De novo Transcriptome Assembly of the Plant-parasitic Nematode Aphelenchoides fragariae

The foliar nematode Aphelenchoides fragariae (Aphelenchida: Aphelenchidae) is an endo- and ectoparasite that feeds on aerial parts of over 250 plant species from 47 families. It is a common and economically-damaging pest of nursery-grown crops including ferns, foliage and flowering plants, and herbaceous and woody perennials.  We used Illumina HiSeq 2000 technology and the Trinity de novo assembler (trinityrnaseq.sourceforge.net/) to produce a transcriptome of A. fragariae from four growth conditions (fungal-fed, plant-fed, diet-changed, and desiccated).  High throughput  sequencing generated 43 million reads with average length of 100-bp.  Assembly of the pooled read set generated 95,930 contigs, corresponding to 50,686 unigenes (mean length = 605 bp) with 45,244 alternate splice variants.  Fifty-two percent of the unigenes (26,389) had homology to known genes or proteins in the NCBI non-redundant database, and 20,558 were assigned GO terms based on these homologies by Blast2Go software (http://www.blast2go.com/b2ghome).  Among the unigenes with blast hits, a large fraction were homologous to Caenorhabditis spp. and Ascaris suum. Differential expression analysis with RSEM (http://deweylab.biostat.wisc.edu/rsem/) and DESeq (http://www-huber.embl.de/users/anders/DESeq/) highlighted differences in gene expression among nematodes from the four growth conditions. For example, expression of the cellulose-degrading enzyme beta-1,4-endoglucanase was more than 1000-fold higher in foliar-feeding than fungal-feeding nematodes, while desiccated nematodes showed enhanced expression of a number of late embryogenesis abundant (LEA) homologs. Our results provide a comprehensive sequence resource for the study of the biology, physiology and control of A. fragariae.