3.4 Repeat annotation
We identified a total of 340.4 Mb of repeats (62.1 % of the genome) in the Chinese walnut genome, of which ~62.42 % were transposable elements (TEs) (Table 1; Table 2). The most abundant repetitive sequences were long terminal repeat retrotransposons (LTR-RTs), which accounted for 41.2 % of the assembled genome (Table 2), followed by LINE (long interspersed nuclear element, 12.22 %), DNA (Class II TEs, 8.96 %), and SINE (short interspersed nuclear element, 0.01 %) (Table 2).