Table 2.
Assembly statistics for 17 Phytophthora cactorum and three Phytophthora idaei isolates sequenced in this study.
| Features | Phytophthora cactorum | Phytophthora idaei | ||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Fragaria ×ananassa crowns | Fragaria ×ananassa fruit | Malus ×domestica | Rubus idaeus | |||||||||||||||||
| P414 | 12–420 | 15–13 | 15–7 | 2003–3 | 4032 | 4040 | P404 | P415 | P421 | PC13/15 | 11–40 | 17–21 | 62471 | P295 | R36/14 | SCRP370 | SCRP371 | SCRP376 | ||
| Coverage | 76.49 | 25.60 | 55.63 | 59.71 | 69.29 | 53.14 | 67.21 | 69.52 | 86.64 | 106.94 | 77.83 | 68.90 | 78.86 | 72.21 | 39.29 | 56.09 | 40.91 | 71.89 | 49.19 | |
| No. of contigs | 194 | 5,509 | 5,421 | 5,457 | 5,467 | 6,726 | 5,326 | 20,136 | 5,695 | 5,485 | 5,278 | 4,571 | 4,452 | 6,173 | 5,088 | 5,952 | 5,356 | 4,720 | 5,313 | |
| Assembly size (Mb) | 66.0 | 59.9 | 60.7 | 60.8 | 60.8 | 61.6 | 60.7 | 75.5 | 60.8 | 60.5 | 60.0 | 61.1 | 59.7 | 59.8 | 61.3 | 60.7 | 60.5 | 61.7 | 60.6 | |
| Longest contig (bp) | 1,749,730 | 272,591 | 358,283 | 300,516 | 353,051 | 299,428 | 238,735 | 346,862 | 313,236 | 251,913 | 346,832 | 288,536 | 347,645 | 285,881 | 357,485 | 345,260 | 247,223 | 295,942 | 230,545 | |
| N50 (bp) | 645,375 | 37,498 | 41,248 | 43,376 | 40,273 | 38,202 | 39,295 | 36,598 | 40,742 | 34,103 | 39,779 | 43,828 | 49,722 | 36,408 | 48,651 | 36,465 | 39,576 | 46,381 | 39,406 | |
| Masked (% bp) | 29.2 | 24.9 | 26.2 | 26.0 | 26.2 | 26.1 | 26.1 | 18.4 | 26.5 | 26.0 | 25.9 | 24.5 | 25.1 | 25.6 | 25.6 | 26.2 | 27.0 | 26.6 | 27.3 | |
| BUSCO | C | 224 | 228 | 227 | 228 | 228 | 228 | 228 | 227 | 228 | 226 | 228 | 227 | 227 | 226 | 227 | 227 | 230 | 230 | 229 |
| % present | 95.7 | 97.4 | 97.0 | 97.4 | 97.4 | 97.4 | 97.4 | 97.0 | 97.4 | 96.6 | 97.4 | 97.0 | 97.0 | 96.6 | 97.0 | 97.0 | 98.3 | 98.3 | 97.9 | |
Isolate P414 represents results from long read sequencing technologies whereas other assemblies are a result of short read sequencing technology. Information on sequencing coverage, assembly size, percentage of bases repeatmasked are shown. Assembly completeness statistics, assessed using Alveolata-Stramenopiles Benchmarking Universal Single-copy Orthologue (BUSCO) genes, detail the number of complete (C) and total percentage of 234 core Eukaryotic genes present in assemblies.