#Complete plastid genome assembly for invasive plant, Centaurea diffusa #Kathryn G. Turner and Chris J. Grassa #June 8, 2014 #Figure 2, Phylogenetic tree of complete plastomes available on NCBI within the Asteraceae #Made using taxize package # Chamberlain S, Szocs E. 2013. taxize - taxonomic search and retrieval in R. F1000Research 2. library(devtools) install_github("taxize_", "ropensci") library(taxize) library(XML) library(reshape2) # Define a species list #from Nucleotide search at https://www.ncbi.nlm.nih.gov/nuccore/ # ("Asteraceae"[Organism] OR ("Asteraceae"[Organism] OR Asteraceae[All Fields])) AND chloroplast[All Fields] AND complete[All Fields] AND genome[All Fields] # visually scan for length of sequence and statement "complete chloroplast" or "complete plastid" spplist <- c("Centaurea diffusa","Artemisia frigida","Jacobaea vulgaris", "Ageratina adenophora","Lactuca sativa","Helianthus annuus", "Guizotia abyssinica","Parthenium argentatum","Helianthus strumosus", "Helianthus decapetalus","Helianthus grosseserratus", "Helianthus tuberosus", "Helianthus divaricatus", "Helianthus giganteus","Helianthus hirsutus", "Helianthus maximiliani", "Chrysanthemum indicum", "Chrysanthemum x morifolium", "Praxelis clematidea") # Praxelis aka Eupatorium catarium # # Make the tree # # species tree with sub-genera detail (Three species do not occur in this tree: # parthenium_argentatum, helianthus_sturmosus, chrysanthemum_xmorifolium) # tree <- phylomatic_tree(taxa = spplist, storedtree='smith2011') tree$tip.label <- taxize_capwords(tree$tip.label) png("fig2Asteraceae_plastome_treeSmith.png", width=600, height = 600, pointsize = 12) plot(tree, cex=1.1, main="Plastomes in the Asteraceae") rect(14.8, 15.5, 20.2, 16.4, border="#66CC00",lwd=3) dev.off()