Analysis of expressed sequence tags and identification of genes encoding cell-wall-degrading enzymes from the fungivorous nematode Aphelenchus avenae
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 5000 ESTs from a mixed-stage A. avenae cDNA library.
Clustering of 5076 high-quality ESTs resulted in a set of 2700 non-redundant sequences comprising 695 contigs and 2005 singletons. Comparative analyses indicated that 1566 (58%) cluster sequences had homologues in Caenorhabditis elegans, 1750 (65%) in other nematodes, 1321(49%) in organisms other than nematodes, and 919 (34%) had no significant match to any sequence in current databases.
In addition, 1100 (41%) 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 cellulase genes encoding family 5 glycosyl hydrolase (GHF5) and two pectate lyase genes encoding polysaccharide lyase family 3 (PL3) proteins were identified and characterized.
Conclusion: We have described at least 2214 putative genes in 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 the 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.
Author: Nurul KarimJohn JonesHiroaki OkadaTaisei Kikuchi
Credits/Source: BMC Genomics 2009, 10:525
Published on: 2009-11-16
Copyright by the authors listed above - made available via BioMedCentral (Open Access). Please
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