Fig. 2

Backbone phylogenies produced using genome guided orthology approach and analysis done with RAxML, trees produced with figtree [41]. a 195 genes, a total length of 131,919 bp for 10 accessions. b gappy supermatrix that contains a putative B genes derived from Eleusine indica to test whether the targeted assembly method biases the assembled transcript to make them take on the characteristics of the genomic sequence used to capture the reads for assembly. It contains 31 false B genes derived from E. indica. Phylogenetic analysis confirms that they have not been biased by the underlying genomic sequence used to capture the reads for assembly. Gappy supermatrix contains 454 total genes and is 261,312 bp in length. c A gappy supermatrix which contains a 457 genes 277,536 bp in length