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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Parasitic Diseases Laboratory » Research » Publications at this Location » Publication #406490
Research Project: Developing Improved Control Strategies for Avian Coccidosis

Location: Animal Parasitic Diseases Laboratory

Title: Chromosomal scale assembly reveals localized structural variants in avian caecal coccidian parasite Eimeria tenella

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

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/15/2023
Publication Date: 12/20/2023
Citation: Srivastava, S.K., Parker, C.C., Obrien, C.N., Tucker, M.S., Thompson, P.C., Rosenthal, B.M., Dubey, J.P., Khan, A., Jenkins, M.C. 2023. Chromosomal scale assembly reveals localized structural variants in avian caecal coccidian parasite Eimeria tenella. Scientific Reports. 13. Article e22802. https://doi.org/10.1038/s41598-023-50117-0.
DOI: https://doi.org/10.1038/s41598-023-50117-0

Interpretive Summary: Avian coccidiosis is a parasitic disease of poultry causing over $14 billion in annual losses to broiler and egg laying industries due to lower weight gain and poorer feed utilization efficiency in affected chickens. The causative organisms are protozoa in the genus Eimeria that are ubiquitous in intensively raised poultry. Eimeria tenella is one of the most pathogenic eimerians causing severe necrosis in the lower intestine and, at high infectious doses, leads to death of afflicted chicks. Combating Eimeria tenella-associated coccidiosis will require understanding its genome for several reasons. Firstly is that efficacious vaccines can be designed based on identifying immune-stimulating protein genes. Secondly is that comparing genomes of different Eimeria tenella isolates may point out genes that are associated with virulence or that arose because of drug-resistance. These may provide a target for rapid idenfication of virulent or drug-resistant parasites. Thirdly is that comparing genomes of Eimeria tenella to other Eimeria, such as Eimeria maxima, may provide insight in why different Eimeria species invade specific regions of the chicken intestine. In the current paper, ARS researchers obtained the complete DNA sequence of the Eimeria tenella genome and assigned these sequences to specific chromosomes of the protozoan. Comparative sequencing identified regions of the Eimeria tenella genome that are highly variable. These sequences may code for immune-stimulating proteins, which complicates vaccine design if the parasite is able to vary what proteins the host responds to during a coccidiosis infection. This information will be useful to pharmaceutical companies attempting to develop an Eimeria vaccine and in turn help poultry farmers combat avian coccidiosis.

Technical Abstract: Eimeria tenella is a major cause of caecal coccidiosis in commercial poultry chickens worldwide. Here, we report chromosomal scale assembly of Eimeria tenella strain APU2, a strain isolated from commercial broiler chickens in the U.S. We obtained 100× sequencing Oxford Nanopore Technology (ONT) and more than 800× Coverage of Illumina Next-Seq. We created the assembly using the hybrid approach implemented in MaSuRCA, achieving a contiguous 51.34 Mb chromosomal-scale scaffolding enabling identification of structural variations. The AUGUSTUS pipeline predicted 8060 genes, and BUSCO deemed the genomes 99% complete; 6278 (78%) genes were annotated with Pfam domains, and 1395 genes were assigned GO-terms. Comparing E. tenella strains (APU2, US isolate and Houghton, UK isolate) derived Houghton strain of E. tenella revealed 62,905 high stringency differences, of which 45,322 are single nucleotide polymorphisms (SNPs) (0.088%). The rate of transitions/transversions among the SNPs are 1.63 ts/tv. The strains possess conserved gene order but have profound sequence heterogeneity in a several chromosomal segments (chr 2, 11 and 15). Genic and intergenic variation in defined gene families was evaluated between the two strains to possibly identify sequences under selection. The average genic nucleotide diversity of 2.8 with average 2 kb gene length (0.145%) at genic level. We examined population structure using available E. tenella sequences in NCBI, revealing that the two E. tenella isolates from the U.S. (E. tenella APU2 and Wisconsin, “ERR296879”) share a common maternal inheritance with the E. tenella Houghton. Our chromosomal level assembly promotes insight into Eimeria biology and evolution, hastening drug discovery and vaccine development.