De novo analysis of the transcriptome of Pratylenchus zeae to identify transcripts for proteins required for structural integrity, sensation, locomotion and parasitism

Abstract

(2015) De novo analysis of the transcriptome of Pratylenchus zeae to identify transcripts for proteins required for structural integrity, sensation, locomotion and parasitism. Molecular Plant Pathology, 17 (4). pp. 532-552. This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1111/mpp.12301 Accepted ArticleThis article is protected by copyright. All rights reserved.Accession numbers: BioProject ID PRJNA268047; SRR1657910 (Short Read Archive); SUB990140 (Transcriptome Shotgun Assembly temporary BioSample submission ID). SummaryThe root lesion nematode Pratylenchus zeae, a migratory endoparasite, is an economically important pest of major crop plants (e.g. cereals, sugarcane). It enters host roots, migrates through root tissues and feeds from cortical cells, and defends itself against biotic and abiotic stresses in the soil and in host tissues. We report de novo sequencing of the P. zeae transcriptome using 454 FLX, and identification of putative transcripts encoding proteins required for movement, response to stimuli, feeding and parasitism. Sequencing generated 347,443 good quality reads which were assembled into 10,163 contigs and 139,104 singletons: 65% of contigs and 28% of singletons matched sequences of free-living and parasitic nematodes. Three quarters of annotated transcripts were common to reference nematodes, mainly representing genes encoding proteins for structural integrity and fundamental biochemical processes. Over 15,000transcripts were similar to Caenorhabditis elegans genes encoding proteins with roles in mechanical and neural control of movement, responses to chemicals, mechanical and thermal stresses. Notably, 766 transcripts matched parasitism genes employed by both migratory and sedentary endoparasites in host interactions, of which three studied hybridised to the gland cell region, suggesting that they might be secreted. Conversely, transcripts for effectors reported to be involved in feeding site formation by sedentary endoparasites were conspicuously absent. Transcripts similar to those encoding some Accepted ArticleThis article is protected by copyright. All rights reserved.secretory-excretory products at the host interface of Brugia malayi, the secretome of Meloidogyne incognita and products of gland cells of Heterodera glycines were also identified. This P. zeae transcriptome provides new information for genome annotation and functional analysis of possible targets for control of pratylenchid nematodes.

Advances in Understanding the Molecular Mechanisms of Root Lesion Nematode Host Interactions

“…There was an implicit expectation that the mode of parasitism and the subset of effectors used for root entry and migration by RLNs would be similar to those used by sedentary endoparasitic nematodes. Now the presence of genes encoding many such cell wall-modifying enzymes has been confirmed in RLNs (32,42,63,85).…”

“…New sequencing technologies have now also been applied to generate RNAseq data for mixed developmental stages of the RLNs P. coffeae, P. thornei, P. zeae, and P. penetrans (32,42,85,112) as well as P. neglectus ( J. Fosu-Nyarko, J. Rana, M. Gonzales, M.G.K. Jones, unpublished results).…”

“…Orthologs of pectate lyase have not been studied in detail in RLNs. Nevertheless, partial transcripts with sequence similarities to pectate lyases of sedentary nematodes have been identified in the transcriptomes of P. coffeae, P. thornei, and P. zeae (32,42,85,105). Evidence for their functionality is that a Pt-pl transcript of P. thornei has been localized to its pharyngeal region, and its downregulation using RNAi resulted in an 86% reduction in nematode reproduction on carrot discs five weeks after inoculation (105).…”

“…An alternative demonstration that such effectors are functional is to use RNAi to downregulate their expression and to demonstrate a possible role in nematode parasitism. This approach has established that knockdown of expression of the cellulases of P. vulnus, P. thornei, and P. zeae reduces their reproduction in a host (26,32,105). However, as yet, there is no confirmatory evidence that knockdown of the transcripts reduces the ability of RLNs to modify cell walls.…”

“…The availability of these transcriptomes has stimulated research on RLNs and has provided new data on genes involved in many activities. These include data on the RNAi pathway (42), on genes possibly required for interaction with the soil environment, for movement through soil, and for migration through host tissues (32), on candidate effectors and carbohydrate active enzymes involved in cell wall modification, and on genes involved in feeding from host cells and evasion of host responses (32,42,85,112).…”