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Table 3 Abundance of major LTR-RTs families in different species of the genus Oryza

From: Transposable element distribution, abundance and role in genome size variation in the genus Oryza

  O. nivara O. rufipogon O. glaberrima O. punctata O. officinalis O. minuta O. alta O. australiensis O. brachyantha O. granulata O. coarctata O. ridleyi
COPIA1 0.35 0.59 0.60 0.57 0.87 0.82 0.57 1.64 0.18 0.69 0.81 0.63
COPIA2 0.19 0.39 0.26 0.19 0.27 0.35 0.54 0.45 0.12 0.70 0.21 0.27
COPIA3 0.13 0.00 0.00 0.19 0.00 0.37 0.32 0.43 0.15 0.07 0.18 0.31
COPIO 0.42 0.31 0.31 0.92 0.60 0.85 0.62 0.48 0.65 0.84 0.71 0.96
Hopscotch 0.03 0.08 0.06 0.03 0.06 0.10 0.05 0.04 0.00 0.10 0.48 0.14
OSTONOR1 0.16 0.04 0.11 0.32 0.37 0.51 0.11 0.79 0.24 0.22 0.02 0.14
RETROFIT4 0.10 0.00 0.06 0.06 0.06 0.06 0.09 0.07 0.06 0.04 0.35 0.06
RIRE1 0.06 0.00 0.00 0.16 0.10 0.60 0.61 4.38 0.03 0.49 0.23 0.46
RIRE5 0.26 0.16 0.26 0.06 0.17 0.18 0.42 0.15 0.06 0.01 0.05 0.15
SC-1 0.06 0.04 0.11 0.10 0.17 0.26 0.46 0.71 0.09 0.34 0.04 0.37
SZ-6 0.03 0.00 0.03 0.03 0.04 0.08 0.17 0.08 0.09 0.12 2.75 0.14
ATALANTYS 1.87 1.49 1.77 6.36 10.15 8.70 7.32 10.98 0.36 7.28 4.08 7.62
BAJIE 0.26 0.39 0.66 0.54 0.74 0.49 0.45 0.15 0.00 0.04 0.04 0.22
RIREX (Dasheng) 0.55 1.06 0.20 1.02 1.49 1.08 0.74 1.24 0.03 1.26 0.05 0.53
GYPSY1 0.48 0.23 0.40 0.22 0.27 0.29 0.16 1.18 0.18 0.30 0.18 0.05
RETRO2 1.68 1.10 0.26 1.08 3.03 1.31 0.72 0.54 0.06 0.96 0.16 1.97
RETROSAT2 1.64 0.78 0.52 0.54 1.65 1.63 0.86 2.74 4.12 1.84 0.05 0.38
RETROSAT3 0.68 0.98 0.66 0.70 1.69 1.62 1.01 2.81 2.13 1.66 0.05 0.37
RETROSAT4 1.29 0.78 0.54 1.02 2.76 0.88 0.70 0.84 0.03 1.75 0.22 1.12
RIRE2 1.61 1.02 0.74 1.69 4.43 2.06 1.70 8.56 0.24 21.50 0.41 2.42
RIRE3 3.42 3.37 1.09 0.25 0.58 0.43 0.17 0.76 0.06 0.60 0.18 0.41
RIRE8 5.90 5.21 2.55 1.18 0.78 1.08 1.49 0.86 0.24 2.59 0.29 0.31
SZ-22 0.19 0.27 0.11 0.32 0.33 0.42 0.19 0.16 0.00 0.06 0.00 0.07
SZ-42 0.23 0.39 0.26 0.06 0.19 0.24 0.21 0.18 0.06 1.11 0.04 0.61
SZ-50 0.77 0.47 0.49 2.19 0.06 0.85 0.07 0.03 0.00 0.36 0.12 0.06
SZ-7 1.03 0.90 1.35 0.57 1.38 1.00 0.92 0.31 0.03 1.05 0.31 0.51
UNC 2.55 3.29 3.18 3.85 4.76 3.41 5.64 3.66 1.63 2.57 1.23 3.21
NHF 1.32 1.14 1.32 1.53 1.84 1.85 2.31 1.59 0.71 2.08 1.50 5.55
Other Families 2.19 1.54 2.57 3.69 3.03 3.11 3.46 4.86 1.18 4.35 3.15 3.70
  1. Figures represent the percentage of significant hits out of the total number of reads for each species. Ty3-gyspy family names are in bold; Ty1-copia ones are not. UNC refers to elements that in RepBase were classified as LTR-RT but without any other detail (i.e. Ty1-copia or Ty3-gypsy); NHF refers to elements that are LTR-RTs related but do not have significant similarity with the major families isolated in the genus Oryza. "Other families" indicates significant hits with other Oryza sativa LTR-RTs elements than those belonging to the families analyzed here.