TABLE 2.
Major virus-like sequences from the barley aphid transcriptomes.
| Contig name1 | Size (nt) | Read no. | Virus or tentative2 virus name | Aphid3 | Accession no. |
| Nege/kita-like virus sequences | |||||
| BaA1_c12 | 10,318 | 328,424 | Wuhan house centipede virus 1 | Rp, Sa | LC516834 |
| BaA3_c894a | 8,890 | 253,596 | barley aphid RNA virus 1 | Rm | LC516835 |
| BaA1_c637 4a | 6,421 | 1,390 | barley aphid RNA virus 1 | Rp, Sa | |
| BaA3_c1889 | 9,398 | 22,346 | barley aphid RNA virus 2 | Rm | LC516836 |
| BaA3_c1334b | 9,321 | 18,472 | barley aphid RNA virus 3 | Rm | LC516837 |
| BaA1_c42/1654b,5 | 9,322 | 303,799 | barley aphid RNA virus 3 | Rp, Rm, Sa | |
| BaA1_c14/635 | 8,395 | 283,449 | barley aphid RNA virus 4 | Rp, | LC516838 |
| Flavi-like virus sequences | |||||
| BaA3_c535 | 3,140 | 43,197 | Wuhan aphid virus 1 S1 | Rp, Rm, Sa | LC516839 |
| BaA3_c172 | 1,168 | 57,745 | Wuhan aphid virus 1 S2 | LC516840 | |
| BaA3_c296 | 2,839 | 77,321 | Wuhan aphid virus 1 S3 | LC516841 | |
| BaA3_c581 | 2,758 | 77,906 | Wuhan aphid virus 1 S4 | LC516842 | |
| BaA1_c359 | 23,141 | 21,307 | Sitobion miscanthi flavi-like virus 1 | Rp, Sa | LC516843 |
| BaA1_c652 | 15,288 | 5,199 | barley aphid RNA virus 9 | Rp, Sa | LC516844 |
| BaA1_c1578 | 3,691 | 1,025 | barley aphid RNA virus 9 | ||
| BaA1_c891 | 3,749 | 742 | barley aphid RNA virus 9 | ||
| BaA3_c3690 4c | 21,997 | 5,333 | barley aphid RNA virus 10 | Rm | LC516845 |
| BaA1_c3264c | 21,210 | 18,335 | barley aphid RNA virus 10 | Rm | |
| BaA1_c33 | 10,551 | 1,440 | barley aphid RNA virus 10 | Rp | LC516846 |
| BaA1_c194 | 5,869 | 877 | barley aphid RNA virus 10 | ||
| Tombus-like virus sequences | |||||
| BaA1_c277 5 | 3,702 | 198,247 | Wuhan insect virus 21, S1 | Rp, Sa | LC516847 |
| BaA1_c31 5 | 2,201 | 690,152 | Wuhan insect virus 21, S2 | LC516848 | |
| Phenui-like virus sequences | |||||
| BaA1_c346 | 7,403 | 2,040 | barley aphid RNA virus 5 | Rp, Rm | LC516849 |
| BaA2_c4524 | 7,402 | 1,329 | barley aphid RNA virus 5 | Rm | LC516850 |
| Other insect virus-like sequences | |||||
| BaA2_c1487 | 2,636 | 4,820 | barley aphid RNA virus 6 | Rm | LC516851 |
| BaA3_c16152 | 2,057 | 239 | barley aphid RNA virus 7 | Rm | LC516852 |
| BaA2_c19028 | 3,552 | 657 | barley aphid RNA virus 8, S1 | Rm | LC516853 |
| BaA2_c18060 | 3,220 | 575 | barley aphid RNA virus 8, S4 | LC516854 | |
| BaA1_c21296 | 1,259 | 105 | a partitivirus-like contig | Rm | LC516855 |
| BaA2_c20409 | 1,605 | 127 | a mononegavirus-like contig | Rm | LC516856 |
1Pool-1: BaA1; Pool-2: BaA2; Pool-3: BaA3. Some other variants of virus-like contigs are shown in Supplementary Figure S7, or not shown. Plant luteovirus-related sequences are not listed here. 2Nucleotide and/or amino acid sequence identity of the contig sequences are shown within Table 3 and Supplementary Table S4. Ten discovered novel viruses were designated as barley aphid RNA viruses 1 to 10 (see main text). S, RNA or dsRNA segment. 3Aphid species in discovery colonies assessed by RT-PCR detection (see Supplementary Figure S1A). Rp: Rhopalosiphum padi; Rm, R. maidis; Sa, Sitobion avenae. 4These sequences are slightly different from each other at the nucleic acid level (4a: 3%, 4b: 1%, and 4c: 5% difference, respectively). 5The gap or unassembled regions were sequenced using RT-PCR (see Figure 2D and Supplementary Figure S7C).