White Paper from the International Arabidopsis Informatics Consortium

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Published on: January 18, 2019

The International Arabidopsis Informatics Consortium (IAIC) has existed since 2010 to facilitate the maintenance, development and evolution of informatics tools that primarily support Arabidopsis researchers.

They have recently published a White paper on the future of Arabidopsis bioinformatics resources.

As we all know the first published plant genome was that of Arabidopsis thaliana in 2000 and since that time Arabidopsis has been used extensively around the globe as the primary plant experimental organism.

At the present time the use of Arabidopsis as a model organism has plateaued in most Western countries but is still on the rise in China and, as reported in the 2018 Multinational Arabidopsis Steering Committee (MASC) Annual Report, there remain more Arabidopsis-focused papers published than those than focus on any other single plant, although rice is catching up fast!!

Therefore with such a large number of researchers requiring effective bioinformatic tools to help their experimental planning and analysis it is essential that these tools are maintained and expanded.

The current situation sees TAIR and Araport existing as two complimentary resources. Active since 1999, TAIR is the older resource and now emphasizes high quality functional annotation. Araport was established in 2014 following a community recommendation from the last IAIC White paper and now focuses on the computational aggregation of diverse resources. TAIR is funded through an innovative subscription model that has maintained the resource over the past 5 years, Araport was funded by NSF and but unfortunately since publication of the White Paper it has emerged that NSF’s currently will not renew this funding.

Both these resources are clearly US-based as a holdover from the early uptake of Arabidopsis research in that country. As mentioned above TAIR received subscriptions from across the world so it remains to be seen how Araport might be funded as there is a clear community need for this resource.


In order to plan for the next phase of bioinformatics support for Arabidopsis and wider plant science researchers, the IAIC met in St Louis in May 2018 and the White Paper resulted from that meeting. One common theme that emerged from the meeting was the importance of metadata standards to facilitate comparable reuse of any deposited data. In addition it became clear that a robust upfront plan for gene ID assignment was critical for the future facile comparison of data from different experiments, across ecotypes and even between species.

Overall the workshop discussions resulted the formulation of the following recommendations:

Integration of data and tools: Identifying a need for a system for standardiSing and integrating data that is sustainable and not overly dependent on a few individuals. This can be achieved by development of a PlantHub or Arabidopsis Super-Portal as well as overseeing a managed expansion of fully integrated analysis tools.

Data formats and standards: This is extremely challenging but there should be community agreement on ontologies, standards and formats, their usage, and enforcement across all types of data. This would allow linkage with independently developed annotation and datasets and thus would require an authority to maintain a gold standard.

Tool development: With more data generation comes the requirement for new ways of browsing genomes that can be integrated with other overlapping ‘omic databases and then compared across genomes and networks. This type of higher level software development will need collaboration with the larger IT community, especially if the end goal is a set of simple GUIs (graphical user interfaces) that encompass more complex underlying information.


As ever the primary challenge lies in obtaining the funding and manpower to meet these recommendations. This should be a global effort given the international uptake of the resources that has been initially developed using US-based funding sources. The TAIR-type funding model is sufficient to maintain their excellent service but development of new tools requires a significant new commitment.

Over the short term the recommendations have resulted in the set up of an Arabidopsis Community Hub hosted by TAIR. This contains a list of software tools that will be of broad interest to plant scientists. They are happy to include additional appropriate links to other well-used tools. This site links to the GARNet Resources page that also contains a similar set of resources, arranged over a broader set of headings.

Please visit the TAIR Arabidopsis Community site and watch this space for updates on how the Arabidopsis bioinformatics community will evolve over the coming years.

GARNet Research Roundup: Jan 11th 2019

The inaugural GARNet Research Roundup of 2019 firstly includes a paper from the University of Sheffield that has identified new pericentromeric epigenetic loci that affect the pathogen response. Secondly is a collaboration between researchers in Birmingham, Nottingham and Oxford that has identified a new mode of regulation of the VRN2 protein. Next are two papers from Jonathan Jones’ lab at The Sainsbury Laboratory in Norwich that firstly provides a toolkit for gene editing in Arabidopsis and secondly characterise the role of the NRG1 gene in the defense response. The penultimate paper is from Paul Devlin’s lab at RHUL and investigates the role of the circadian clock in the control of leaf overtopping whilst the final paper is a meeting report from a recent GARNet workshop on gene editing.


Furci L, Jain R, Stassen J, Berkowitz O, Whelan J, Roquis D, Baillet V, Colot V, Johannes F, Ton J (2019) Identification and characterisation of hypomethylated DNA loci controlling quantitative resistance in Arabidopsis. Elife. doi: 10.7554/eLife.40655.

Open Access

Leonardo Furci and Ritushree Jain are the lead authors on this study conducted at the University of Sheffield. The authors used a population of epigenetic recombinant inbred lines (epiRILs) to screen for resistance to the oomycete pathogen Hyaloperonospora arabidopsidis. These lines each share genetic information but have varied epigenetic changes. This analysis enabled the identification of plants with hypomethylated pericentromeric regions that were primed to better respond to the presence of this pathogen. The authors discuss the mechanism through which this might affect the defence response albeit without altering other aspects of plant growth.

https://elifesciences.org/articles/40655

Gibbs DJ, Tedds HM, Labandera AM, Bailey M, White MD, Hartman S, Sprigg C, Mogg SL, Osborne R, Dambire C, Boeckx T, Paling Z, Voesenek LACJ, Flashman E, Holdsworth MJ (2018) Oxygen-dependent proteolysis regulates the stability of angiosperm polycomb repressive complex 2 subunit VERNALIZATION 2. Nat Commun. doi: 10.1038/s41467-018-07875-7

Open Access

This collaboration between the Universities of Birmingham, Nottingham, Oxford and colleagues in Utrecht is led by Daniel Gibbs. They demonstrate that the amount of VRN2 protein, which is a member of the Polycomb Repressive Complex2, is controlled by the N-end rule pathway and that this regulation responses to both cold and hypoxia stress. Whilst the VRN2 gene is expressed throughout the plant, the N-end rule degradation pathway ensures that the protein is restricted to meristematic regions until the plant senses the appropriate abiotic stress. Classically VRN2 has been linked to the regulation of flowering time by altering gene expression at the FLC locus so this study introduces new complexity into this process through the involvement of the N-end rule pathway. More information on this linkage will undoubtedly follow over the coming years.

Daniel kindly discusses this paper on the GARNet YouTube channel.


Castel B, Tomlinson L, Locci F, Yang Y, Jones JDG (2019) Optimization of T-DNA architecture for Cas9-mediated mutagenesis in Arabidopsis. PLoS One. doi: 10.1371/journal.pone.0204778

Open Access

Baptiste Castel is lead author of this work conducted at the Sainsbury Laboratory, Norwich in Jonathan Jones’ group. They have conducted a detailed analysis of the factors that contribute to successful gene editing by CRISPR-Cas9, specifically in Arabidopsis. This includes assessing the efficacy of different promotor sequences, guideRNAs, versions of Cas9 enzyme and associated regulatory sequences in the editing of a specific locus. Given that researchers are finding that different plants have different requirements when it comes to successful gene editing, this type of analysis will be invaluable for anyone who plans to conduct a gene editing experiment in Arabidopsis.

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0204778

Castel B, Ngou PM, Cevik V, Redkar A, Kim DS, Yang Y, Ding P, Jones JDG (2018) Diverse NLR immune receptors activate defence via the RPW8-NLR NRG1. New Phytol. doi: 10.1111/nph.15659

In this second paper led by Baptiste Castel, they used the techniques outlined in the paper above to generate a set of CRISPR mutants deficient in NRG1, which is a RPW8-NLR resistance (R) gene. These nrg1 mutants have compromised signalling in all tested downstream TIR-NLR resistance genes. In addition the authors demonstrate that this signalling is needed for resistance to oomycete but not bacterial infection. Therefore this study reveals some significant details regarding the components of the disease response that are influenced by the activity of NRG1.


Woodley Of Menie MA, Pawlik P, Webb MT, Bruce KD, Devlin PF (2018) Circadian leaf movements facilitate overtopping of neighbors. Prog Biophys Mol Biol. doi: 10.1016/j.pbiomolbio.2018.12.012

This work is led by Michael Woodley Of Menie from Paul Devlin’s lab at Royal Holloway College and investigates the role of circadian leaf movements during shade avoidance and overtopping. Arabidopsis plants were grow in a grid system that meant leaves would interact with their neighbours and the authors show that plants with a normal circadian rhythm gained an advantage over those adapted to a longer period in which they were grown. This overtopping was additive to the advantage gained through shade avoidance and overall this paper shows that maintainance of clock-aligned leaf movements are beneficial to growth.


Parry G, Harrison CJ (2019) GARNet gene editing workshop. New Phytol. doi: 10.1111/nph.15573

Open Access

GARNet advisory committee member Jill Harrison and GARNet coordinator Geraint Parry are authors on this meeting report resulting from a GARNet organised workshop on gene editing that took place in March 2018 at the University of Bristol. Coincidentally part of the paper discusses the work that was presented at the meeting by Baptiste Castel, which is published in the paper described above.

Daniel Gibbs talks to GARNet

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Published on: January 9, 2019

Daniel Gibbs discusses a recent paper published in Nature Communications entitled ‘Oxygen-dependent proteolysis regulates the stability of angiosperm polycomb repressive complex 2 subunit VERNALIZATION 2

Grants to support Conference Travel to China and Oxford.

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Published on: January 7, 2019

As the festive period passes, thoughts turn to warmer times and summer conference plans. GARNet are delighted to provide and administer grants to support attendance at two major upcoming conferences.

Royal Microscopy Society Botanical Microscopy 2019. Oxford Brookes University, April 14th-18th 2019.

Scientific Organising Committee: Chris Hawes, Beatrice Satiat-Jeunemaitre, Verena Kriechbaumer, Katja Graumann, Louise Hughes, Imogen Sparkes.

GARNet are supporting the New Technologies session of this meeting that will include invited speaker Dr Sarah Robinson as well as a tribute to Professor Ian Moore.

GARNet will also supply 10x £150 travel grants to support ECRs travel to this meeting. More details about these awards can be found here in the ‘Delegate Information’ tab:

https://www.rms.org.uk/discover-engage/event-calendar/botanical-microscopy-2019.html


International Conference on Arabidopsis Research (ICAR2019): Wuhan, China, June 16th-21st 2019.

ICAR is the largest annual conference that focuses on discovery-led research. GARNet are administering four £500 travel grants available for UK-based PhD students to attend this meeting. Please contact the GARNet coordinator Geraint Parry to obtain an application form for these awards. The early registration date for this meeting means the deadline for these travel awards is January 28th.

Any other questions about these awards then please contact Geraint Parry.

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