Table 1 . Summary of W05 genome assembly and annotation
Categories | Type | Length (Mb) | No. | Percentage (%) |
|---|---|---|---|---|
Assembly | Contigs | 988.6 | 1870 | − |
Contig N50 | 3.3 | 58 | − | |
Contig N90 | 0.4 | 432 | − | |
Scaffolds | 1013.2 | 1118 | − | |
Scaffold N50 | 50.7 | 10 | − | |
Scaffold N90 | 38.4 | 19 | − | |
Protein-coding genes | Total transcripts | − | 89,477 | 100.0 |
Function assigned transcripts | − | 82,567 | 92.3 | |
Non-coding RNAs | miRNA | 0.036 | 288 | 0.004 |
snRNA | 0.216 | 1988 | 0.021 | |
rRNA | 0.032 | 147 | 0.003 | |
tRNA | 0.067 | 892 | 0.007 | |
Transposable elements | Class I: Retroelements | 359.6 | − | 35.5 |
SINEs | 1.1 | − | 0.1 | |
LINEs | 13.3 | − | 1.3 | |
LTR elements | 345.2 | − | 34.1 | |
Ty1/Copia | 93.5 | − | 9.2 | |
Ty3/gypsy | 248.0 | − | 24.5 | |
Others | 3.8 | − | 0.4 | |
Class II: DNA transposons | 74.8 | − | 7.4 | |
CMC-EnSpm | 29.7 | − | 2.9 | |
MULE | 27.9 | − | 2.8 | |
TcMar | 0.8 | − | 0.1 | |
hAT | 8.7 | − | 0.9 | |
Helitron | 4.2 | − | 0.4 | |
Others | 3.5 | − | 0.3 | |
Satellites | 4.9 | − | 0.5 | |
Simple repeats | 44.1 | − | 4.4 | |
Low complexity | 3.1 | − | 0.3 | |
Unknown | 59.8 | − | 5.9 | |
Total transposable elements | 546.4 | − | 53.9 |
