Journal standards and trends in crop genomics

Transcription

1 Journal standards and trends in crop genomics Myles Axton Chief Editor Nature Genetics ICRISAT Hyderabad, India February 18 th 2015 Maciej Tomczak

2 Nature's mission statement written in 1869 still guides us today First, to serve scientists through prompt publication of significant advances in any branch of science, and to provide a forum for the reporting and discussion of news and issues concerning science. Second, to ensure that the results of science are rapidly disseminated to the public throughout the world, in a fashion that conveys their significance for knowledge, culture and daily life.

3 Your best work yet Gloucester Old Spot by John Miles,1834. Gloucester Museums Service Art Collection.

4 Organizing the paper

5 Writing the paper

6 Organizing the paper Jiang, N. et al An active DNA transposon family in rice. Nature 421: , HYPOTHESIS EVIDENCE METHOD Nipponbare rice genome contains active and inactive transposable elements (TEs) Repeats are present in genome Genomic sequencing Active TEs will show little intrafamily divergence Nipponbare rice genome contains an active MITE named mping mping element is actively transposing mping is related to other TEs mping is mechanistically related to Ping mping is mechanistically related to Pong Ping is not the source of transposase for mping Pong is actively transposing mping has been differentially active in rice strains from different latitudes There are repeats with various levels of identity, including identical interspersed repeats Sequence of 430bp with 26 identical copies in available Nipponbare sequence 42 new mping insertion sites in cell culture DNA Identified the larger Ping and Pong elements in the Nipponbare genomic sequence mping is a derived from Ping by deletion Pong is more distantly related to mping than is Ping Ping is not present in the sequenced indica (93-11) genome New Pong insertions in cell culture DNA mping element has undergone more extensive amplification in temperate rice strains Computational search for repeats, filtering by sequence identity % Manual inspection of 1257 repeat families in Nipponbare sequence Transposon display technique used with rice cell culture DNA Computational search of Nipponbare sequence using the mping sequence Sequence comparison among copies of two types of element Sequence comparison among copies of three types of element Sequence analysis of (93-11) by BLAST with Ping sequence Transposon display technique used with rice cell culture DNA Transposon display technique used with DNA from diverse rice strains

7 Navigating the editorial process Tayfun Özçelic

8 Genetics and genomics in Nature journals - Professional editors choose which papers to publish - Peer referees provide technical guidance to improve the work - Editorial standards and decision criteria are constantly revised in light of referee advice, author comments, conference presentations and lab visits - Standards of the journal constantly get higher All Nature Research Journals use two basic criteria for decisions: Novelty: new data, new resource, new ideas, new strategies Conceptual advance: How much is new compared to existing publications? Plus: Nature: Is this work of general interest to all scientists, to decision makers or to the public? Nature Genetics: How many other researchers will do their research differently as a result of this work?

9 Scope of Nature Genetics

10 Scope of Nature Genetics: vision and fields Common diseases/complex traits Gene networks - Risk calculator - Wiring diagram Cancer Human disease genetics Pharmacological genomics Epigenetics Developmental genetics Functional genomics Stem cell genetics Genetic technology Genome evolution Plant genome variation Genome x environment Human-plant co-evolution Allopolyploid/hybrid function Metabolic trait networks

11 Trends in agricultural genomics Rachel Meyer

12 From reference genomes to genome diversity

13 Drought resistance through deep root trait Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions Yusaku Uga et al. Cloning of DRO1 deep rooting QTL DRO1 is negatively regulated by auxin and controls cell elongation such that the deep root allele induces asymmetrical growth downward DRO1 QTL crossed into shallow rooting rice confers increased drought resistance

14 Tuning tomato productivity with florigen alleles Optimization of crop productivity in tomato using induced mutations in the florigen pathway Soon Ju Park et al. Nat. Genet. (2014) doi: /ng November 2014

15 Soil is familiar Cornell University Cooperative Extension

16 But we do not understand enough about soil to keep ourselves alive Phillip Beesley

17 Nature Plants Societal questions Economics Sociology Food security Environmental change Basic research Biochemistry Biophysics Cell Biology Ecology Genetics Molecular Biology Physiology Techniques Genomics Proteomics Systems biology Scientific questions Development Evolution Metabolism Defense Secondary metabolism Metabolomics Plant-microbe Photosynthesis Symbiosis Translational research Agriculture Agronomy Forestry Applications Crops Biofuels Environmental engineering Water use

18 Nature Outlook on Rice

19 Access to data Eve Stockton

20 Access to phenotype data as well as genotypes journal.pbio

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22 Author responsibilities Birgit Woelker

23 Avoid distorting citations Conversion of hypothesis to fact through citation alone BMJ 339, 2680 (2009)

24 Avoid fabrication and falsification Same photo, different genotype Nature Genetics 2007 Intra- and intercellular RNA interference in Arabidopsis thaliana requires components of the microrna and heterochromatic silencing pathways 90 o Science May 2010 Small RNA Duplexes Function as Mobile Silencing Signals Between Plant Cells

25 Display unprocessed data Nature Genetics 36, (2004) p53* (second row) shows the normalized amount of p53 in the four samples. Normalization was done after densitometric analyses of p53 (third row) and GFP (fourth row) band intensities in each lane, using Scion Image and NIH Image software.

26 Author contributions ICMJE Authorship requires: Substantial contributions to: the conception or design of the work; or the acquisition, analysis, or interpretation of data for the work; AND Drafting the work or revising it critically for important intellectual content; AND Final approval of the version to be published; AND Agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. NCBI/NLM The National Library of Medicine has indicated that regardless of the byline s wording, it will index individual authors or contributors /collaborators provided there is a note associated with the byline indicating that individual roles are listed elsewhere. Nature journals Submission to a Nature journal is taken by the journal to mean that all the listed authors have agreed all of the contents. Authors are required to include a statement of responsibility in the manuscript that specifies the contribution of every author.

27 Author contributions in Nature journals Study conception: Ideas; formulation of research question; statement of hypothesis Methodology: Development or design of methodology; creation of models Formal analysis: Application of statistical, mathematical or other formal techniques to analyze study data Computation: Programming, software development; designing computer programs; implementation of the computer code and supporting algorithms Investigation: Conducting the research and investigation process Performed the experiments Data/evidence collection Other investigatory role: please specify in space provided Resources: Provision of study materials, reagents, materials, patients, laboratory samples, animals, instrumentation or other analysis tools. Data curation: Management activities to annotate (produce metadata) and maintain research data for initial use and later re-use. Publication: Preparation, creation, and/or presentation of the published work. Writing the initial draft Critical review, commentary or revision Visualization/data presentation Other presentational role: please specify in the space provided Supervision: Responsibility for supervising research; project orchestration; principal investigator other lead stakeholder. Project administration: Coordination or management of research activities leading to this publication. Funding acquisition

28 Thank you! Alexander Davis