Table 1 Genome assembly statistics for three strains of Verticillium dahliae
From: Dynamics of Verticillium dahliae race 1 population under managed agricultural ecosystems
Strain | VdLs.16 | JR2 | VdLs.17 | ||||
|---|---|---|---|---|---|---|---|
Genome assembly | Â | Scaffold | Contig | Scaffold | Contig | Scaffold | Contig |
Total number | 14 | 17 | 8 | 8 | 8 | 8 | |
Total length of (bp) | 36,092,517 | 36,089,483 | 36,150,287 | 36,150,287 | 35,973,870 | 35,973,870 | |
Gap number (bp) | 3034 | – | 0 | – | 0 | – | |
Average length (bp) | 2,578,037 | 2,122,911 | 4,518,786 | 4,518,786 | 4,496,734 | 4,496,734 | |
N50 length (bp) | 4,722,744 | 3,663,785 | 4,168,633 | 4,168,633 | 5,894,008 | 5,894,008 | |
N90 length (bp) | 2,532,149 | 2,375,583 | 3,361,230 | 3,361,230 | 3,290,897 | 3,290,897 | |
Maximum length (bp) | 8,087,087 | 8,087,087 | 9,275,483 | 9,275,483 | 6,210,300 | 6,210,300 | |
Minimum length (bp) | 50,807 | 41,068 | 3,277,570 | 3,277,570 | 3,272,870 | 3,272,870 | |
GC content (%) | 53.8 | 53.8 | 53.88 | 53.88 | 54 | 54 | |
Genome prediction | Protein-coding genes | 10,799 | 10,875 | 10,825 | |||
Length of genes (bp) | 18,863,221 | 19,050,607 | 19,146,372 | ||||
Mean gene length (bp) | 1,747 | 1752 | 1769 | ||||
Gene GC % | 58.56 | 58.49 | 58.46 | ||||
Length of CDS (bp) | 16,527,821 | 16,720,002 | 16,761,722 | ||||
Mean length of CDS (bp) | 1530 | 1537 | 1548 | ||||
CDS GC % | 59.41 | 59.31 | 59.29 | ||||
Exon no. | 31,232 | 31,303 | 31,696 | ||||
Coding gene with introns | 1.89 | 1.87 | 1.92 | ||||
Mean exons per gene | 2.89 | 2.87 | 2.92 | ||||
Mean exons length (bp) | 529 | 534 | 529 | ||||
Intron no. | 20,433 | 20,428 | 20,871 | ||||
Mean intron length (bp) | 114 | 114 | 114 | ||||
Intron GC % | 52.26 | 52.25 | 52.29 | ||||
Mean intergenic length (bp) | 1584 | 1571 | 1553 | ||||
No. of transposons | 4870 | 4665 | 5262 | ||||
Total length of transposons (bp) | 3,879,742 | 4,057,098 | 4,803,307 | ||||
Percentage in genome | 10.7494 | 11.2228 | 13.3522 | ||||
Genome annotation | Secretome | 797 | 803 | 803 | |||
CAZymes | 588 | 589 | 590 | ||||
Pectin degradation | 36 | 35 | 35 | ||||
Cellulose degradation | 84 | 84 | 82 | ||||
Hemicellulose degradation | 67 | 67 | 65 | ||||
Ligin degradation | 4 | 5 | 4 | ||||
CAZymes (secreted) | 266 | 268 | 270 | ||||
SCRPs | 302 | 313 | 297 | ||||
LysM effectors | 6 | 6 | 7 | ||||
NLPs | 7 | 7 | 8 | ||||
Protein kinases | 150 | 156 | 154 | ||||
Transcription factors | 432 | 482 | 500 | ||||
PHI homologs | 2797 | 2778 | 2789 | ||||