Table 5. Relative RPKMs of RNAi-related genes.
| RNAi factors | Closest homolog in B. mori | GenBank Accession Number | Gene ID | 2inf vs 2c RPKM | 4inf vs 4c RPKM |
|---|---|---|---|---|---|
| Intracellular auxiliary factors | |||||
| Arginine methyltransferase PRMT5 (dPRMT5, also called capsuleen or dart5) | protein arginine N-methyltransferase 5-like isoform X1 or X2 (predicted) | XP_004928553.1/ XP_004928554.1 | BGIBMGA007842 | 1.11 | 1.46 |
| Armitage | probable RNA helicase armi-like (predicted)* | XP_004933936.1 | BGIBMGA005056 | 1.13 | 0.95 |
| ATP-dependent RNA helicase Belle | ATP-dependent RNA helicase DDX3X isoform X1 or X2 (predicted) | XP_004924684.1/ XP_004924685.1 | BGIBMGA007594 | 1.05 | 1.26 |
| Clp1 homolog (kinase) | protein CLP1 homolog (predicted) | XP_004923397.1 | BGIBMGA004784 | 1.03 | 1.20 |
| Drosophila homolog of p68 RNA helicase | DEAD box polypeptide 5 isoform 1 or 2 | NP_001037582.1/ NP_001166829.1 | BGIBMGA011746 | 1.31 | 1.42 |
| DEAD box polypeptide 5 isoform 1 or 2 | NP_001037582.1/ NP_001166829.1 | BGIBMGA011754 | 1.12 | 1.15 | |
| DEAD box polypeptide 5 isoform 1 or 2 | NP_001037582.1/ NP_001166829.1 | BGIBMGA011965 | 1.05 | 1.22 | |
| DEAD box polypeptide 5 isoform 1 or 2 | NP_001037582.1/ NP_001166829.1 | BGIBMGA012013 | 0.88 | 0.87 | |
| Elp-1 | elongator complex protein 1 | NP_001182006.1 | BGIBMGA001538 | 0.94 | 0.97 |
| Eukaryotic initiation factor 4E-1 | eukaryotic initiation factor 4E-1 | NP_001091832.1 | BGIBMGA012675 | 4.89 | 2.16 |
| Gawky CG31992-PA (similar) | trinucleotide repeat-containing gene 6B protein-like (predicted)/ protein Gawky-like (predicted) | XP_004922030.1/ XP_004922029.1 | BGIBMGA005589 | 1.12 | 0.90 |
| Gemin 3 homolog | probable ATP-dependent RNA helicase DDX20-like (predicted) | XP_004931522.1 | BGIBMGA011804 | 0.77 | 1.41 |
| HEN1 | small RNA 2'-O-methyltransferase-like (predicted) | XP_004928786.1 | BGIBMGA007679 | 1.21 | 0.79 |
| Homeless (spindle-E) | probable ATP-dependent RNA helicase spindle-E-like (predicted) | XP_004924494.1 | BGIBMGA004949 | 0.92 | 1.43 |
| Maelstrom | protein maelstrom homolog (predicted) | XP_004928380.1 | BGIBMGA008424 | 1.08 | 1.32 |
| Putative translin-associated factor X | translin-associated protein X-like (predicted) | XP_004927402.1 | BGIBMGA004644 | nd | nd |
| Staufen | maternal effect protein staufen-like (predicted) | XP_004932448.1 | BGIBMGA002695 | 1.12 | 0.88 |
| Translin | translin | ABD36365.1 | BGIBMGA009726 | 1.07 | 1.38 |
| Tudor-SN | tudor staphylococcus/micrococcal nuclease | NP_001182009.1 | BGIBMGA013328 | 0.69 | 0.85 |
| Vasa intronic gene (VIG) | plasminogen activator inhibitor 1 RNA-binding protein-like | NP_001266293.1 | BGIBMGA006704 | 1.07 | 0.86 |
| DsRNA uptake | |||||
| CG4966 (orthologous to the Hermansky- Pudlak Syndrome 4, HPS4) | uncharacterized protein LOC101743016 (predicted)* | XP_004923697.1 | BGIBMGA009850 | 1.16 | 0.51 |
| Eater | neurogenic locus notch homolog protein 1-like (predicted) * | XP_004931260.1 | BGIBMGA002383 | 1.33 | 0.79 |
| FBX011 ortholog | F-box only protein 11-like isoform X1 or X2 (predicted) | XP_004924574.1/ XP_004924575.1 | BGIBMGA005003 | 1.09 | 1.12 |
| Scavenger receptor SR-C-like protein | scavenger receptor type C precursor | NP_001128387.1 | BGIBMGA004577 | 2.15 | 0.33 |
| Sid-1-like protein 1 | sid-1-related gene 1 precursor/ low quality protein: SID1 transmembrane family member 1 (predicted) | NP_001106735.1 / XP_004930735.1 | BGIBMGA011251 | 1.14 | 0.95 |
| sid-1-related gene 1 precursor | NP_001106735.1 | BGIBMGA011160 | 0.92 | 0.87 | |
| sid-1-related gene 1 precursor | NP_001106735.1 | BGIBMGA011161 | 0.71 | 1.15 | |
| low quality protein: SID1 transmembrane family member 1 (predicted) | XP_004930735.1 | BGIBMGA011250 | 0.99 | 1.08 | |
| Sid-1-like protein 2 | sid-1-like protein 2 | BAF95807.1 | BGIBMGA011251 | 1.14 | 0.95 |
| Sid-1-like protein 3 | sid-1-related gene 3 precursor | NP_001106736.1 | BGIBMGA005847 | 0.93 | 0.84 |
| Antiviral RNAi | |||||
| Ars2 | low quality protein: serrate RNA effector molecule homolog (predicted) | XP_004930189.1 | BGIBMGA003480 | 0.94 | 1.08 |
| CG4572 | venom serine carboxypeptidase-like (predicted) | XP_004929002.1 | BGIBMGA013085 | 1.01 | 1.85 |
| Egghead | glycosyltransferase precursor | NP_001243979.1 | BGIBMGA001169 | 1.34 | 1.52 |
| NinaC | myosin-IIIa-like (predicted) | XP_004930229.1 | BGIBMGA003454 | 1.46 | 0.67 |
| Nucleases | |||||
| dsRNase | alkaline nuclease precursor | NP_001091744.1 | BGIBMGA001173 | 0.55 | 0.85 |
| Exosome | PM-Scl autoantigen-like protein | NP_001108472.1 | BGIBMGA000626 | 1.34 | 0.77 |
| Nibbler | probable exonuclease mut-7 homolog (predicted) | XP_004931095.1 | BGIBMGA002947 | 0.84 | 0.94 |
| Poly(A) polymerase (Pla1 homolog Schizosaccharomyces) | poly(A) polymerase gamma-like isoform X1 (predicted) | XP_004923145.1 | BGIBMGA000084 | 1.29 | 1.02 |
| Sdn1-like (small RNA-degrading nuclease 1) | putative RNA exonuclease NEF-sp-like (predicted) | XP_004931480.1 | BGIBMGA011782 | 0.84 | 1.31 |
| Other factors | |||||
| Exportin-5 | exportin-5-like (predicted) | XP_004928015.1 | BGIBMGA001123 | 0.92 | 1.02 |
| HSP90 | HSP90, partial | AEB39782.1 | BGIBMGA004612 | 0.96 | 2.24 |
Ratios of RPKM values from pathogenically versus persistently infected midgut tissue of 2nd and 4th instar larvae obtained by deep sequencing analysis (2c, 2inf, 4c and 4inf samples) are presented for selected genes with a role in the RNAi mechanism. Listed are intracellular auxiliary factors, dsRNA uptake genes, antiviral RNAi genes, nucleases and unclassified factors [64]. Genes presenting higher than 1.5-fold up- or down-regulation are marked with bold letters. Abbreviation: nd: not detected.