Transcriptomic analysis of the rice white tip nematode, Aphelenchoides besseyi (Nematoda: Aphelenchoididae)

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-rel...

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Veröffentlicht in:PloS one 2014-03, Vol.9 (3), p.e91591-e91591
Hauptverfasser: Wang, Feng, Li, Danlei, Wang, Zhiying, Dong, Airong, Liu, Lihong, Wang, Buyong, Chen, Qiaoli, Liu, Xiaohan
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container_title PloS one
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Li, Danlei
Wang, Zhiying
Dong, Airong
Liu, Lihong
Wang, Buyong
Chen, Qiaoli
Liu, Xiaohan
description 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 resistance-overcoming genes in this nematode. Using 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. The 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.
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Finally, comparative analyses were conducted between A. besseyi contigs and Caenorhabditis elegans genes to look for orthologs of RNAi phenotypes, neuropeptides and peptidases. The 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. 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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. Using 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. The 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.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>24637831</pmid><doi>10.1371/journal.pone.0091591</doi><tpages>e91591</tpages><oa>free_for_read</oa></addata></record>
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subjects Agricultural production
Amino Acid Sequence
Analysis
Animals
Aphelenchoides besseyi
Barley
Biology and Life Sciences
Caenorhabditis elegans
Carbohydrates
Cell Wall - metabolism
Cellulase
Cellulase - chemistry
Cellulase - genetics
Computational Biology
Databases, Nucleic Acid
Esterases
Gene expression
Gene Expression Profiling
Gene Regulatory Networks
Gene sequencing
Genes
Genomes
Genomics
Glycoside hydrolase
Health aspects
Homology
Hydrolases
Medicine and Health Sciences
Molecular modelling
Molecular Sequence Data
Mortality
Nematoda - classification
Nematoda - genetics
Nematoda - metabolism
Nematodes
Neuropeptides
Neuropeptides - genetics
Neuropeptides - metabolism
Orthology
Oryza - parasitology
Parasitism
Peptidases
Peptide Hydrolases - genetics
Peptide Hydrolases - metabolism
Phylogeny
Proteins
Quality
Rice
RNA Interference
RNA, Messenger - genetics
RNA-mediated interference
Roundworms
Sequence Alignment
Transcriptome
title Transcriptomic analysis of the rice white tip nematode, Aphelenchoides besseyi (Nematoda: Aphelenchoididae)
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