Skip to main content
ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Parasitic Diseases Laboratory » Research » Publications at this Location » Publication #417688
Research Project: Developing Improved Control Strategies for Avian Coccidosis

Location: Animal Parasitic Diseases Laboratory

Title: Chromosomal scale assembly and functional annotation of the apicomplexan parasite Eimeria acervulina

Author
item SRIVASTAVA, SUBODH - Oak Ridge Institute For Science And Education (ORISE)
item Parker, Carolyn
item Thompson, Peter
item Tucker, Matthew
item Rosenthal, Benjamin
item Khan, Asis
item Valente, Matthew
item Jenkins, Mark

Submitted to: Scientific Data
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/14/2025
Publication Date: 5/23/2025
Citation: Srivastava, S.K., Parker, C.C., Thompson, P.C., Tucker, M.S., Rosenthal, B.M., Khan, A., Valente, M., Jenkins, M.C. 2025. Chromosomal scale assembly and functional annotation of the apicomplexan parasite Eimeria acervulina. Scientific Data. 12. Article e852. https://doi.org/10.1038/s41597-025-04653-1.
DOI: https://doi.org/10.1038/s41597-025-04653-1

Interpretive Summary: Avian coccidiosis is devastating disease of poultry caused by protozoan parasites in the genus Eimeria. Coccidiois is regularly listed by poultry veterinarians as the most important disease problem affecting broiler and layer chickens, causing over $3 billion in annual losses in the U.S. alone. One of the most prevalent species, namely Eimeria acervulina, is found in virtually all poultry houses and has been controlled for years by medication of feed with anticoccidial drugs or vaccines. However, the emergence of drug resistance and immunovariability in Eimeria is affecting the ability of poultry companies to prevent coccidiosis. Knowing the complete sequence of the Eimeria acervulina genome will help identify genes that are involved in drug resistance and immunovariablity. In this work, the DNA sequence of Eimeria acervulina genome organized to the chromosome level was acquired using various technologies developed in our laboratory. The sequencing effort revealed 15 chromosomes in this parasite and allowed the identification of protein-coding genes that may be involved in various biological processes such as parasite development, resistance to drugs, and genetic variability to escape host immunity. This research will assist pharmaceutical and vaccine companies in developing treatments against avian coccidiosis caused by Eimeria acervulina, and in turn help poultry producers combat this disease.

Technical Abstract: Apicomplexan parasites are single-celled obligate intracellular eukaryotic organisms that cause significant animal and human disease and pose a substantial health and socioeconomic burden worldwide. Eimeria acervulina is one such parasite of chickens, representative of several Eimeria species causing coccidiosis disease. A complete assembly of the E. acervulina genome may help identify markers of drug-resistance and design recombinant vaccines. We sequenced E. acervulina APU1 strain using Oxford Nanopore Sequencing and Illumina technology in combination with a Hi-C (Omni-C) proximity linkage library and achieved a chromosomal scale assembly using the MaSuRCA assembler. The final assembly was 52'Mb. with 15 chromosomes and 99% BUSCO completeness. A total of 7,621 genes were predicted using a pipeline of BRAKER3, GeneMark-ETP and AUGUSTUS, of which 4,647 (60.97%) have a predicted Pfam function and 1,962 (25.74%) have Gene Ontology (GO) terms matching molecular, biological, and functional classes. Stage-specific transcriptome analysis revealed 9,761 transcripts. This genome assembly and transcriptome analysis provides the foundation for identifying biologically important candidates for anticoccidial drug and vaccine development.