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. 2017 Apr 14;7(6):1875–1885. doi: 10.1534/g3.116.037572

Figure 2.

Figure 2

Phylogenetic trees of representative LTR retrotransposon lineages across the eight AA-genome Oryza species. Neighbor joining and unrooted trees were constructed based on sequences of RT genes for Ty1-copia (A) and Ty3-gypsy (B). The backbone of the RT trees and retroelements from SAT are shown in black, while colored branches indicate those from other seven species. LTR retrotransposons from NIV and RUF (the closest to SAT), GLA and BAR (similar divergence time to SAT), GLU, LON, and MER are colored in red, orange, green, light blue, and dark blue, respectively. BAR, O. barthii; GLA, O. glaberrima; GLU, O. glumaepatula; LON, O. longistaminata; LTR, long terminal repeat; MER, O. meridionalis; MY, million years; Mya, million years ago; NIV, O. nivara; OAL, Oryza AA genome of LTR retrotransposons; RT, reverse transcriptase; RUF, O. rufipogon; SAT, O. sativa ssp. japonica. cv. Nipponbare (Release 7).