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Detoxification-related gene expression accompanies anhydrobiosis in the foliar nematode (Aphelenchoides fragariae)

Zhen Fu
Zhen Fu
, 
Paula Agudelo
Paula Agudelo
 und 
Christina E. Wells
Christina E. Wells
   | 25. Mai 2020
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Online veröffentlicht: 25. Mai 2020
Seitenbereich: 1 - 12
Eingereicht: 10. Feb. 2020
DOI: https://doi.org/10.21307/jofnem-2020-047
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© 2020 Zhen Fu et al., published by Sciendo.
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

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.
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.

Figure S1:

Top blastx hit species for 48,541 putative protein-coding genes from Aphelenchoides fragariae.
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.
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.
Differentially expressed genes of A. fragariae that function as chaperones in A and respond to unfolded proteins in B.

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

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%
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