TABLE 3. Summary of repeated sequences annotated with Repeat Detector (Red) (Girgis, 2015) and RepeatMasker (Smit et al., 2015) with the libraries nrTEplants and REdat (Nussbaumer et al., 2013) and with custom libraries obtained for some species by RepeatModeler (Flynn et al., 2020). Total repeats and N50 is the sequence length of the shortest contig at 50% of the total sequence length (N50) estimates of repeats are shown.
| Species | Red | nrTEplants | REdat | RepMod | ||||
|---|---|---|---|---|---|---|---|---|
| Repeats | N50 | Repeats | N50 | Repeats | N50 | Repeats | N50 | |
| Arabidopsis thaliana | 172,935 | 445 | 48,144 | 1,779 | 28,797 | 2,211 | 72,138 | 1,178 |
| Arabidopsis halleri | 226,080 | 554 | 81,857 | 1,380 | 57,901 | 1,431 | - | - |
| Prunus dulcis | 190,357 | 1,627 | 105,546 | 2,528 | 36,891 | 1,025 | 243,499 | 1,422 |
| Brachypodium distachyon | 150,191 | 4,986 | 74,215 | 6,260 | 67,632 | 6,665 | 222,710 | 2,125 |
| Brassica rapa | 348,258 | 642 | 160,157 | 1,046 | 69,345 | 777 | 303,119 | 628 |
| Trifolium pratense | 277,811 | 555 | 139,254 | 326 | 155,808 | 265 | - | - |
| Arabis alpina | 279,129 | 1,040 | 146,057 | 2,245 | 98,017 | 1,050 | - | |
| Cucumis melo | 305,083 | 1,939 | 148,925 | 3,141 | 51,833 | 1,338 | 407,579 | 1,819 |
| Citrullus lanatus | 323,894 | 2,596 | 151,980 | 1,020 | 52,941 | 1,103 | - | - |
| Oryza sativa | 278,406 | 2,931 | 160,371 | 4,479 | 129,121 | 6,077 | - | - |
| Setaria viridis | 247,732 | 3,124 | 116,459 | 1,727 | 105,088 | 1,722 | - | - |
| Vitis vinifera | 423,876 | 1,753 | 185,204 | 3,369 | 69,315 | 1,550 | 496,352 | 1,604 |
| Rosa chinensis | 463,880 | 2,125 | 189,086 | 1,479 | 93,715 | 950 | 499,475 | 1,958 |
| Camelina sativa | 709,160 | 878 | 267,290 | 1,272 | 201,059 | 1,176 | 611,700 | 1,105 |
| Malus domestica | 531,496 | 2,416 | 211,929 | 4,729 | 126,487 | 1,268 | - | - |
| Olea europaea | 901,519 | 3,153 | 291,445 | 1,956 | 375,614 | 1,218 | - | - |
| Zea mays | 847,205 | 13,137 | 365,978 | 11,806 | 372,467 | 11,419 | 853,432 | 1,1380 |
| Helianthus annuus | 2,387,122 | 5,018 | 355,890 | 8,716 | 479,400 | 1,317 | - | - |
| Aegilops tauschii | 1,506,690 | 10,133 | 777,962 | 9,973 | 847,592 | 9,431 | 1,758,407 | 7,894 |
| Triticum turgidum | 4,291,533 | 9,066 | 1,914,776 | 9,947 | 1,784,719 | 10,124 | 72,138 | 1,178 |