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

Journal of Nematology
Volume 52 (2020): Issue 1 (January 2020)
By:
Open Access
|May 2020

Figures & Tables

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 IDPredicted length (aa)Mean FPKM desiccatedMean FPKM controlFold-changeAdjusted P-value% disordered residuesGRAVY hydropathy valueBlastx hits to LEA database
DN15064_c0_g1175398.80.41020.93.15E−64 88.1−1.836−
DN14203_c3_g311945.40.588.71.92E−15 74.8−0.977−
DN10042_c0_g2128366.85.072.93.61E−28 82.8−0.108 Sophora davidii dehydrin DHN, E = 2e−13
DN10455_c1_g1191928.214.064.19.30E−99 90.6−0.503 Sophora davidii dehydrin DHN, E = 8e−09
DN9957_c2_g13357.90.241.11.66E−17 94.6−1.104 Sorghum bicolor dehydrin-like SORBIDRAFT_10g003700, E = 2e−14
DN10923_c0_g117117.00.725.51.23E−12 81.9−1.607 Trifolium repens dehydrin b, E = 0.002
DN9863_c0_g125021.70.923.41.70E−43 85.2−0.951 Arabidopsis thaliana dehydrin rab18, E = 2e−10
DN9710_c0_g116728.11.320.64.50E−07 93.5−1.185−
DN12711_c2_g213192.86.413.84.35E−12 77.1−0.204 Sophora davidii dehydrin DHN, E = 7e−07
DN11488_c0_g119216.401.3011.502.52E−03 86.5−1.167−
DN12459_c0_g4172173.614.411.57.31E−17 98.3−0.793 Eucalyptus grandis dehydrin 1, E = 5e−07
DN15965_c0_g1140294.525.710.72.28E−10 72.9−0.450 Hordeum vulgare dehydrin dhn4, E = 8e−12
DN12325_c1_g19615.51.98.11.38E−17 75.0−0.672−
DN9469_c2_g113346.89.74.71.44E−14 100.0−1.520 Phaseolis vulgaris dehydrin PHAVU_009G004400g, E = 3e−05

Summary statistics for Aphelenchoides fragariae transcriptome assembly_

Basic sequence statisticsNumber
Total raw reads324,895,970
Mean read length (bp)125
Raw read GC content42%
Mean read PHRED score after filtering and trimming36
Number of genes48,541
Number of isoforms147,621
Assembly N50 (of all isoforms)1293 bp
Ex90N501470 bp
Mean length of all isoforms882 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 annotation23%
DOI: https://doi.org/10.21307/jofnem-2020-047 | Journal eISSN: 2640-396X | Journal ISSN: 0022-300X
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Language: English
Page range: 1 - 12
Submitted on: Feb 10, 2020
Published on: May 25, 2020
Published by: Society of Nematologists, Inc.
In partnership with: Paradigm Publishing Services
Publication frequency: 1 issue per year
Keywords:
Anhydrobiosis,
Detoxification,
Extended life span,
Foliar nematode,
RNA-seq,
Transcriptome
Related subjects:
Life sciences,
Life sciences, other

© 2020 Zhen Fu, Paula Agudelo, Christina E. Wells, published by Society of Nematologists, Inc.
This work is licensed under the Creative Commons Attribution 4.0 License.

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