Table 3 Genome summary statistics of representative ophiostomatoid isolates sequenced in this study
Species | Ceratocystiopsis | Graphilbum | Leptographium s. l.. | Ophiostoma s. l. | |||
|---|---|---|---|---|---|---|---|
Ceratocystiopsis sp. | G. fragrans | G. ipis-grandicollis sp. nov | G. cf. rectangulosporium | Gro. huntii | Gro. radiaticola | O. angusticollis | |
Taxon | Taxon 1 | Taxon 2 | Taxon 3 | Taxon 4 | Taxon 5 | Taxon 6 | Taxon 7 |
Sequenced strain | VPRI43766 | VPRI43528 | VPRI43762 | VPRI43763 | VPRI43530 | VPRI43523 | VPRI43764 |
GenBank Accession | JADHKF010000000 | JADHKG010000000 | JADHKH010000000 | JADHKI010000000 | JADHKJ010000000 | JADHKK010000000 | JADHKL010000000 |
Total reads after QC | 27,063,242 | 50,135,289 | 49,429,518 | 46,778,484 | 94,294,776 | 114,599,394 | 10 454 088 |
Number of scaffolds | 79 | 237 | 178 | 117 | 254 | 85 | 317 |
Longest contig (bp) | 1,540,000 | 999,956 | 1,555,217 | 1,343,814 | 1,099,032 | 2,583,828 | 651 020 |
Est. genome size (Mb) | 20.45 | 34.04 | 24.02 | 23.61 | 28.05 | 27.56 | 23.80 |
N50 (bp) | 471,680 | 323,198 | 601,306 | 298,270 | 343,842 | 883,760 | 236 362 |
L50 | 12 | 32 | 13 | 22 | 25 | 11 | 34 |
# N's per 100 kbp | 10 | 7 | 14 | 6 | 8 | 5 | 14 |
GC (%) | 61.48 | 55.75 | 55.53 | 60.91 | 54.63 | 57.09 | 57.89 |
Avg. coverage depth | 197 | 218 | 305 | 296 | 493 | 619 | 61 |
No. of predicted genes | 6967 | 9034 | 7221 | 7270 | 7836 | 7867 | 8022 |
Est. gene density | 341 | 265 | 301 | 308 | 279 | 286 | 337 |
Complete BUSCO (%) | 95.20 | 97.10 | 95.60 | 95.70 | 97.40 | 96.40 | 96.60 |
Complete BUSCO (n) | 3636 | 3706 | 3647 | 3651 | 3716 | 3680 | 3686 |
Complete—single | 3631 | 3699 | 3644 | 3648 | 3710 | 3673 | 3680 |
Complete—duplicated | 5 | 7 | 3 | 3 | 6 | 7 | 6 |
Fragmented | 17 | 23 | 29 | 18 | 17 | 21 | 18 |
Missing | 164 | 88 | 141 | 148 | 84 | 116 | 113 |
Species | Ophiostoma s. lat. | Raffaelea | Sporothrix | Graphium | ||||
|---|---|---|---|---|---|---|---|---|
O. fasciatum | O. ips | O. pallidulum | R. deltoideospora | S. euskadiensis | S. cf. nigrograna | S. pseudoabietina | Graphium sp. | |
Taxon | Taxon 8 | Taxon 9 | Taxon 10 | Taxon 11 | Taxon 12 | Taxon 13 | Taxon 14 | Taxon 15 |
Sequenced strain | VPRI43845 | VPRI43529 | VPRI43846 | VPRI43720 | VPRI43754 | VPRI43755 | VPRI43531 | VPRI43844 |
GenBank Accession | JADHKM010000000 | JADHKN010000000 | JADHKO010000000 | JADHKP010000000 | JADHKQ010000000 | JADHKR010000000 | JADHKS010000000 | JADHKT010000000 |
Total reads after QC | 51,287,508 | 37,261,588 | 36,666,452 | 35,927,882 | 29,627,312 | 37,781,794 | 36,719,768 | 28,160,580 |
Number of scaffolds | 36 | 208 | 473 | 120 | 92 | 125 | 51 | 490 |
Longest contig (Mb) | 2,360,849 | 1,117,630 | 543,815 | 1,965,135 | 1,881,930 | 1,307,617 | 3,412,636 | 1,008,604 |
Est. genome size (Mb) | 22.54 | 26.01 | 32.66 | 30.95 | 36.13 | 27.34 | 35.20 | 31.65 |
N50 (bp) | 966,108 | 283,044 | 126,120 | 416,364 | 790,753 | 398,989 | 1,285,428 | 190,968 |
L50 | 9 | 29 | 84 | 25 | 16 | 23 | 9 | 49 |
# N's per 100 kbp | 4 | 8 | 12 | 18 | 11 | 12 | 8 | 12 |
GC (%) | 65.26 | 56.88 | 57.93 | 54.55 | 52.70 | 59.54 | 53.27 | 50.12 |
Avg. coverage depth | 341 | 209 | 167 | 173 | 122 | 205 | 154 | 132 |
No. of predicted genes | 7498 | 7470 | 8757 | 7428 | 9348 | 7908 | 9190 | 9482 |
Est. gene density | 333 | 287 | 268 | 240 | 259 | 289 | 261 | 300 |
Complete BUSCO (%) | 96.60 | 96.90 | 97.20 | 94.90 | 98.10 | 97.20 | 97.80 | 96.60 |
Complete BUSCO (n) | 3688 | 3696 | 3710 | 3621 | 3743 | 3710 | 3734 | 3686 |
Complete—single | 3685 | 3690 | 3705 | 3613 | 3739 | 3703 | 3729 | 3679 |
Complete—duplicated | 3 | 6 | 5 | 8 | 4 | 7 | 5 | 7 |
Fragmented | 16 | 16 | 28 | 30 | 10 | 23 | 12 | 40 |
Missing | 113 | 105 | 79 | 166 | 64 | 84 | 71 | 91 |