R.M. Parsons Laboratory
Environmental Science and Engineering


We are part of a large collaborative effort to deeply resequence the genomes of 54 natural accessions of the model grass species Brachypodium distachyon. These genomes were assembled independently of the reference genome, thereby allowing us to identify sequences not present in the reference. Collectively, these sequenced accessions constitute the “pan-genome” of Brachypodium distachyon. The studies are reported in Gordon et al. (2014 and in review). The genomes can be visualized here: https://brachypan.jgi.doe.gov

All of the data and scripts necessary to recapitulate our results from Des Marais et al. 2017 Proc Roy Sci 284: 20170914 are available here: https://github.com/scarpino/arab_net

I am frequently asked how we made Figure 4 of our 2013 Annual Reviews paper, showing thousands of genes in a “triplot” representing the proportion of experimental variance in transcript abundance attributable to G, E, and GxE. That figure was made by my co-author, Kyle Hernandez, in R. Script and example data file are here.


Our 2016 Plant Science paper (Des Marais et al. 2016 Plant Science 251: 2-11) reported a new linkage map for the publicly available Brachypodium distachyon Bd3-1 x Bd21 RIL population. This map added new SNP markers to a previously published dataset, and corrected several errors in that earlier set, and updated marker positions on the physical Bd21 v3.0 reference genome. The map is here.