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Transcriptomic Analysis of the Rice White Tip Nematode, Aphelenchoides besseyi (Nematoda: Aphelenchoididae)

BACKGROUND: 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...

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Autores principales: Wang, Feng, Li, Danlei, Wang, Zhiying, Dong, Airong, Liu, Lihong, Wang, Buyong, Chen, Qiaoli, Liu, Xiaohan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3956754/
https://www.ncbi.nlm.nih.gov/pubmed/24637831
http://dx.doi.org/10.1371/journal.pone.0091591
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author Wang, Feng
Li, Danlei
Wang, Zhiying
Dong, Airong
Liu, Lihong
Wang, Buyong
Chen, Qiaoli
Liu, Xiaohan
author_facet Wang, Feng
Li, Danlei
Wang, Zhiying
Dong, Airong
Liu, Lihong
Wang, Buyong
Chen, Qiaoli
Liu, Xiaohan
author_sort Wang, Feng
collection PubMed
description BACKGROUND: 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. METHODOLOGY AND PRINCIPAL FINDINGS: 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. CONCLUSIONS AND SIGNIFICANCE: 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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spelling pubmed-39567542014-03-18 Transcriptomic Analysis of the Rice White Tip Nematode, Aphelenchoides besseyi (Nematoda: Aphelenchoididae) Wang, Feng Li, Danlei Wang, Zhiying Dong, Airong Liu, Lihong Wang, Buyong Chen, Qiaoli Liu, Xiaohan PLoS One Research Article BACKGROUND: 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. METHODOLOGY AND PRINCIPAL FINDINGS: 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. CONCLUSIONS AND SIGNIFICANCE: 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. Public Library of Science 2014-03-17 /pmc/articles/PMC3956754/ /pubmed/24637831 http://dx.doi.org/10.1371/journal.pone.0091591 Text en © 2014 Wang et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Wang, Feng
Li, Danlei
Wang, Zhiying
Dong, Airong
Liu, Lihong
Wang, Buyong
Chen, Qiaoli
Liu, Xiaohan
Transcriptomic Analysis of the Rice White Tip Nematode, Aphelenchoides besseyi (Nematoda: Aphelenchoididae)
title Transcriptomic Analysis of the Rice White Tip Nematode, Aphelenchoides besseyi (Nematoda: Aphelenchoididae)
title_full Transcriptomic Analysis of the Rice White Tip Nematode, Aphelenchoides besseyi (Nematoda: Aphelenchoididae)
title_fullStr Transcriptomic Analysis of the Rice White Tip Nematode, Aphelenchoides besseyi (Nematoda: Aphelenchoididae)
title_full_unstemmed Transcriptomic Analysis of the Rice White Tip Nematode, Aphelenchoides besseyi (Nematoda: Aphelenchoididae)
title_short Transcriptomic Analysis of the Rice White Tip Nematode, Aphelenchoides besseyi (Nematoda: Aphelenchoididae)
title_sort transcriptomic analysis of the rice white tip nematode, aphelenchoides besseyi (nematoda: aphelenchoididae)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3956754/
https://www.ncbi.nlm.nih.gov/pubmed/24637831
http://dx.doi.org/10.1371/journal.pone.0091591
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