Table 1 Summarised assembly (A) and gene model (B) statistics for F. oxysporum (Fo) and F. oxysporum f. sp. cepae (Foc) isolates. Gene models predicted in this study show values predicted by Braker and additional genes predicted by CodingQuarry. Reference values are shown for the published Fo isolate Fo47 and F. oxysporum f. sp. lycopersici (Fol) isolate 4287 genomes.
Organism | Foc | Foc | Foc | Fo | Fo | Fo | Fo | Fo | Fol |
|---|---|---|---|---|---|---|---|---|---|
Isolate | Fus2 | 125 | A23 | A13 | A28 | CB3 | PG | Fo471 | 42871 |
(A) Assembly stats: | |||||||||
Total coverage (fold) | 214 | 63 | 47 | 33 | 53 | 30 | 69 | — | — |
Technology | PacBio + MiSeq | MiSeq | MiSeq | MiSeq | MiSeq | MiSeq | MiSeq | — | — |
Assembly size (Mb) | 53.4 | 51.4 | 51.0 | 54.8 | 53.1 | 50.5 | 50.3 | 49.7 | 61.5 |
Contigs | 34 | 2121 | 1999 | 3121 | 2375 | 1720 | 920 | 124 | 15 + 73* |
Largest contig (Kb) | 6,434 | 573 | 538 | 806 | 1,221 | 1,006 | 2,304 | 6,199 | 6,855 |
N50 (Kb) | 414 | 128 | 147 | 167 | 297 | 237 | 413 | 3,844 | 4,590 |
Sodariomycete genes (BUSCO) | 3687 | 3686 | 3688 | 3692 | 3683 | 3679 | 3684 | 3687 | 3599 |
% Sodariomycete genes (BUSCO) | 99 | 99 | 99 | 99 | 99 | 99 | 99 | 99 | 97 |
% Repeatmasked | 10.54 | 7.36 | 6.96 | 9.03 | 8.35 | 5.67 | 6.11 | 5.68 | 16.42 |
(B) Gene models: | |||||||||
Total genes | 18855 | 18505 | 18323 | 18790 | 18629 | 17943 | 17830 | 18191 | 20925 |
Total proteins | 19371 | 18743 | 18557 | 18934 | 18874 | 18178 | 18101 | 24818 | 27347 |
Braker transcripts | 17823 | 17197 | 17006 | 17986 | 17426 | 16833 | 16811 | — | — |
CodingQuarry transcripts | 1548 | 1546 | 1551 | 948 | 1448 | 1345 | 1290 | — | — |
Sodariomycete genes (BUSCO) | 3668 | 3671 | 3663 | 3673 | 3627 | 3663 | 3664 | 3687 | 3577 |
% Sodariomycete genes (BUSCO) | 98 | 99 | 98 | 99 | 97 | 98 | 98 | 99 | 96 |
Secreted Genes | 1449 | 1439 | 1431 | 1505 | 1442 | 1433 | 1429 | 1409 | 1493 |
