DOI: 10.5061/dryad.8pk0p2njc
title: Detoxification-related gene expression accompanies anhydrobiosis in the foliar nematode (Aphelenchoides fragariae)

description: 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.
description: We used RNA sequencing and <i>de novo</i>
 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. 
description: <b>Supplementary File
 1</b> Transcriptome assembly of
 <i>A. fragariae</i> in fasta format. 
 Note: all 147,621
 sequences, including splicing isoforms, are included in this file.
   <b>Supplementary File
 2</b> Annotation table of <i>A.
 fragariae</i> 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. 
   <b>Supplementary File
 3</b>. Gene expression data of <i>A. fragariae</i> 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. 
 <b>Supplementary File
 4</b>. Gene ontology (GO) terms enriched in the desiccation
 treatment (“desiccation” tab) and control (“control” tab). Nominal
 <i>p</i>-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.