title: Transcriptomic analysis of the rice white tip nematode, Aphelenchoides besseyi (Nematoda: Aphelenchoididae).
abstract: 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.
  
  
  RESULTS
  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
  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.
authors.affiliation: College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China.
authors.forename: Feng
authors.initials: F
authors.lastname: Wang
authors.affiliation: College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China.
authors.forename: Danlei
authors.initials: D
authors.lastname: Li
authors.affiliation: College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China.
authors.forename: Zhiying
authors.initials: Z
authors.lastname: Wang
authors.affiliation: College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China.
authors.forename: Airong
authors.initials: A
authors.lastname: Dong
authors.affiliation: College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China.
authors.forename: Lihong
authors.initials: L
authors.lastname: Liu
authors.affiliation: College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China.
authors.forename: Buyong
authors.initials: B
authors.lastname: Wang
authors.affiliation: College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China.
authors.forename: Qiaoli
authors.initials: Q
authors.lastname: Chen
authors.affiliation: College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China.
authors.forename: Xiaohan
authors.initials: X
authors.lastname: Liu
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002473:Cell Wall / Q000378:metabolism; D002480:Cellulase / Q000737:chemistry / Q000235:genetics; D019295:Computational Biology; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D008969:Molecular Sequence Data; D009348:Nematoda / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D009479:Neuropeptides / Q000235:genetics / Q000378:metabolism; D012275:Oryza / Q000469:parasitology*; D010447:Peptide Hydrolases / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D034622:RNA Interference; D012333:RNA, Messenger / Q000235:genetics; D016415:Sequence Alignment; D059467:Transcriptome
chemical_list: D009479:Neuropeptides; D012333:RNA, Messenger; D002480:Cellulase; D010447:Peptide Hydrolases