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

Author
item HEIZER, ESLEY - Washington University School Of Medicine
item Zarlenga, Dante
item GASSER, ROBIN - University Of Melbourne
item DEGRAEF, JESSIE - University Of Melbourne
item GELDHOF, PETER - Ghent University
item MITREVA, MAKEDONKA - Washington University School Of Medicine

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/11/2013
Publication Date: 2/22/2013
Publication URL: http://handle.nal.usda.gov/10113/56753
Citation: Heizer, E., Zarlenga, D.S., Gasser, R., Degraef, J., Geldhof, P., Mitreva, M. 2013. Transcriptome analyses reveal protein and domain families that delineate stage-related development in the economically important parasitic nematodes, Ostertagia ostertagi and Cooperia oncophora. Biomed Central (BMC) Genomics. 14:118.

Interpretive Summary: Little is known of the structure, organization and content of nematode genomes beyond that of the free-living nematode, Caenorhabditis elegans. In particular, information is lacking on parasitic nematodes that are both highly pathogenic and infectious for cattle. Ostertagi ostertagi and Cooperia oncophora are two such nematodes that contribute substantially to the cost of raising cows in the US and abroad. Herein we present the first comprehensive analysis of genes expressed in both the parasitic and free-living stages of both parasites in an effort to examine gene regulation as it is influenced by the environment and host factors. Among the many findings, it was concluded that protein domains previously implicated in growth and development tended to dominate in the free-living stages of these organisms. In contrast, domains believed involved in feeding such as the zinc finger and CAP domains dominated in the parasitic stages. Results further demonstrate that 66% of the most abundantly expressed genes have orthologues in C. elegans and that conserved biological pathways are in many instances conserved among the broader group of Metazoa. These data will form the foundation for sequencing the entire genomes of these organisms, generating a comparative framework upon which the entire group of gastrointestinal nematode species infecting ruminants can be referenced, and hopefully lead to identifying genetic markers for key phenotypic traits among this group of organisms. These data will be used initially by scientists but eventually filter over to drug companies interested in looking for nematode–specific sequences and proteins that can be targeted for drug intervention.

Technical Abstract: 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. The assembly of 8.7 million and 11.0 million sequences from C. oncophora and O. ostertagi, respectively, encoded 29,900 and 34,792 polypeptides. Among these, 68.8.0% and 73.0% of the polypeptides 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 polypeptides that were stage specific were much smaller (1% of the polypeptides expressed in a stage). Approximately 21% of the polypeptides in C. oncophora and 22% in O. ostertagi were up-regulated in a particular stage. InterPro signatures were detected for 46.2% and 35.3% of the predicted polypeptides of 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 L3sheathed) and parasitic (L3exsheathed, 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. This study characterized transcriptomes from multiple life stages from both C. oncophora and O. ostertagi. These transcriptomic data represent an important resource for studying these parasites. The data produced will allow future comparative analyses of the biology, evolution and adaptation to parasitism in nematodes.