Figure 3

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 [22] 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 [22] due to the lower (<70%) confidence values at the respective nodes. Two nodes representing horizontal transfer events proposed by Zupunski et al. [22] 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.