Abstract
BackgroundThe rice white tip nematode Aphelenchoides besseyi, a devastating nematode whose genome has not been sequenced, is distributed widely throughout almost all the rice-growing regions of the world. The aims of the present study were to define the transcriptome of A. besseyi and to identify parasite-related, mortality-related or host resistance-overcoming genes in this nematode.Methodology and Principal FindingsUsing Solexa/Illumina sequencing, we profiled the transcriptome of mixed-stage populations of A. besseyi. A total of 51,270 transcripts without gaps were produced based on high-quality clean reads. Of all the A. besseyi transcripts, 9,132 KEGG Orthology assignments were annotated. Carbohydrate-active enzymes of glycoside hydrolases (GHs), glycosyltransferases (GTs), carbohydrate esterases (CEs) and carbohydrate-binding modules (CBMs) were identified. The presence of the A. besseyi GH45 cellulase gene was verified by in situ hybridization. Given that 13 unique A. besseyi potential effector genes were identified from 41 candidate effector homologs, further studies of these homologs are merited. Finally, comparative analyses were conducted between A. besseyi contigs and Caenorhabditis elegans genes to look for orthologs of RNAi phenotypes, neuropeptides and peptidases.Conclusions and SignificanceThe present results provide comprehensive insight into the genetic makeup of A. besseyi. Many of this species' genes are parasite related, nematode mortality-related or necessary to overcome host resistance. The generated transcriptome dataset of A. besseyi reported here lays the foundation for further studies of the molecular mechanisms related to parasitism and facilitates the development of new control strategies for this species.
Highlights
Parasitic nematodes that prey on plants cause devastating losses in agricultural production and contribute to a significant reduction in yield
The generated transcriptome dataset of A. besseyi reported here lays the foundation for further studies of the molecular mechanisms related to parasitism and facilitates the development of new control strategies for this species
Illumina Sequencing and De Novo Assembly A total of 46,826,350 raw reads were obtained by Solexa (Illumina GAIIX) RNA paired-end sequencing, and 36,905,372 high-quality clean reads were obtained after a strict filtering process
Summary
Parasitic nematodes that prey on plants cause devastating losses in agricultural production and contribute to a significant reduction in yield. As a seed-borne nematode, A. besseyi can survive on stored grain in anhydrobiosis for several years [7]. This species is a facultative migratory ecto- and endoparasite of the leaf or young tissue of rice, causing whitening of the top of the leaf, which later becomes necrotic, and a crinkling and distortion of the flag leaf enclosing the panicle, which dies off and disintegrates [4,8]. The rice white tip nematode Aphelenchoides besseyi, a devastating nematode whose genome has not been sequenced, is distributed widely throughout almost all the rice-growing regions of the world. The aims of the present study were to define the transcriptome of A. besseyi and to identify parasite-related, mortality-related or host resistanceovercoming genes in this nematode
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