Table 2 Draft genome assembly size, number of contigs, N50 value and genome completeness percentage of the six sequenced Heterodera species from the genomic DNA of field isolated fifty cysts compared to a published genome of Heterodera carotae (GenBank BioProject accession number PRJNA774818)
From: Insights from draft genomes of Heterodera species isolated from field soil samples
| Â | Assembly statistics | H. australis | H. avenae | H. filipjevi | H. humuli | H. mani | H. trifolii | H. carotae [43] |
|---|---|---|---|---|---|---|---|---|
Minimum contig value = 500 bp | Common name | Australian cereal cyst nematode | Cereal cyst nematode | Filipjev’s cereal cyst nematode | Hop cyst nematode | Ryegrass cyst nematode | Clover cyst nematode | Carrot cyst nematode |
NCBI GenBank Genome Assembly Accession Number | JBDLPM000000000 | JBDLPL000000000 | JBDLPK000000000 | JBDLPJ000000000 | JBDLPI000000000 | JBDLPH000000000 | GCA_024500135.1 | |
Assembly Size (bp) | 82,886,899 | 116,811,496 | 45,419,541 | 116,750,469 | 105,775,809 | 100,475,064 | 95,118,078 | |
Assembly size (Mb) | 82.8 | 116.8 | 45.4 | 116.7 | 105.7 | 100.4 | 95.1 | |
Number of scaffolds | 18,642 | 70,665 | 57,668 | 95,680 | 41,671 | 98,793 | 17,839 | |
Number of contigs | 18,642 | 70,664 | 57,631 | 95,857 | 41,671 | 98,793 | 17,845 | |
Largest scaffold (bp) | 66,318 | 64,296 | 19,717 | 143,716 | 43,969 | 47,397 | 113,425 | |
N50 value (bp) | 7,074 | 2,351 | 741 | 1,362 | 5,925 | 1,052 | 13,935 | |
No. contigs > 5,000 bp | 5,474 | 3,620 | 160 | 3,201 | 6,115 | 1,140 | 5,030 | |
No. contigs > 10,000 bp | 1,858 | 845 | 31 | 1,595 | 2,052 | 183 | 2,755 | |
No. contigs > 25,000 bp | 123 | 53 | 0 | 294 | 101 | 2 | 699 | |
No. contigs > 50,000 bp | 5 | 1 | 0 | 29 | 0 | 0 | 103 | |
GC content (%) | 36.32 | 37.57 | 41.77 | 47.8 | 37.89 | 44.44 | 39.39 | |
Total reads | 194,388,316 | 78,179,649 | 18,875,672 | 120,062,124 | 52,100,830 | 64,320,364 | Â | |
Genome Mapped %* | 15.57 | 63.32 | 24.27 | 47.47 | 61.73 | 25.95 | Â | |
Coverage > = 1x (%) | 99.44 | 98.2 | 92.02 | 93.26 | 99.07 | 89.95 |  | |
Average coverage depth | 31 | 44 | 9 | 44 | 37 | 11 | Â | |
Eukaryota_db (n = 255) | Complete BUSCOs (%) | 165 (64.7) | 108 (42.4) | 14 (5.5) | 173 (67.8) | 164 (64.3) | 69 (27.1) | 149 (58.4) |
Complete and single-copy BUSCOs (%) | 165 (64.7) | 108 (42.4) | 14 (5.5) | 168 (65.9) | 164 (64.3) | 60 (23.5) | 149 (0.0) | |
Complete and duplicated BUSCOs (%) | 0 | 0 | 0 | 5 (2.0) | 2 (0.8) | 9 (3.5) | 0 | |
Fragmented BUSCOs (%) | 29 (11.4) | 72 (28.2) | 99 (38.8) | 29 (11.4) | 39 (15.3) | 115 (45.1) | 52 (20.4) | |
Missing BUSCOs (%) | 61 (23.9) | 75 (29.4) | 142 (55.7) | 53 (20.8) | 52 (20.4) | 71 (27.8) | 54 (21.2) | |
Nematoda_db (n = 3131) | Complete BUSCOs (%) | 1468 (46.9) | 973 (31.1) | 128 (4.1) | 1568 (50.1) | 1468 (46.9) | 407 (13.0) | 1742 (55.1) |
Complete and single-copy BUSCOs (%) | 1458 (46.6) | 969 (30.9) | 128 (4.1) | 1552 (49.6) | 1438 (45.9) | 403 (12.9) | 1702 (54.4) | |
Complete and duplicated BUSCOs (%) | 10 (0.3) | 4 (0.1) | 0 | 16 (0.5) | 30 (1.0) | 4 (0.1) | 22 (0.7) | |
Fragmented BUSCOs (%) | 155 (5.0) | 191 (6.1) | 95 (3.0) | 129 (4.1) | 143 (4.6) | 174 (5.6) | 154 (4.9) | |
Missing BUSCOs (%) | 1508 (48.2) | 1967 (62.8) | 2908 (92.9) | 1434 (45.8) | 1520 (48.5) | 2550 (81.4) | 1253 (40.0) | |
| Â | Predicted protein coding genes usingH. schachtiispecies model | 18,975 | 44,321 | 35,303 | 1,01,081 | 33,265 | 77,832 | 17,212 |