The foliar nematode (Aphelenchoides fragariae) is a quarantined pest that infects a broad range of herbaceous and woody plants. Previous work has demonstrated its remarkable ability to survive rapid and extreme desiccation, although the specific mechanisms underlying its anhydrobiotic response have not been characterized. We used RNA sequencing and de novo transcriptome assembly to compare patterns of gene expression between hydrated and 24-hr desiccated nematodes. Two thousand eighty-three and 953 genes were significantly up- and downregulated, respectively, in desiccated nematodes. Of the one hundred annotated genes with the largest positive fold-changes, more than one third encoded putative detoxification-related proteins. Genes encoding enzymes of Phase I and Phase II detoxification systems were among the most strongly upregulated in the transcriptome, including 35 cytochrome p450s, 23 short chain dehydrogenase/reductases, five glutathione-S-transferases, and 22 UDP-glucuronosyltransferases. Genes encoding heat shock proteins, unfolded protein response enzymes, and intrinsically-disordered proteins were also upregulated. Anhydrobiosis in A. fragariae appears to involve both (1) strategies to minimize protein misfolding and aggregation and (2) wholesale induction of the cellular detoxification machinery. These processes may be controlled in part through the activity of forkhead transcription factors similar to C. elegans’ daf-16, a number of which were differentially expressed under desiccation.

We used RNA sequencing and de novo transcriptome assembly to compare patterns of gene expression between hydrated and 24-hr desiccated foliar nematodes. We performed differetinal gene expression analysis using R library edgeR. Additionaly, we conducted Gene Set Enrichment Analysis to examine which gene sets that were asssgiend to gene ontology terms were enriched in desiccation treatment. 

Supplementary File 1

Transcriptome assembly of A. fragariae in fasta format.

Note: all 147,621 sequences, including splicing isoforms, are included in this file.

Supplementary File 2

Annotation table of A. fragariae transcriptome.

Note: Annotation was performed on the longest isoforms only (48,541 sequences). Information in this file includes sequence names, closest match to known genes in the nr database (description), lowest e-value to known genes, number of gene ontology (GO) terms assigned, enzyme code and names, detailed GO information, and InterPro annotation.

Supplementary File 3. Gene expression data of A. fragariae under desiccated and control conditions.

Note: Genes with low expression were removed. Fragments per kilobase of transcript per million mapped reads (FPKM) of each condition was averaged across three biological replicates. In the fold change column, positive and negative values indicate genes were up-regulated and down-regulated in the desiccated condition, respectively; Differential expression was determined in R package edgeR using exact tests (Robinson et al., 2010). Differentially expressed transcriptional factors and their GO annotations were presented in the second tab.

Supplementary File 4. Gene ontology (GO) terms enriched in the desiccation treatment (“desiccation” tab) and control (“control” tab). Nominal p-value, false discovery rate (FDR), and normalized enrichment score (NES) were determined in GSEA (Subramanian et al., 2005). Abbreviations in the category column: BP, biological process; CC, cellular component; MF, molecular function.