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Table 2 Repeat composition of the pea genome estimated from genomic abundance of reconstructed contigs

From: Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula

  Genome representationa Copy numbersb
  Clusters (contigs) Total GR Genome proportion [%] Copies/1C (domain) Element length [bp] Genome proportion [%]
Retroelements       
   Ty3/gypsy       
Ogre-like 77 (632) 6,754,965 20.30 65,000 (RT, PBS) 22,000 33.26
Peabody 5 (42) 703,484 2.11 16,000 (RT) 8,000 2.98
PIGY 23 (70) 361,389 1.09 4,700 (RT) 13,600 1.49
Cyclops 15 (52) 221,925 0.67 2,700 (RT) 12,300 0.77
   Ty1/copia       
Ps-copia-1/751 6 (14) 690,339 2.07    
full-length     8,000 (RT) 8,000 1.49
solo-LTR     9,000 1,400 0.29
SIRE 9 (87) 548,280 1.65    (1.65)
PDR 6 (24) 214,755 0.65 1,100 (RT) 4,000 0.10
Other copia 16 (26) 101,805 0.31    (0.31)
   Other RE 17 (111) 878,773 2.64    (2.64)
DNA transposons       
   MuDR 7 (24) 68,247 0.21    (0.21)
   En/Spm 5 (9) 50,845 0.15    (0.15)
Tandem repeats       
   45S rDNA 1 (6) 348,987 1.05 5,300 8,680 1.07
   5S rDNA 1 (3) 13,134 0.04    (0.04)
   PisTR-B 1 (7) 147,113 0.44    (0.44)
   Other satellites 16 (73) 381,148 1.15    (1.15)
   Total : 34.5 %    48.0 %
  1. aGenome proportion of individual groups of repeats was estimated from the sum of genome representation (GR) values of corresponding clusters of contigs.
  2. b Estimates based on genomic copy numbers inferred from the read depth of contigs including conserved sequence domains (RT, reverse transcriptase; PBS, primer binding site). Genome proportion of the repeats was calculated using the length of the complete elements and therefore it is provided only for repeat families with known full-length copies in the pea genome.
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