Table 1.
Genome-wide Repeat-Induced Point (RIP) mutation statistics for different versions of the Fusarium circinatum (FSP34) genome assembly.
| Genome and RIP statistics | Version of the genome assembly | ||
|---|---|---|---|
| 2012 | 2018 | 2020 | |
| Genome size (bp) | 42,457,838 | 43,949,211 | 45,100,144 |
| Number of scaffolds/contigs in the genome assembly | 4,509 | 420 | 28 |
| BUSCO genome completeness (%)1 | 91.1 | 92.3 | 98.1 |
| Number of windows investigated | 88,515 | 87,898 | 90,200 |
| GC content (%) for the assembly | 47.3 | 47.4 | 46.9 |
| Number of RIP affected windows2 | 3,582 | 3,628 | 5,685 |
| RIP-affected genomic proportion (%)3 | 4.0 | 4.1 | 6.3 |
| Predicted repeat content (%)4 | 4.6 | 4.3 | 8.0 |
| Number of LRARs5 | 45 | 106 | 168 |
| Average size (bp) of LRARs | 7085.4 | 9547.2 | 14975.5 |
| Average GC content (%) of LRARs | 22.8 | 22.2 | 20.8 |
| Genomic proportion (bp) of LRARs | 318,842 | 1,012,006 | 2,515,882 |
| Product index value for LRARs6 | 1.6 | 1.6 | 1.6 |
| Substrate index value for LRARs7 | 0.3 | 0.3 | 0.2 |
| Composite index value for LRARs8 | 1.3 | 1.3 | 1.3 |
Benchmarking universal single-copy orthologs (Simão et al., 2015; Waterhouse et al., 2017).
Based on RIP index values.
Proportion of the genome affected by RIP. Calculated using the total number of windows indicating RIP-positive index values against the total number of windows investigated for the entire genome sequence.
Estimated using REPET (Quesneville et al., 2005; Flutre et al., 2011).
LRAR, large RIP affected genomic regions. More than 4,000 bp that are consecutively RIP affected.
Product index value (TpA/ApT): x > 1.15.
Substrate index value (CpA + TpG/ApC + GpT): 0.75 ≥ x.
Composite index value [(TpA/ApT) − (CpA + TpG/ApC + GpT)]: x > 0.