title: Analysis of expressed sequence tags and identification of genes encoding cell-wall-degrading enzymes from the fungivorous nematode Aphelenchus avenae.
abstract: BACKGROUND
  The fungivorus nematode, Aphelenchus avenae is widespread in soil and is found in association with decaying plant material. This nematode is also found in association with plants but its ability to cause plant disease remains largely undetermined. The taxonomic position and intermediate lifestyle of A. avenae make it an important model for studying the evolution of plant parasitism within the Nematoda. In addition, the exceptional capacity of this nematode to survive desiccation makes it an important system for study of anhydrobiosis. Expressed sequence tag (EST) analysis may therefore be useful in providing an initial insight into the poorly understood genetic background of A. avenae.
  
  
  RESULTS
  We present the generation, analysis and annotation of over 5,000 ESTs from a mixed-stage A. avenae cDNA library. Clustering of 5,076 high-quality ESTs resulted in a set of 2,700 non-redundant sequences comprising 695 contigs and 2,005 singletons. Comparative analyses indicated that 1,567 (58.0%) of the cluster sequences had homologues in Caenorhabditis elegans, 1,750 (64.8%) in other nematodes, 1,321(48.9%) in organisms other than nematodes, and 862 (31.9%) had no significant match to any sequence in current protein or nucleotide databases. In addition, 1,100 (40.7%) of the sequences were functionally classified using Gene Ontology (GO) hierarchy. Similarity searches of the cluster sequences identified a set of genes with significant homology to genes encoding enzymes that degrade plant or fungal cell walls. The full length sequences of two genes encoding glycosyl hydrolase family 5 (GHF5) cellulases and two pectate lyase genes encoding polysaccharide lyase family 3 (PL3) proteins were identified and characterized.
  
  
  CONCLUSIONS
  We have described at least 2,214 putative genes from A. avenae and identified a set of genes encoding a range of cell-wall-degrading enzymes. This EST dataset represents a starting point for studies in a number of different fundamental and applied areas. The presence of genes encoding a battery of cell-wall-degrading enzymes in A. avenae and their similarities with genes from other plant parasitic nematodes suggest that this nematode can act not only as a fungal feeder but also a plant parasite. Further studies on genes encoding cell-wall-degrading enzymes in A. avenae will accelerate our understanding of the complex evolutionary histories of plant parasitism and the use of genes obtained by horizontal gene transfer from prokaryotes.
authors.affiliation: Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan. nkarim@affrc.go.jp
authors.forename: Nurul
authors.initials: N
authors.lastname: Karim
authors.forename: John T
authors.initials: JT
authors.lastname: Jones
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Okada
authors.forename: Taisei
authors.initials: T
authors.lastname: Kikuchi
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D002473:Cell Wall / Q000378:metabolism*; D002480:Cellulase / Q000235:genetics; D016000:Cluster Analysis; D030562:Databases, Protein; D003890:Desiccation; D020224:Expressed Sequence Tags; D005786:Gene Expression Regulation; D015723:Gene Library; D008969:Molecular Sequence Data; D010802:Phylogeny; D011133:Polysaccharide-Lyases / Q000737:chemistry / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D013312:Stress, Physiological / Q000235:genetics; D017187:Tylenchida / Q000166:cytology / Q000201:enzymology* / Q000235:genetics*
chemical_list: D012333:RNA, Messenger; D002480:Cellulase; D011133:Polysaccharide-Lyases; C023911:pectate lyase