Table 2.
Repeat composition of the pea genome estimated from genomic abundance of reconstructed contigs
| 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 % | ||||
aGenome proportion of individual groups of repeats was estimated from the sum of genome representation (GR) values of corresponding clusters of contigs.
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.