Neighbour-joining RTE clade phylogenetic tree. The NJ tree is a 50% consensus tree, with bootstrap values of >70 from 2,000 bootstrap replications indicated at respective nodes. Alignment of complete RT conserved domain used the Kalign sequence alignment program [51, 52] in EMBL-EBI. The Neurospora Group II intron (GenBank: S07649) was used as the outgroup. 14 representative BmRTE sequences used in Figure 2 have been included, along with newly described RTE elements as listed in the Methods, indicated with an asterisk. The RTE elements were broadly clustered as reported in Figure 5 of  although the higher number of BmRTEs identified and included in this analysis, and together with the lower numbers of Bov-B LINEs included have altered the tree topology. Overall, the elements were grouped into four sister groups of animal/plant RTE, Rex3/RTE, Bov-B LINE/RTE, and Caenorhabditis/Bombyx RTE. Although basal to the Plant/Animal RTE and Rex3/RTE subgroups, the positions of JAM1 and SR2 remained uncertain  due to the lower (<70%) confidence values at the respective nodes. Two nodes representing horizontal transfer events proposed by Zupunski et al.  are indicated. (A) from plants to some fishes, (B) from arthropods to reptiles and then to ruminant mammals. Note that the medaka fish Oryzias has both a Rex3 RTE element similar to other fishes, and a plant-like RTE element.