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Sequences with C. elegans, other nematodes and non-nematode protein sequence databases using SimiTri. The numbers at each vertex indicate the number of cluster sequences matching only that specific database. The numbers on the edges indicate the number of cluster sequences matching the two databases linked by that edge. The number within the triangle indicates the number of A. avenae genes with matches to sequences in all three databases.Page 5 of(page number not for citation purposes)BMC Genomics 2009, 10:http://www.biomedcentral.com/1471-2164/10/UBQ-1, elongation factor,) and metabolism (for example, enolase, cytochrome c oxidase). Representation of these clusters in the A. avenae EST collection varied from 81 ESTs to 2 ESTs. None of these most conserved gene products were nematode specific. Out of all clusters, 461 (17.1 ) had homology only to nematodes, either C. elegans (4), other nematodes (137), or both (320) (Fig. 3). The most conserved (1e-111) of these nematode-specific proteins was a homolog of a serine proteinase inhibitor, previously characterized from C. elegans (K10D3.4) and parasitic nematodes [49,50]. Among the other most conserved nematode-specific clusters were homologs of previously characterized C. elegans structural proteins (for example cluster, AAC01973 matched to a collagen family protein, COL-176) as well as uncharacterized C. elegans hypothetical proteins (for example, cluster, AAC01948 matched C. elegans gene, C34E7.4 which has no known function). The 137 cluster sequences where homologs were present only in other nematodes were further categorized based on their BLAST (BLASTX and TBLASTX) results (Additional file 1). Matches were found in plant parasitic, animal parasitic and free living nematodes. 24.8 of sequences (34 of 137) had homology only to sequences from plant parasitic nematodes. Some of these sequences were similar to previously characterized cell-wall-degrading enzymes, which are known to be involved in the parasitism process of these nematodes. For example, cluster, AAC01592 matched an expansin-like protein from B. xylophilus [19] and cluster, AAC02968 matched a -1,4endoglucanase precursor from Globodera rostochiensis [20]. Further analysis of some of the cell-wall-degrading enzymes present in A. avenae is presented below.Identification of transcripts similar to stress-response genes related to desiccation BLASTX (E < 1e-5) searches of A. avenae cluster sequences against nr protein databases allowed identification of genes that can encode proteins or enzymes important in providing protection against desiccation or other environmental-stress (Additional file 2). One notable observation was the presence of sequences similar to late embryonic abundant (LEA) proteins, which are known to be associated with tolerance to water stress resulting from desiccation [9]. Protein aggregation during desiccation is likely to be a major potential hazard for anhydrobiotes; LEA proteins may act as molecular chaperones or molecular shields and play an important role in the prevention of this aggregation [51]. Thirteen ESTs, distributed in three clusters, (AAC00729, Vorinostat AAC00888, and AAC01781) were identified as having significant similarity PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/17139194 to LEA proteins. Cluster, AAC01781 which was identified as a singleton matched a previously characterized LEA protein from desiccated A. avenae [9]. In addition, we also identified multiple copies of cytochrome P450, superoxide dismutase, glutathione peroxidase, and glutathione S-.