Table 2.
Genomic repeat elements metrics of rust pathogen genomes.
| Pn | Ps | Pgt 21–0 | Pgt Ug99 | Pgt 75-36-700-3 | Pst 38S102 | Pst CY32 | Pst 78 | Pt | Ph | Pc | Ml | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Genome size (bp) | 99,934,463 | 99,534,058 | 176,850,170 | 176,235,062 | 88,724,376 | 75,577,821 | 130,484,873 | 117,391,083 | 135,343,689 | 206,919,034 | 150,467,806 | 101,129,028 |
| Retroelements | 1521 | 2109 | 3439 | 3449 | 1542 | 964 | 2024 | 1384 | 2289 | 7644 | 4365 | 1709 |
| SINEs: | 57 | 61 | 37 | 42 | 20 | 39 | 61 | 41 | 19 | 67 | 17 | 21 |
| Penelope | 17 | 7 | 45 | 41 | 21 | 1 | 2 | 1 | 13 | 89 | 165 | 10 |
| LINEs: | 202 | 150 | 343 | 303 | 147 | 102 | 187 | 155 | 106 | 482 | 432 | 268 |
| CRE/SLACS | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| L2/CR1/Rex | 12 | 16 | 42 | 32 | 16 | 15 | 23 | 35 | 5 | 34 | 40 | 16 |
| R1/LOA/Jockey | 21 | 12 | 39 | 33 | 15 | 10 | 23 | 23 | 17 | 71 | 23 | 14 |
| R2/R4/NeSL | 5 | 1 | 7 | 4 | 3 | 1 | 1 | 1 | 2 | 2 | 0 | 2 |
| RTE/Bov-B | 5 | 2 | 3 | 1 | 1 | 4 | 5 | 6 | 2 | 8 | 10 | 7 |
| L1/CIN4 | 80 | 86 | 144 | 125 | 62 | 49 | 91 | 60 | 58 | 223 | 150 | 203 |
| LTR elements: | 1262 | 1898 | 3059 | 3104 | 1375 | 823 | 1776 | 1188 | 2164 | 7095 | 3916 | 1420 |
| BEL/Pao | 32 | 27 | 64 | 63 | 27 | 18 | 33 | 64 | 40 | 47 | 55 | 27 |
| Ty1/Copia | 249 | 165 | 280 | 286 | 142 | 61 | 114 | 132 | 287 | 469 | 279 | 157 |
| Gypsy/DIRS1 | 765 | 1489 | 2249 | 2264 | 987 | 600 | 1385 | 849 | 1597 | 5993 | 3116 | 1099 |
| Retroviral | 117 | 130 | 293 | 324 | 155 | 81 | 146 | 86 | 169 | 368 | 305 | 90 |
| DNA transposons | 511 | 436 | 853 | 855 | 402 | 253 | 398 | 281 | 228 | 1117 | 2830 | 251 |
| hobo-Activator | 160 | 129 | 272 | 278 | 139 | 86 | 127 | 92 | 95 | 217 | 288 | 79 |
| Tc1-IS630-Pogo | 68 | 81 | 83 | 80 | 35 | 49 | 77 | 47 | 13 | 82 | 1760 | 49 |
| En-Spm | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| MuDR-IS905 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| PiggyBac | 9 | 3 | 4 | 8 | 1 | 0 | 0 | 2 | 1 | 7 | 3 | 3 |
| Tourist/Harbinger | 58 | 28 | 62 | 58 | 24 | 17 | 26 | 20 | 14 | 84 | 69 | 18 |
| Other (Mirage) | 3 | 0 | 3 | 3 | 3 | 0 | 1 | 0 | 0 | 4 | 8 | 0 |
| Rolling-circles | 71 | 13 | 146 | 133 | 48 | 25 | 45 | 36 | 90 | 470 | 75 | 51 |
| Unclassified: | 2 | 4 | 11 | 7 | 2 | 2 | 4 | 3 | 6 | 6 | 3 | 1 |
| Small RNA: | 214 | 118 | 589 | 383 | 143 | 182 | 211 | 209 | 409 | 265 | 210 | 289 |
| Satellites: | 246 | 60 | 102 | 113 | 47 | 69 | 91 | 72 | 91 | 79 | 118 | 62 |
| Simple repeats: | 31,718 | 20,098 | 58,386 | 59,308 | 25,531 | 18,926 | 27,874 | 19,902 | 19,756 | 73,766 | 44,612 | 20,398 |
| Low complexity: | 6496 | 4585 | 12623 | 12588 | 5569 | 4180 | 6115 | 4516 | 4033 | 15956 | 7700 | 4463 |
Repeats were analyzed using RepeatMasker v4.1.2. RepeatModeler v2.0.3 [50,51,52] was used to model the repeats. Most repeats fragmented by insertions or deletions have been counted as one element. Abbr: Puccinia graminis tritici (Pgt); Puccinia striiformis tritici (Pst); Puccinia triticina (Pt); Puccinia coronata avenae (Pc); Puccinia novopanici (Pn); Puccinia sorghi (Ps); Puccinia hordei (Ph); Melampsora laricis (Ml).