Table 1.
Predicted peach mRNAs, annotated as transcripts, targeted by PLMVd-sRNAs containing the pathogenic determinant for PYM strictly associated with U238 (or the complementary A238).
| sRNAa | sRNA 5´endb |
Viroid strand |
sRNA RPMc |
mRNA target:sRNA duplexd | mfee | Scoref | mRNA target accession numberg | Target predicted functiong | EST assembly of target transcriptg | Chloroplast localization of the encoded proteinh |
|---|---|---|---|---|---|---|---|---|---|---|
| PYM-sRNA15 | 269 | (+) | 109.7/9.0/3.7 |  |
−34.8 | 2.5 | Prupe.1G480500 | Phospholipase D alpha1, hormonal action and stress-response | asmbl_18654.peachv21_pasa0 | No |
| PYM-sRNA16 | 268 | (+) | 49.7/3.2/2.4 |  |
−34.8 | 2.5 | Prupe.1G480500 | Phospholipase D alpha1, hormonal action and stress-response | asmbl_18654.peachv21_pasa0 | No |
| PYM-sRNA16 | 268 | (+) | 49.7/3.2/2.4 |  |
−27.7 | 2.5 | Prupe.2G151200 | MADS-box protein SOC1, RNA-polymerase II regulator | asmbl_7685.peachv21_pasa1 | No |
| PYM-sRNA17 | 267 | (+) | 19.2/1.3/0.7 |  |
−36.3 | 2.5 | Prupe.3G302400 | COP9 signalosome complex subunit 3 | asmbl_12131.peachv21_pasa2 | No |
| PYM-sRNA18 | 266 | (+) | 0.6/0.1/0.0 |  |
−36.2 | 1.5 | Prupe.3G302400 | COP9 signalosome complex subunit 3 | asmbl_12131.peachv21_pasa2 | No |
| PYM-sRNA19 | 265 | (+) | 0.1/0.0/0.0 |  |
−34.2 | 2.5 | Prupe.3G302400 | COP9 signalosome complex subunit 3 | asmbl_12131.peachv21_pasa2 | No |
| PYM-sRNA41 | 284 | (−) | 0.1/0.0/0.0 |  |
−35.4 | 2.0 | Prupe.3G002700 | Protein translocase subunit SecA1 | asmbl_124.peachv21_pasa2 | Yes |
| PYM-sRNA40 | 285 | (−) | 14.6/0.8/0.5 |  |
−35.6 | 1.5 | Prupe.3G002700 | Protein translocase subunit SecA1 | asmbl_124.peachv21_pasa2 | Yes |
| PYM-sRNA39 | 286 | (−) | 64.1/3.2/1.6 |  |
−35.7 | 2.5 | Prupe.3G002700 | Protein translocase subunit SecA1 | asmbl_124.peachv21_pasa2 | Yes |
| PYM-sRNA38 | 287 | (−) | 31.2/2.5/1.3 |  |
−35.0 | 2.0 | Prupe.3G002700 | Protein translocase subunit SecA1 | asmbl_124.peachv21_pasa2 | Yes |
| PYM-sRNA37 | 288 | (−) | 16.1/1.6/0.7 |  |
−33.1 | 2.0 | Prupe.3G002700 | Protein translocase subunit SecA1 | asmbl_124.peachv21_pasa2 | Yes |
| PYM-sRNA32 | 293 | (−) | 12.8/0.9/0.3 |  |
−26.2 | 2.5 | Prupe.8G251600 | RNA-binding protein BRN1, floral development, mRNA catabolism | asmbl_9675.peachv21_pasa7 | No |
| PYM-sRNA29 | 296 | (−) | 4.8/0.7/0.2 |  |
−38.0 | 2.0 | Prupe.1G553100 | RING domain-containing protein 2, proteins traffic across vacuole system | asmbl_21682.peachv21_pasa0 | Yes |
| PYM-sRNA28 | 297 | (−) | 21.7/0.7/0.8 |  |
−39.4 | 2.0 | Prupe.1G553100 | RING domain-containing protein 2, proteins traffic across vacuole system | asmbl_21682.peachv21_pasa0 | Yes |
| PYM-sRNA27 | 298 | (−) | 65.6/2.4/1.9 |  |
−38.3 | 1.5 | Prupe.1G553100 | RING domain-containing protein 2, proteins traffic across vacuole system | asmbl_21682.peachv21_pasa0 | Yes |
| PYM-sRNA26 | 299 | (−) | 676.3/29.8/11.1 |  |
−36.9 | 1.5 | Prupe.1G553100 | RING domain-containing protein 2, proteins traffic across vacuole system | asmbl_21682.peachv21_pasa0 | Yes |
| PYM-sRNA26 | 299 | (−) | 676.3/29.8/11.1 |  |
−33.5 | 2.0 | Prupe.8G265600 | Kinesin-like protein KIN-14I, ATPase in microtubules activity | asmbl_10074.peachv21_pasa7 | No |
| PYM-sRNA725 | 300 | (−) | 0.6/0.1/0.0 |  |
−36.9 | 2.0 | Prupe.1G553100 | RING domain-containing protein 2, proteins traffic across vacuole system | asmbl_21682.peachv21_pasa0 | Yes |
| PYM-sRNA25 | 300 | (−) | 0.6/0.1/0.0 |  |
−33.5 | 2.0 | Prupe.8G265600 | Kinesin-like protein KIN-14I, ATPase in microtubules activity | asmbl_10074.peachv21_pasa7 | No |
| PYM-sRNA24 | 301 | (−) | 0.9/0.1 |  |
−37.2 | 2.0 | Prupe.8G265600 | Kinesin-like protein KIN-14I, ATPase in microtubules activity | asmbl_10074.peachv21_pasa7 | No |
asRNAs containing U283/A283 in (+) and (−) polarities, respectively
bLocation of sRNA 5´-termini in the genomic RNA of variant y4
cRPM of sRNA in yellow sector/green sector/green leaf libraries
dmRNA:sRNA duplexes predicted by psRNATarget (Xinbin Dai et al., 2018); targeted host mRNAs are on top (5´-3´ orientation) and sRNAs below (3´-5´orientation); U283/A283 are in bold; |, Watson-Crick base pairs; o, G:U wobble base pairs; -, mismatches or bulges
eMinimum free energy (mfe, kcal mol−1) predicted by RNA hybrid (Rehmsmeier et al., 2004) for the mRNA target:sRNA duplex
fScore of the mRNA target:sRNA duplex, estimated by psRNATarget (Xinbin Dai et al., 2018); the lower the score, the more reliable the prediction
gAnnotations from Prunus persica Whole Genome Assembly v2.0 & Annotation v2.1 (v2.0.a1) (https://www.rosaceae.org/analysis/154)
hChloroplast targeting of the protein predicted by CHLOROP software (http://www.cbs.dtu.dk/sevices/ChloroP)