishment of the – to environmental conditions. The research carried out under this communication interface, and plant-microbe co-evolution. Building on ISP will be critically important for improving the stability of crop this knowledge we will develop strategies for reducing crop losses and our yields which are strongly infl uenced by changes in weather and reliance on agrochemicals that have negative impacts on the environment, other environmental factors. thus enhancing agricultural yield and sustainability. FEATURED PROJECT POD SHATTER FEATURED PROJECT FIELD PATHOGENOMICS Oilseed rape pods can open in the field and disperse their seeds. This As part of our Plant Health ISP Dr Diane Saunders’ lab is studying process, known as ‘pod shatter’, leads to annual yield losses of around (re-)emerging plant pathogens that pose a significant threat to 15 per cent, totalling roughly £165 million every year. Professor Lars UK agriculture. Recently the lab pioneered a revolutionary Østergaard and his team have studied fruit development in the model genomics-based pathogen surveillance technique that uses the latest plant Arabidopsis. Previously involved in identifying the genes for DNA sequencing technology to rapidly generate high-resolution Arabidopsis fruit opening, since arriving at JIC Professor Østergaard data for describing the diversity in a pathogen population directly and his team have developed resources to translate knowledge of from infected field samples. Using this new technique, and in gene function in this model system to modify certain genes and collaboration with the National Institute for Agricultural Botany improve pod shatter in oilseed rape. Recently, in collaboration with (NIAB) in Cambridge, the teams uncovered a dramatic shift in the Dr Vinod Kumar’s group population of yellow rust in the UK in recent years, largely due to an at JIC, his team discovered influx of fungal spores from pod shatter is accelerated outside the country. This at higher temperatures. information is essential to Their current work is aimed help breeders develop at understanding the wheat varieties resistant to genetic mechanisms the range of yellow rust underlying this e ect to isolates, and will positively inform the development of impact the sustainability of oilseed rape that is more the UK arable industry. resilient to climate change. Advances | Summer 2017 ISP News spread__John Innes Advances 4 06/07/2017 17:06 Molecules from Nature FEATURED PROJECT PLANTS AS FACTORIES Our Molecules from Nature ISP, led by Professor Professor George Lomonosso’s group focuses on utilising Alison Smith, will investigate the vast diversity plant viruses in bio- and nano-technology.
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    bioRxiv preprint doi: https://doi.org/10.1101/2021.06.03.446950; this version posted June 3, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Discovery, Article A fast, general synteny detection engine Joseph B. Ahrens1*, Kristen J. Wade1 and David D. Pollock1* 1Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, Denver, Colorado, USA * Corresponding authors Joseph B. Ahrens E-mail: [email protected] David D. Pollock E-mail: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.06.03.446950; this version posted June 3, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract The increasingly widespread availability of genomic data has created a growing need for fast, sensitive and scalable comparative analysis methods. A key aspect of comparative genomic analysis is the study of synteny, co-localized gene clusters shared among genomes due to descent from common ancestors. Synteny can provide unique insight into the origin, function, and evolution of genome architectures, but methods to identify syntenic patterns in genomic datasets are often inflexible and slow, and use diverse definitions of what counts as likely synteny. Moreover, the reliable identification of putatively syntenic regions (i.e., whether they are truly indicative of homology) with different lengths and signal to noise ratios can be difficult to quantify.
  • Identifying Regions of Conserved Synteny Between

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    IDENTIFYING REGIONS OF CONSERVED SYNTENY BETWEEN PEA (PISUM SPP.), LENTIL (LENS SPP.), AND BEAN (PHASEOLUS SPP.) by Matthew Durwin Moffet A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Plant Sciences MONTANA STATE UNIVERSITY Bozeman, Montana August 2006 © COPYRIGHT by Matthew Durwin Moffet 2006 All Rights Reserved ii APPROVAL of a thesis submitted by Matthew Durwin Moffet This thesis has been read by each member of the thesis committee and has been found to be satisfactory regarding content, English usage, format, citations, bibliographic style, and consistency, and is ready for submission to the Division of Graduate Education. Dr. Norman Weeden Approved for the Department of Plant Sciences and Plant Pathology Dr. John Sherwood Approved for the Division of Graduate Education Dr. Carl A. Fox iii STATEMENT OF PERMISSION TO USE In presenting this thesis in partial fulfillment of the requirements for a master’s degree at Montana State University, I agree that the Library shall make it available to borrowers under rules of the Library. If I have indicated my intention to copyright this thesis by including a copyright notice page, copying is allowable only for scholarly purposes, consistent with “fair use” as prescribed in the U.S. Copyright Law. Requests for permission for extended quotation from or reproduction of this thesis in whole or in parts may be granted only by the copyright holder. Matthew Durwin Moffet August 2006 iv ACKNOWLEDGEMENTS I would like to acknowledge and thank the following individuals: my past and present academic advisors Dr. Dan Bergey, Dr.