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Table 1 Genomic repeat contents in genome assembly and after clustering in comparison

From: Repeat Composition of CenH3-chromatin and H3K9me2-marked heterochromatin in Sugar Beet (Beta vulgaris)

   Genome Assembly RepeatExplorer (758 Mb)   ChIP enrichment
  RefBeet 1.1 (567 Mb)
   genome proportion size genome proportion size Δ   
   [%] [Mb] [%] [Mb] [Mb] CenH3 H3K9me2
Repeat         
Superfamily
  family        
Ty3-gypsy retrotransposons   7.61 43.15 4.37 33.09 −10.23 0.8–7.81 0.42–3.38
  Beetle2 0.12 0.68 0.48 3.67 2.99 3.00 2.01
  Beetle4 0.00 0.00 0.10 0.74 0.74 4.54 2.07
  Beetle7 0.08 0.45 0.65 4.92 4.47 5.34 1.58
  Total Beetle 0.50 2.84 1.25 9.50 6.66 3.0–5.34 0.75–2.07
  Bongo3 2.02 11.45 1.90 14.42 2.96 0.28 0.63–1.62
Ty1- copia retrotransposons   4.56 25.86 4.99 37.82 11.97 0.11–0.49 0.8–2.37
  Cotzilla 1.72 9.75 3.02 22.89 13.14 0.25–0.15 0.8–1.83
  Salire 0.34 1.93 0.49 3.71 1.79 0.16 1.83
  Patty 0.18 1.02 0.10 0.72 −0.30 0.11 2.37
ENV-like retrotransposons   4.05 22.96 2.14 16.22 −6.74 0.10–0.42 1.01–2.55
  Elbe family 3.01 17.07 2.03 15.41 −1.66 0.10–0.42 1.01–2.43
LINE   3.77 21.38 0.14 1.06 −20.31 0.16 2.65
Tandem Repeat   3.31 18.77 11.15 84.52 65.75 0.08–3.22 0.33–3.61
  pBV 0.27 1.53 6.17 46.75 45.21 2.34–3.22 0.87–1.2
  pEV 0.17 0.96 3.58 27.14 26.17 0.13 2.6
  Niobe 0.02 0.11 0.06 0.46 0.35 0.14 1.81
  BvSat04 0.03 0.17 0.03 0.19 0.02 0.08 3.61
DNA transposons   2.07 11.74 3.93 29.79 18.05 0.11–1.02 0.25–3.15
  Mutator 0.00 0.00 2.01 15.24 15.24 0.11–1.02 0.26–3.15
  En/Spm (CACTA superfamily) 0.00 0.00 0.89 6.78 6.78 0.12–0.17 1.84–2.14
Helitron   0.56 3.18 0.10 0.76 −2.42 0.12 1.51
SINE   0.49 2.78 0.05 0.38 −2.40 0.31–0-64 0.37–0.46
rDNA   0.15 0.85 1.56 11.82 10.97 0.17–0.42 0.47–1.05
Pararetrovirus   0.06 0.34 0.09 0.68 0.34 0.5 1.55
Unclassified Dispersed Repeats   0.08 0.45 0.00 0.00 −0.45 - -
plastid DNA   0.00 0.00 9.58 72.62 72.62 1.77–3.09 1.62–1.79
Unknown   6.28 35.61 4.69 35.55 −0.06 0.08–4.10 0.23–3.64