DOCSLIB.ORG

The Earth Under Our Feet Botanical Boudicas

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Earth Under Our Feet Botanical Boudicas 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.
Load more

Recommended publications
  • Constraints on Genes Shape Long-Term Conservation of Macro-Synteny in Metazoan Genomes
    Lv et al. BMC Bioinformatics 2011, 12(Suppl 9):S11 http://www.biomedcentral.com/1471-2105/12/S9/S11 PROCEEDINGS Open Access Constraints on genes shape long-term conservation of macro-synteny in metazoan genomes Jie Lv, Paul Havlak, Nicholas H Putnam* From Ninth Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Com- parative Genomics Galway, Ireland. 8-10 October 2011 Abstract Background: Many metazoan genomes conserve chromosome-scale gene linkage relationships (“macro-synteny”) from the common ancestor of multicellular animal life [1-4], but the biological explanation for this conservation is still unknown. Double cut and join (DCJ) is a simple, well-studied model of neutral genome evolution amenable to both simulation and mathematical analysis [5], but as we show here, it is not sufficent to explain long-term macro- synteny conservation. Results: We examine a family of simple (one-parameter) extensions of DCJ to identify models and choices of parameters consistent with the levels of macro- and micro-synteny conservation observed among animal genomes. Our software implements a flexible strategy for incorporating genomic context into the DCJ model to incorporate various types of genomic context (“DCJ-[C]”), and is available as open source software from http://github.com/ putnamlab/dcj-c. Conclusions: A simple model of genome evolution, in which DCJ moves are allowed only if they maintain chromosomal linkage among a set of constrained genes, can simultaneously account for the level of macro- synteny conservation and for correlated conservation among multiple pairs of species. Simulations under this model indicate that a constraint on approximately 7% of metazoan genes is sufficient to constrain genome rearrangement to an average rate of 25 inversions and 1.7 translocations per million years.
    [Show full text]
  • Securing a Safer, Healthier and More Sustainable
    Healthy Plants. Healthy People. Healthy Planet. Securing a safer, healthier and more sustainable future through the power of plant and microbial science The Healthy Plants, The John Innes Centre and The Sainsbury Healthy People, Healthy Laboratory are at the forefront of efforts Planet (HP³) project is to bring this vision to life, but getting there requires a step change in capability that is only our vision for achieving a achievable through new ways of working. safer, healthier and more We are working with UKRI’s Biotechnology and sustainable future through Biological Sciences Research Council (BBSRC) the power of plant and to develop the case for investment in our new infrastructure, and are seeking private capital microbial science. investment alongside public funding to enable us to realise our exciting and ambitious vision. Here, we lay out the near and very real threats facing humankind and the planet more widely, the potential for plant and microbial science The John Innes Centre is an independent, to overcome them, and why a UK hub for plant and microbial science would provide pivotal international research centre specialising resource for developing solutions. in plant science and microbiology. It is a registered charity funded by UKRI-BBSRC, the European Research Council and other charitable sources including the John Innes Foundation. The John Innes Centre uses genetic approaches to answer fundamental questions of bioscience, and to translate the answers into environmental and societal benefits. For more information, please contact Felicity Perry, Head of The Sainsbury Laboratory is a Communications and Engagement world-leading independent research at the John Innes Centre: institute that specialises in plant-microbe Email: [email protected] interactions, funded by The Gatsby Charitable Telephone: +44 (0) 1603 450 269 Mail: John Innes Centre, Foundation, The University of East Anglia and Norwich, UKRI-BBSRC.
    [Show full text]
  • About Synteny Analysis
    Chris Shaffer Last update: 08/11/2021 About Synteny Analysis In eukaryotes, synteny analysis is really the investigation of how chromosomes, or large sections of chromosomes evolve over time. To investigate this, scientists compare the order and orientation of either genes or DNA sequences between homologous chromosomes from two or more species (syntenic blocks). Genes within a syntenic region may have similar functional constraints or regulatory regimes that function best when they are kept together. In the lab, flies exhibit chromosomal changes such as duplications, deletions, and inversions, particularly when exposed to mutagens such as x-rays; the question is what kinds of changes happen in the wild, and at what rate? Analysis of such changes gives us information about what changes can be tolerated and provides insights into speciation. To search for chromosome changes that occurred over the course of fruit fly evolution, you can compare the order and orientation of the genes in your project with the order and orientation of the orthologous genes in Drosophila melanogaster. There are three basic steps to the process: 1. Determine orthologs If you are going to decide how genes change order/orientation you first need to make sure you are looking at orthologous genes in each species. If you have assigned orthology during annotation you can use that assignment. If not, you will need to do cross-species BLAST searches. 2. Assess position Once you have the orthology assigned, use your favorite genome browser (e.g. GBrowse or JBrowse on FlyBase) to find the position and orientation of each gene in your project.
    [Show full text]
  • “Parent-Daughter” Relationships Among Vertebrate Paralogs
    Reconstruction of the deep history of “Parent-Daughter” relationships among vertebrate paralogs Haiming Tang*, Angela Wilkins Mercury Data Science, Houston, TX, 77098 * Corresponding author Abstract: Gene duplication is a major mechanism through which new genetic material is generated. Although numerous methods have been developed to differentiate the ortholog and paralogs, very few differentiate the “Parent-Daughter” relationship among paralogous pairs. As coined by the Mira et al, we refer the “Parent” copy as the paralogous copy that stays at the original genomic position of the “original copy” before the duplication event, while the “Daughter” copy occupies a new genomic locus. Here we present a novel method which combines the phylogenetic reconstruction of duplications at different evolutionary periods and the synteny evidence collected from the preserved homologous gene orders. We reconstructed for the first time a deep evolutionary history of “Parent-Daughter” relationships among genes that were descendants from 2 rounds of whole genome duplications (2R WGDs) at early vertebrates and were further duplicated in later ceancestors like early Mammalia and early Primates. Our analysis reveals that the “Parent” copy has significantly fewer accumulated mutations compared with the “Daughter” copy since their divergence after the duplication event. More strikingly, we found that the “Parent” copy in a duplication event continues to be the “Parent” of the younger successive duplication events which lead to “grand-daughters”. Data availability: we have made the “Parent-Daughter” relationships publicly available at https://github.com/haimingt/Parent-Daughter-In-Paralogs/ Introduction Gene duplication has been widely accepted as a shaping force in evolution (Zhang, et al.
    [Show full text]
  • Uk Plant Science Research Strategy a Green Roadmap for the Next Ten Years Contents
    UK PLANT SCIENCE RESEARCH STRATEGY A GREEN ROADMAP FOR THE NEXT TEN YEARS CONTENTS Foreword . 1 Introduction . 3 Context . 4 Deliverables . .5 1 Securing. a Pipeline of Transformative Discoveries . 5 2 Strategic. Research to Solve Grand Challenges . .8 3 Innovation. 11 4 Diverse. People and Skills . .18 5 National. Infrastructure . 20 6 International. Landscape . .21 List of Recommendations . 23 Appendix 1: List of people consulted . .25 FOREWORD In many ways the idea of a national strategy I also held a workshop with twenty independent is counterintuitive – science is global and research fellows . I am extremely grateful to more than ever we need to be working across everyone who gave their time and thoughtful national boundaries to solve the enormous input during a very challenging period of environmental and societal challenges that we national lockdown . The issues we discussed face . However, to collaborate more effectively in revolved around what plant science research the international arena we first need increased can and should contribute to society, and what investment and better co-ordination across the mechanisms are needed to ensure effective UK . In April 2020, following discussions with delivery of those contributions . After the colleagues, I proposed a community-driven consultation, I distilled many pages of informal approach to develop a plant science research notes into a two page summary of the core strategy for the UK . I engaged with no personal messages that would underpin the strategy . In or professional agenda, no vested interest and the second phase, this summary was circulated an open mind1 . Melanie Welham, Executive to all consultees, with a request to consult more Chair of the UK Biotechnology and Biological widely within their local constituency and to Sciences Research Council (BBSRC), part feedback any further comments .
    [Show full text]
  • Calcisponges Have a Parahox Gene and Dynamic Expression of 2 Dispersed NK Homeobox Genes 3
    1 Calcisponges have a ParaHox gene and dynamic expression of 2 dispersed NK homeobox genes 3 4 Sofia A.V. Fortunato1, 2, Marcin Adamski1, Olivia Mendivil Ramos3, †, Sven Leininger1, , 5 Jing Liu1, David E.K. Ferrier3 and Maja Adamska1§ 6 1Sars International Centre for Marine Molecular Biology, University of Bergen, 7 Thormøhlensgate 55, 5008 Bergen, Norway 8 2Department of Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, 9 Norway 10 3 The Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of 11 St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK. 12 † Current address: Stanley Institute for Cognitive Genomics, Cold Spring Harbor 13 Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA. 14 Current address: Institute of Marine Research, Nordnesgaten 50, 5005 Bergen, Norway 15 §Corresponding author 16 Email address: [email protected] 17 18 Summary 19 Sponges are simple animals with few cell types, but their genomes paradoxically 20 contain a wide variety of developmental transcription factors1‐4, including 21 homeobox genes belonging to the Antennapedia (ANTP)class5,6, which in 22 bilaterians encompass Hox, ParaHox and NK genes. In the genome of the 23 demosponge Amphimedon queenslandica, no Hox or ParaHox genes are present, 24 but NK genes are linked in a tight cluster similar to the NK clusters of bilaterians5. 25 It has been proposed that Hox and ParaHox genes originated from NK cluster 26 genes after divergence of sponges from the lineage leading to cnidarians and 27 bilaterians5,7. On the other hand, synteny analysis gives support to the notion that 28 absence of Hox and ParaHox genes in Amphimedon is a result of secondary loss 29 (the ghost locus hypothesis)8.
    [Show full text]
  • The Third Base
    Appendix The Third Base Donald Forsdyke If I thought that by learning more and more I should ever arrive at the knowledge of absolute truth, I would leave off studying. But I believe I am pretty safe. Samuel Butler, Notebooks Darwin’s mentor, the geologist Charles Lyell, and Darwin himself, both con- sidered the relationship between the evolution of biological species and the evolution of languages [1]. But neither took the subject to the deep informa- tional level of Butler and Hering. In the twentieth century the emergence of a new science – Evolutionary Bioinformatics (EB) – was heralded by two dis- coveries. First, that DNA – a linear polymer of four base units – was the chromosomal component conveying hereditary information. Second, that much of this information was “a phenomenon of arrangement” – determined by the sequence of the four bases. We conclude with a brief sketch of the new work as it relates to William Bateson’s evolutionary ideas. However, imbued with true Batesonian caution (“I will believe when I must”), it is relegated to an Appendix to indicate its provisional nature. Modern languages have similarities that indicate branching evolution from common ancestral languages [2]. We recognize early variations within a language as dialects or accents. When accents are incompatible, communi- cation is impaired. As accents get more disparate, mutual comprehension de- creases and at some point, when comprehension is largely lost, we declare that there are two languages where there was initially one. The origin of lan- guage begins with differences in accent. If we understand how differences in accent arise, then we may come to understand something fundamental about the origin of language (and hence of a text written in that language).
    [Show full text]
  • Annual Report for the Year Ended 31St March 2018
    Annual Report for the year ended 31st March 2018 Registered charity number: 223852 Registered company number: 00511709 ANNUAL REPORT Contents Trustees’ Report including the Strategic Report Introduction to the Annual Report 03 Achievements and Highlights 05-19 Future Plans 20 Financial Review 21-22 Risk Assessment and Management 23-24 Structure, Governance and Management 25-28 Independent Auditor’s Report 29-30 Financial Statements 31-50 Charity Information 51 John Innes Centre (‘JIC’) is a company limited by guarantee and a registered charity. The Annual Report provides information on the legal purposes of the charity, the activities it undertakes and its main achievements. The financial statements have been prepared in accordance with the Charities Act 2011, the Companies Act 2006, the Memorandum and Articles of Association, and Accounting and Reporting by Charities: Statement of Recommended Practice applicable to charities preparing their accounts in accordance with the Financial Reporting Standard applicable in the UK and Republic of Ireland (FRS 102) (effective 1 January 2015). 2 Annual Report | Year ended 31 March 2018 ANNUAL REPORT Trustees’ Report including the Strategic Report The Board of Trustees of John Innes Centre (Governing Council) presents its Annual Report and Financial Statements for the year ended 31 March 2018. The Annual Report provides details of the John Innes Centre’s objectives, achievements, scientific and financial performance in the year, future plans, risk management and its governance and management structure. About us The John Innes Centre (JIC) is an independent, • To use a wide range of contemporary world-leading international centre of excellence approaches to develop dialogue with in plant science and microbiology.
    [Show full text]
  • Breakup of a Homeobox Cluster After Genome Duplication in Teleosts
    Breakup of a homeobox cluster after genome duplication in teleosts John F. Mulley*, Chi-hua Chiu†, and Peter W. H. Holland*‡ *Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, United Kingdom; and †Rutgers University, Department of Genetics, Life Sciences Building, Piscataway, NJ 08854 Edited by Eric H. Davidson, California Institute of Technology, Pasadena, CA, and approved May 11, 2006 (received for review January 13, 2006) Several families of homeobox genes are arranged in genomic been active throughout vertebrate history, we show that in the clusters in metazoan genomes, including the Hox, ParaHox, NK, ray-finned fish clade, the ParaHox gene cluster was lost in the Rhox, and Iroquois gene clusters. The selective pressures respon- evolution of teleosts after divergence from more basal ray- sible for maintenance of these gene clusters are poorly under- finned fish. stood. The ParaHox gene cluster is evolutionarily conserved be- tween amphioxus and human but is fragmented in teleost fishes. Results We show that two basal ray-finned fish, Polypterus and Amia, each We searched the emerging genome sequences of zebrafish possess an intact ParaHox cluster; this implies that the selective (Danio rerio; www.sanger.ac.uk͞Projects͞D࿝rerio) and two pressure maintaining clustering was lost after whole-genome pufferfish [Tetraodon nigroviridis (10) and Takifugu rubripes duplication in teleosts. Cluster breakup is because of gene loss, not (11)] for DNA sequences assignable to the Gsx, Xlox, and Cdx transposition or inversion, and the total number of ParaHox genes gene families. Comparison between species gave a consistent is the same in teleosts, human, mouse, and frog.
    [Show full text]
  • Inferring Synteny Between Genome Assemblies: a Systematic Evaluation Dang Liu1,2, Martin Hunt3,4 and Isheng J Tsai1,2*
    Liu et al. BMC Bioinformatics (2018) 19:26 DOI 10.1186/s12859-018-2026-4 RESEARCH ARTICLE Open Access Inferring synteny between genome assemblies: a systematic evaluation Dang Liu1,2, Martin Hunt3,4 and Isheng J Tsai1,2* Abstract Background: Genome assemblies across all domains of life are being produced routinely. Initial analysis of a new genome usually includes annotation and comparative genomics. Synteny provides a framework in which conservation of homologous genes and gene order is identified between genomes of different species. The availability of human and mouse genomes paved the way for algorithm development in large-scale synteny mapping, which eventually became an integral part of comparative genomics. Synteny analysis is regularly performed on assembled sequences that are fragmented, neglecting the fact that most methods were developed using complete genomes. It is unknown to what extent draft assemblies lead to errors in such analysis. Results: We fragmented genome assemblies of model nematodes to various extents and conducted synteny identification and downstream analysis. We first show that synteny between species can be underestimated up to 40% and find disagreements between popular tools that infer synteny blocks. This inconsistency and further demonstration of erroneous gene ontology enrichment tests raise questions about the robustness of previous synteny analysis when gold standard genome sequences remain limited. In addition, assembly scaffolding using a reference guided approach with a closely related species may result in chimeric scaffolds with inflated assembly metrics if a true evolutionary relationship was overlooked. Annotation quality, however, has minimal effect on synteny if the assembled genome is highly contiguous. Conclusions: Our results show that a minimum N50 of 1 Mb is required for robust downstream synteny analysis, which emphasizes the importance of gold standard genomes to the science community, and should be achieved given the current progress in sequencing technology.
    [Show full text]
  • A Fast, General Synteny Detection Engine
    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.
    [Show full text]
  • Identifying Regions of Conserved Synteny Between
    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.
    [Show full text]