Exploring the transcriptome of the burrowing nematode Radopholus similis

Abstract

Radopholus similis is an important nematode pest on fruit crops in the tropics. Unraveling the transcriptome of this migratory plant-parasitic nematode can provide insight in the parasitism process and lead to more eYcient control measures. For the Wrst high throughput molecular characterization of this devastating nematode, 5,853 expressed sequence tags from a mixed stage population were generated. Adding 1,154 tags from the EST division of GenBank for subsequent analysis, resulted in a total of 7,007 ESTs, which represent approximately 3,200 genes. The mean G + C content of the nucleotides at the third codon position (GC3%) was calculated to be as high as 64.8%, the highest for nematodes reported to date. BLAST-searches resulted in about 70% of the clustered ESTs having homology to (DNA and protein) sequences from the GenBank database, whereas one-third of them did not match to any known sequence. Roughly 40% of these latter sequences are predicted to be coding, representing putative novel protein coding genes. Functional annotation of the sequences by GO annotation revealed the abundance of genes involved in reproduction and development, which reXects the nematode population biology. Genes with a role in the parasitism process are identiWed, as well as genes essential for nematode survival, providing information useful for parasite control. No evidence was found for the presence of trans-spliced leader sequences commonly occurring in nematodes, despite the use of various approaches. In conclusion, we found three diVerent sources for the EST sequences: the majority has a nuclear origin, approximately 1% of the EST sequences are derived from the mitochondrial transcriptome, and interestingly, 1% of the tags are with high probability derived from Wolbachia, providing the Wrst molecular indication for the presence of this endosymbiont in a plant-parasitic nematode.Keywords Expressed sequence tag analysis · Trans-spliced leader · Parasitism · G + C content · Wolbachia · Endoparasitic migratory nematode

Transcriptomes of Plant-Parasitic Nematodes

“…Little parasitism gene research has focused on PPN species with other types of parasitic behaviour, although some progress has been made (Uehara et al 2001;Mitreva et al 2004b;Kikuchi et al 2005;Jacob et al 2008). Nevertheless, the accumulated knowledge and insights from parasitism genes identified in sedentary PPN may provide a basis for the identification of parasitism genes in migratory PPN (Opperman and Bird 1998).…”

“…Of course, when the genome sequence of the species under consideration is available, the fragmentation level can be calculated exactly. On average, a typical degree of fragmentation is between 8 and 18% (Mitreva et al 2004a(Mitreva et al , b, 2005Jacob et al 2008;Karim et al 2009). For example, a fragmentation error of 12% means that 12% of the unigenes represent genes which have already been covered by one or several other unigenes in the data set.…”

“…Secondly, sometimes technical artifacts or impurities can cause an aberrantly large cluster of ESTs. As an example of the latter, in a Radopholus similis EST dataset, 8% of all unigenes were derived from mitochondrial rRNA (Jacob et al 2008). Interestingly, many of these systemic biases in cDNA libraries can be detected through visualization and application of statistics.…”

“…For example, enrichment of sequences with a certain length (visible in length distribution graphs) can point to the inclusion of normalization steps (Liu and Graber 2006). Plotting histograms of GC content can differentiate between sequences of different sources (Jacob et al 2008). And the observation of aberrantly large clusters in a cluster size distribution may point to overrepresentation of certain genes, mostly due to artifacts during library construction (Kikuchi et al 2007) (Fig.…”

Characterization of the venom allergen—like protein (vap-1) and the fatty acid and retinol binding protein (far-1) genes in Meloidogyne hispanica

“…FAR-1 induces susceptibility to RKN through the manipulation of jasmonate-dependent defence response (Iberkleid et al 2013). FAR-1 has also been identified in H. schachtii, M. chitwoodi, M. hapla, M. incognita, P. coffeae and Radopholus similis (Vanholme et al 2006;Bellafiore et al 2008;Jacob et al 2008;Opperman et al 2008;Roze et al 2008;Haegeman et al 2009Haegeman et al , 2011.…”