Table 1. Number of sequence reads and mean read coverage of viral genomes from mined transcriptome data sets.
Sequence coverage was determined in Geneious software version 9.1.7 with BBMap using de novo assemblies generated by VirFind [9]. Abbreviations: J2 (second-stage juvenile), SCN (soybean cyst nematode), BCN (beet cyst nematode), CCN (cereal cyst nematode), PCN (potato cyst nematode), Gp (Globodera pallida), Gr (G. rostochiensis), NLV (nyami-like virus), BLV (bunya-like virus), PLV (picorna-like virus). Mean describes average sequence read coverage for each nucleotide position. ND (not detected) denotes the virus was not found in the specified nematode sample.
| SCN NLV | SCN BLV | PCN PLV | ||||||
|---|---|---|---|---|---|---|---|---|
| Sample | Run ref # | Reads | Reads | Mean | Reads | Mean | Reads | Mean |
| SCN OP25 J2s | SRR6269844 | 11.4 mil | 22,989 | 557 | 5845 | 168 | ND | ND |
| SCN OP50 J2s | SRR6269845 | 12.7 mil | 34,351 | 820 | 5619 | 161 | ND | ND |
| SCN MM8 J2s | SRR6232814-16 | 71.3 mila | 7391 | 50 | 305b | 3 | ND | ND |
| BCN J2s | SRR1125017 | 184,024 | 1714 | 3 | ND | ND | ND | ND |
| CCN J2s + females | ERR414136 | 46.1 mil | ND | ND | ND | ND | ND | ND |
| PCN (Gp) males | ERR202422 | 33.7 mil | ND | ND | ND | ND | 88,829 | 731 |
| PCN (Gp) females | ERR202423 | 33.5 mil | ND | ND | ND | ND | 12,138 | 99 |
| PCN (Gr) females | ERR1173512 | 41.2 mil | ND | ND | ND | ND | 1751 | 19 |
a Read information represents three pooled biological replicates.
b Sequence data spans the length of the genome; however, there is poor coverage within A-T rich regions creating several large, undermined gaps in the genome.