Nary history of these genes within nematodes. To address these issues, we have generated over 5,000 high quality ESTs from a mixed-stage A. avenae cDNA library. We report the identification of genes that could encode enzymes that degrade the cell walls of plants or fungi. We have also analysed the clustered A. avenae sequences using the Gene Ontology (GO) classification system and undertaken comparative analysis with C. elegans and other nematode protein databases.(650 out of 695) were composed of 2-10 ESTs. 89 clusters were found to contain multiple contig members, revealing potential splice isoforms. By eliminating redundancy during this contig building, the total number of nucleotides used for further analysis was reduced from 2.82 million to 1.61 million. In addition, this process significantly increased the length of assembled transcript sequences from 468 ?114 nt for submitted ESTs alone to 595 ?321 nt for contigs. The longest sequence generated also increased from 724 to 2,154 nt. Based on the identified clusters 2,700 A. avenae genes were identified, corresponding to a new gene discovery rate of 53 (2,700/5,076). However, 2700 clusters is likely to be an overestimate of the true gene discovery rate, as one gene could be represented by multiple nonoverlapping clusters. Such “fragmentation” has been estimated at 18 using C. elegans as a reference genome [39]. After allowing for such potential fragmentation, we estimated that the A. avenae sequences derived from minimum of 2,214 genes giving a discovery rate of 44 (2,214/5,076). Assuming between 14,000 and 21,000 total genes, the range encompassed by Meloidogyne hapla [40], M. incognita [41] and C. elegans (Wormpep v. 203), the cluster dataset could represent approximately 11-16 of A. avenae genes.Transcript abundance and highly represented genes A high level of representation in a cDNA library usually correlates with high transcript abundance in the original biological sample [42], although artifacts of library construction can result in a selection for or against some transcripts. The A. avenae clusters were ranked according to the number of contributing ESTs, and the top 25 clusters are summarized in Table 2. Each of these clusters contained fifteen or more EST copies and represented 16 of the total number of ESTs obtained. Eighteen of the clusters had significant matches to Calcitriol genes with annotated functions based on BLASTX (E < 1e-5) against the non-redundant database, and all of these had homologues in nematodes. Transcripts abundantly represented in the A. avenae library included genes encoding structural proteins (such as actin, collagen, tropomyosin and troponin C) and proteins which carry out core metabolic processes (e.g. cytochrome c oxidase, ATP synthase). Other abundant ESTs included a small heat shock protein and phosphoenolpyruvate carboxykinase. The latter enzyme has previously been cloned from the parasitic nematodes, Haemonchus contortus and Ascaris suum [43,44]. Cluster AAC00541, containing 23 ESTs, was similar to an SXP/ RAL-2 family protein from the parasitic nematode, Anisakis simplex. Similar genes have previously been characterized from plant parasitic nematodes [45], and individual PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/17139194 genes have been shown to be expressed in a range of secretory tissues including the gland cells sur-Results and DiscussionGeneration of ESTs from an A. avenae cDNA library A mixed-stage A. avenae cDNA library (Aamk) was constructed to generate ESTs (Table 1). Sixteen clones wer.