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Background   Cooperia oncophora  and  Ostertagia ostertagi  are among the most important gastrointestinal nematodes of cattle worldwide. The economic losses caused by these parasites are on the order of hundreds of millions of dollars per year. Conventional treatment of these parasites is through anthelmintic drugs; however, as resistance to anthelmintics increases, overall effectiveness has begun decreasing. New methods of control and alternative drug targets are necessary. In-depth analysis of transcriptomic data can help provide these targets.    Results  The assembly of 8.7 million and 11 million sequences from  C. oncophora  and  O. ostertagi , respectively, resulted in 29,900 and 34,792 transcripts. Among these, 69% and 73% of the predicted peptides encoded by  C. oncophora  and  O. ostertagi  had homologues in other nematodes. Approximately 21% and 24% were constitutively expressed in both species, respectively; however, the numbers of transcripts that were stage specific were much smaller (~1% of the transcripts expressed in a stage). Approximately 21% of the transcripts in  C. oncophora  and 22% in  O. ostertagi  were up-regulated in a particular stage. Functional molecular signatures were detected for 46% and 35% of the transcripts in  C. oncophora  and  O. ostertagi , respectively. More in-depth examinations of the most prevalent domains led to knowledge of gene expression changes between the free-living (egg, L1, L2 and L3 sheathed) and parasitic (L3 exsheathed, L4, and adult) stages. Domains previously implicated in growth and development such as chromo domains and the MADF domain tended to dominate in the free-living stages. In contrast, domains potentially involved in feeding such as the zinc finger and CAP domains dominated in the parasitic stages. Pathway analyses showed significant associations between life-cycle stages and peptides involved in energy metabolism in  O. ostertagi  whereas metabolism of cofactors and vitamins were specifically up-regulated in the parasitic stages of  C. oncophora.  Substantial differences were observed also between Gene Ontology terms associated with free-living and parasitic stages.    Conclusions  This study characterized transcriptomes from multiple life stages from both  C. oncophora  and  O. ostertagi.  These data represent an important resource for studying these parasites. The results of this study show distinct differences in the genes involved in the free-living and parasitic life cycle stages. The data produced will enable better annotation of the upcoming genome sequences and will allow future comparative analyses of the biology, evolution and adaptation to parasitism in nematodes.

bmc genomics

Transcriptome analyses reveal protein and domain families that delineate stage-related development in the economically important parasitic nematodes, Ostertagia ostertagi and Cooperia oncophora