The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode

Abstract

BackgroundGlobodera pallida is a devastating pathogen of potato crops, making it one of the most economically important plant parasitic nematodes. It is also an important model for the biology of cyst nematodes. Cyst nematodes and root-knot nematodes are the two most important plant parasitic nematode groups and together represent a global threat to food security.ResultsWe present the complete genome sequence of G. pallida, together with transcriptomic data from most of the nematode life cycle, particularly focusing on the life cycle stages involved in root invasion and establishment of the biotrophic feeding site. Despite the relatively close phylogenetic relationship with root-knot nematodes, we describe a very different gene family content between the two groups and in particular extensive differences in the repertoire of effectors, including an enormous expansion of the SPRY domain protein family in G. pallida, which includes the SPRYSEC family of effectors. This highlights the distinct biology of cyst nematodes compared to the root-knot nematodes that were, until now, the only sedentary plant parasitic nematodes for which genome information was available. We also present in-depth descriptions of the repertoires of other genes likely to be important in understanding the unique biology of cyst nematodes and of potential drug targets and other targets for their control.ConclusionsThe data and analyses we present will be central in exploiting post-genomic approaches in the development of much-needed novel strategies for the control of G. pallida and related pathogens.

TheDitylenchus destructorgenome provides new insights into the evolution of plant parasitic nematodes

“…Compared with other plant nematodes and C. elegans, no obvious extreme gene family expansions, like G protein-coupled receptor (GPCR) in M. halpa [8] and SPRY domain (domain in SP1a and the ryanodine receptor) proteins in G. pallida [9], were found. In the list of the top 25 Pfam hits featured from D. destructor compared with the other clade 12 plant nematodes, more proteins containing trypsin (PF00089), ABC transporter (PF00005), sugar (and other) transporter (PF00083) and short chain dehydrogenase (PF00106) domains (electronic supplementary material, table S3) were found.…”

“…This result is in accordance with its two different lifestyles (free-living and facultative plant parasitism). Second, some effectors from root-knot and cyst nematodes have homologies in D. destructor, but there is little overlap between the two sedentary nematodes [9]. These common effectors may originate from nematodes such as Ditylenchus spp.…”

“…The assembly was cleared of contaminants as described by Cotton et al [9] in two steps. Before gene model prediction, all scaffolds were searched against the NCBI non-redundant (nr) database with BlastX using an e-value of 10 25 .…”

“…For the control of plant nematodes, it can be applied in transgenic plants to promote resistance against parasites [46]. Caenorhabditis elegans has 78 RNAi effectors, but all plant nematodes contain less than half of these effectors [9,38]. The two migratory plant nematodes have more RNAi effectors than the sedentary plant nematodes (table 2; electronic supplementary material, table S14).…”

“…To gain in-depth insights into the parasitic mechanism, genome sequences of nematodes with different life cycles were considered. Genome sequences are available for three sedentary endoparasitic nematodes (M. incognita, M. hapla and G. pallida) and one migratory endoparasite (Pratylenchus coffeae) in this clade [7][8][9][10]. In this study, we sequenced another migratory endoparasitic nematode (Ditylenchus destructor) that was positioned at the base of the most economically important plant nematodes, including root-knot and cyst nematodes, on the SSU rDNA tree [6].…”