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Published on: January 11, 2015

Happy New Year! We at GARNet enjoyed a long Christmas break and some of us have returned to work via California! Ruth, Jim and I are in San Diego this week for the Plant and Animal Genome Conference (PAG).

PAG is an enormous conference – take a look at the Twitter stream (PAGXXIII) for an idea of how many sessions run at any one time. Yesterday I went to sessions on Ontologies, Brassica and Tritaceae, and I thought I’d quickly update our blog readers about a workshop about the CoGe online tool. I mentioned CoGe in this post about the EPIC conference and it’s also featured in the June 2013 edition of GARNish.

Eric Lyons, one of the creators of CoGe, began the session by explaining that CoGe is a platform for managing, visualising, analysing and comparing genomes. It can deal with unlimited numbers of genomes of unlimited size—though there is a limit for the number of annotations per genome—and while there are tools set up for ease of use, users can perform custom, on-the-fly analysis too.

Throughout the session, Lyons was clear that CoGe is ‘Powered by iPlant.’ It uses iPlant middleware to enable data storage, universal log-in and much more functionality that the user might not be aware of but which makes their experience smooth and relatively stress-free. (more…)

Arabidopsis Research Round-up

There are three new and exciting Arabidopsis papers from the UK research community this week. The University of Bath makes two appearances, once with a Genetics paper, and once in collaboration with the University of Oxford in Genome Research. Representing Norwich this week, Jonathan Jones heads up a Sainsbury Lab/John Innes Centre collaboration to investigate simultaneous changes in gene expression between Arabidopsis and a pathogen.


  • Gnan S, Priest A and Kover PX. The genetic basis of natural variation in seed size and seed number and their trade-off using Arabidopsis thalianaMAGIC lines. Genetics, 13 October 2014. DOI: 10.1534/genetics.114.170746.

This team from the University of Bath explored the natural variation in genes affecting seed size and seed number in Arabidopsis. Both seed size and seed number were found to be affected by non-overlapping QTLs, therefore suggesting these two traits can evolve independently of each other. Trade-off between these two traits in terms of fecundity and yield is dependent upon life history traits.


  • Jiang C, Mithani A, Belfield EJ, Mott R, Hurst LD and Harberd NP. Environmentally responsive genome-wide accumulation of de novo Arabidopsis thaliana mutations and epimutations. Genome Research, 14 October 2014. DOI: 10.1101/gr.177659.114. [Open Access]

GARNet committee member Nick Harberd led on this Genome Research paper, along with co-corresponding author Caifu Jiang from China, and colleagues from theUniversity of Bath and Pakistan. In animal cells, repeated or prolonged presentation of a stressor often leads to increased mutations, which can increase the risk of cancer. Being sessile, plants do not get cancer in the same way that humans do, but do they acquire more mutations? Does stress – here the example of high soil salinity is used – drive the evolution of plants through increased phenotypic diversity? Yes, it seems so.


  • Asai S, Rallapalli G, Piquerez SJM, Caillaud M-C, Furzer OJ, Ishaque N, Wirthmueller L, Fabro G, Shirasu K and Jones JDG. Expression profiling during Arabidopsis/downy mildew interaction reveals a highly expressed effector that attenuates responses to salicylic acid. PLOS Pathogens, 16 October 2014. DOI: 10.1371/journal.ppat.1004443. [Open Access]

Led by Jonathan Jones, scientists from The Sainsbury Laboratory in Norwich worked with Lennart Wirthmueller from the John Innes Centre, and two Japanese collaborators, to produce this PLOS Genetics paper. Though gene expression patterns have been studied independently in the pathogen Hyaloperenospora arabidopsidis, and in its host Arabidopsis thaliana, they have not been compared simultaneously. Using a high-throughput cDNA tag sequencing method, this paper describes simultaneous changes in gene expression profiles in both host and pathogen.

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