Figure 1:
A. fragariae aggregated into a compact, dried cluster of “nematode wool” following 24-hr desiccation treatment at 60 ± 2% relative humidity and 23 ± 2°C.
Table S1.
Summary statistics for Aphelenchoides fragariae transcriptome assembly.
| Basic sequence statistics | Number |
|---|---|
| Total raw reads | 324,895,970 |
| Mean read length (bp) | 125 |
| Raw read GC content | 42% |
| Mean read PHRED score after filtering and trimming | 36 |
| Number of genes | 48,541 |
| Number of isoforms | 147,621 |
| Assembly N50 (of all isoforms) | 1293 bp |
| Ex90N50 | 1470 bp |
| Mean length of all isoforms | 882 bp |
| Top BLASTx-hit species | Toxocara canis |
| Percent of gene with at least one BLASTx hit (E ≤ 1.0-3) | 35% |
| Percent of gene with at least one GO annotation | 23% |
Figure S1:
Top blastx hit species for 48,541 putative protein-coding genes from Aphelenchoides fragariae.
Figure 2:
A: Volcano plot of differentially expressed genes between control and desiccated A. fragariae. Black: genes that were not differentially expressed; green: upregulated genes in desiccation; red: downregulated genes in desiccation (FDR = 0.05). Box encloses 100 genes with the largest positive fold changes; B: Number of A. fragariae genes from five families with documented roles in detoxification: cytochrome P450s (CYP), short chain dehydrogenase/reductases (SDR), UDP-glucuronosyltransferases (UGT), glutathione-S-transferases (GST), and nuclear hormone receptors (NHR). Green: genes upregulated in desiccation; red: genes downregulated in desiccation; grey: genes that were not differentially expressed (FDR = 0.05); C: Nine gene sets, defined based on shared gene ontology terms, whose expression was significantly enriched under desiccation (FDR = 0.05). Orange bar: normalized enrichment score for each set (Subramanian et al., 2005); D: Heat map of log10(FPKM) values in green and log2(fold-change) values in purple for 100 genes with the largest positive fold-changes in response to desiccation. Genes marked with orange bars have putative roles in detoxification.
Figure 3:
Differentially expressed genes of A. fragariae that function as chaperones in A and respond to unfolded proteins in B.
Table 1.
Characteristics of 14 putative intrinsically disordered proteins whose expression was significantly upregulated under desiccation in Aphelenchoides fragariae.
| Gene ID | Predicted length (aa) | Mean FPKM desiccated | Mean FPKM control | Fold-change | Adjusted P-value | % disordered residues | GRAVY hydropathy value | Blastx hits to LEA database |
|---|---|---|---|---|---|---|---|---|
| DN15064_c0_g1 | 175 | 398.8 | 0.4 | 1020.9 | 3.15E−64 | 88.1 | −1.836 | − |
| DN14203_c3_g3 | 119 | 45.4 | 0.5 | 88.7 | 1.92E−15 | 74.8 | −0.977 | − |
| DN10042_c0_g2 | 128 | 366.8 | 5.0 | 72.9 | 3.61E−28 | 82.8 | −0.108 | Sophora davidii dehydrin DHN, E = 2e−13 |
| DN10455_c1_g1 | 191 | 928.2 | 14.0 | 64.1 | 9.30E−99 | 90.6 | −0.503 | Sophora davidii dehydrin DHN, E = 8e−09 |
| DN9957_c2_g1 | 335 | 7.9 | 0.2 | 41.1 | 1.66E−17 | 94.6 | −1.104 | Sorghum bicolor dehydrin-like SORBIDRAFT_10g003700, E = 2e−14 |
| DN10923_c0_g1 | 171 | 17.0 | 0.7 | 25.5 | 1.23E−12 | 81.9 | −1.607 | Trifolium repens dehydrin b, E = 0.002 |
| DN9863_c0_g1 | 250 | 21.7 | 0.9 | 23.4 | 1.70E−43 | 85.2 | −0.951 | Arabidopsis thaliana dehydrin rab18, E = 2e−10 |
| DN9710_c0_g1 | 167 | 28.1 | 1.3 | 20.6 | 4.50E−07 | 93.5 | −1.185 | − |
| DN12711_c2_g2 | 131 | 92.8 | 6.4 | 13.8 | 4.35E−12 | 77.1 | −0.204 | Sophora davidii dehydrin DHN, E = 7e−07 |
| DN11488_c0_g1 | 192 | 16.40 | 1.30 | 11.50 | 2.52E−03 | 86.5 | −1.167 | − |
| DN12459_c0_g4 | 172 | 173.6 | 14.4 | 11.5 | 7.31E−17 | 98.3 | −0.793 | Eucalyptus grandis dehydrin 1, E = 5e−07 |
| DN15965_c0_g1 | 140 | 294.5 | 25.7 | 10.7 | 2.28E−10 | 72.9 | −0.450 | Hordeum vulgare dehydrin dhn4, E = 8e−12 |
| DN12325_c1_g1 | 96 | 15.5 | 1.9 | 8.1 | 1.38E−17 | 75.0 | −0.672 | − |
| DN9469_c2_g1 | 133 | 46.8 | 9.7 | 4.7 | 1.44E−14 | 100.0 | −1.520 | Phaseolis vulgaris dehydrin PHAVU_009G004400g, E = 3e−05 |