O’Neill, B. C. et al. Global demographic trends and future carbon emissions. Proc. Natl. Acad. Sci. U S A. 107, 17521–17526 (2010).Article
ADS
PubMed
PubMed Central
Google Scholar
Smil, V. Worldwide transformation of diets, burdens of meat production and opportunities for novel food proteins. Enzyme Microb. Technol. 30, 305–311 (2002).Article
CAS
Google Scholar
Augustine, P. C. Cell: sporozoite interactions and invasion by apicomplexan parasites of the genus Eimeria. Int. J. Parasitol. 31, 1–8 (2001).Article
CAS
PubMed
Google Scholar
Antonissen, G. et al. Microbial shifts associated with necrotic enteritis. Avian Pathol. 45, 308–312 (2016).Article
CAS
PubMed
Google Scholar
Blake, D. P. et al. Re-calculating the cost of coccidiosis in chickens. Vet. Res. 51, 115 (2020).Article
PubMed
PubMed Central
Google Scholar
Chapman, H. D. Biochemical, genetic and applied aspects of drug resistance in Eimeria parasites of the fowl. Avian Pathol. 26, 221–244 (1997).Article
CAS
PubMed
Google Scholar
Kant, V. et al. Anticoccidial drugs used in the poultry: an overview. Sci. Int. 1, 261–265 (2013).Article
CAS
Google Scholar
Lee, X. W., Lam, S. D., Firdaus-Raih, M. & Wan, K. L. Molecular characterisation of Eimeria tenella porin, a potential anticoccidial drug target. Sains Malays. 49, 755–764 (2020).Article
CAS
Google Scholar
Noack, S., Chapman, H. D. & Selzer, P. M. Anticoccidial drugs of the livestock industry. Parasitol. Res. 118, 2009–2026 (2019).Article
PubMed
PubMed Central
Google Scholar
Squadrone, S., Mauro, C., Ferro, G. L., Amato, G. & Abete, M. C. Determination of amprolium in feed by a liquid chromatography-mass spectrometry method. J. Pharm. Biomed. Anal. 48, 1457–1461 (2008).Article
CAS
PubMed
Google Scholar
Blake, D. P. & Tomley, F. M. Securing poultry production from the ever-present Eimeria challenge. Trends Parasitol. 30, 12–19 (2014).Article
PubMed
Google Scholar
Soutter, F., Werling, D., Tomley, F. M. & Blake, D. P. Poultry coccidiosis: design and interpretation of vaccine studies. Front. Vet. Sci. 7, 101 (2020).Article
PubMed
PubMed Central
Google Scholar
Blake, D. P., Pastor-Fernández, I., Nolan, M. J. & Tomley, F. M. Recombinant anticoccidial vaccines – a cup half full? Infect. Genet. Evol. 55, 358–365 (2017).Article
CAS
PubMed
Google Scholar
Shirley, M. W., Smith, A. L. & Tomley, F. M. The biology of avian Eimeria with an emphasis on their control by vaccination. Adv. Parasitol. 60, 285–330 (2005).Article
PubMed
Google Scholar
Blake, D. P. et al. Genetic and biological characterisation of three cryptic Eimeria operational taxonomic units that infect chickens (Gallus gallus domesticus). Int. J. Parasitol. 51, 621–634 (2021).Article
CAS
PubMed
PubMed Central
Google Scholar
Clark, E. L. et al. Cryptic Eimeria genotypes are common across the southern but not northern hemisphere. Int. J. Parasitol. 46, 537–544 (2016).Article
PubMed
PubMed Central
Google Scholar
Tabarés, E. et al. Eimeria tenella sporozoites and merozoites differentially express glycosylphosphatidylinositol-anchored variant surface proteins. Mol. Biochem. Parasitol. 135, 123–132 (2004).Article
PubMed
Google Scholar
Reid, A. J. et al. Genomic analysis of the causative agents of coccidiosis in domestic chickens. Genome Res. 24, 1676–1685 (2014).Article
CAS
PubMed
PubMed Central
Google Scholar
Chow, Y. P., Wan, K. L., Blake, D. P., Tomley, F. & Nathan, S. Immunogenic Eimeria tenella glycosylphosphatidylinositol-anchored surface antigens (SAGs) induce inflammatory responses in avian macrophages. PloS One 6, e25233 (2011).Article
ADS
CAS
PubMed
PubMed Central
Google Scholar
Jahn, D. et al. Model structure of the immunodominant surface antigen of Eimeria tenella identified as a target for sporozoite-neutralizing monoclonal antibody. Parasitol. Res. 105, 655–668 (2009).Article
PubMed
Google Scholar
Ho, S. K., Singh, M., Nathan, S. & Wan, K. L. Immunisation of Eimeria tenella SAG2 recombinant protein protects chickens against the effects of coccidiosis. Sains Malays. 49, 971–978 (2020).Article
CAS
Google Scholar
Arnott, A. et al. Distinct patterns of diversity, population structure and evolution in the AMA1 genes of sympatric Plasmodium falciparum and Plasmodium vivax populations of Papua New Guinea from an area of similarly high transmission. Malar. J. 13, 1–16 (2014).Article
Google Scholar
Takala, S. L. & Plowe, C. V. Genetic diversity and malaria vaccine design, testing and efficacy: preventing and overcoming ‘vaccine resistant malaria’. Parasite Immunol. 31, 560–573 (2009).Article
CAS
PubMed
PubMed Central
Google Scholar
Blake, D. P. et al. Population, genetic, and antigenic diversity of the apicomplexan Eimeria tenella and their relevance to vaccine development. Proc. Natl. Acad. Sci. U.S.A. 112, E5343–E5350 (2015).Article
CAS
PubMed
PubMed Central
Google Scholar
Fitz-Coy, S. H. Antigenic variation among strains of Eimeria maxima and E. tenella of the chicken. Avian Dis. 36, 40–43 (1992).Article
CAS
PubMed
Google Scholar
Abu-Akkada, S. S. & Awad, A. M. Isolation, propagation, identification and comparative pathogenicity of five Egyptian field strains of Eimeria tenella from broiler chickens in five different provinces in Egypt. Res. Vet. Sci. 92, 92–95 (2012).Article
PubMed
Google Scholar
Awad, A. M., El-Nahas, A. F. & Abu-Akkada, S. S. Evaluation of the protective efficacy of the anticoccidial vaccine Coccivac-B in broilers, when challenged with Egyptian field isolates of E. tenella. Parasitol. Res. 112, 113–121 (2013).Article
PubMed
Google Scholar
Tan, L. et al. Genetic diversity and drug sensitivity studies on Eimeria tenella field isolates from Hubei Province of China. Parasit. Vectors. 10, 1–10 (2017).Article
Google Scholar
Võ, T. C. et al. Genetic diversity of microneme protein 2 and surface antigen 1 of Eimeria tenella. Genes. 12, 1418 (2021).Article
PubMed
PubMed Central
Google Scholar
McDougald, L. R. & Jeffers, T. K. Eimeria tenella (sporozoa, coccidia): gametogony following a single asexual generation. Science. 192, 258–259 (1976).Article
ADS
CAS
PubMed
Google Scholar
Loo, S. S., Mohamed, M., Mohd-Taib, F. S., Khoo, C. K. & Wan, K. L. Isolation and establishment of Eimeria tenella populations from local broiler chicken farms. Sains Malays. 51, 1677–1686 (2022).Article
Google Scholar
Loo, S. S., Mohd-Taib, F. S., Khoo, C. K. & Wan, K. L. Characterization of internal transcribed spacer-1 and apical membrane antigen-1 sequences provides insights into the genetic diversity of Eimeria tenella strains. Trop. Biomed. 39, 476–482 (2022).Article
PubMed
Google Scholar
Joshi, N. A. & Fass, J. N. Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files. (GitHub, 2011). https://github.com/najoshi/sickle.Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at arXiv (2013). https://arxiv.org/abs/1303.3997Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience. 10, giab008 (2021).Article
PubMed
PubMed Central
Google Scholar
Li, H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 27, 2987–2993 (2021).Article
Google Scholar
Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 31, 3210–3212 (2015).Article
PubMed
Google Scholar
Slater, G. & Birney, E. Automated generation of heuristics for biological sequence comparison. BMC Bioinform. 6, 31 (2005).Article
Google Scholar
Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly. 6, 80–92 (2012).Article
CAS
PubMed
PubMed Central
Google Scholar
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 841–842 (2010).Article
CAS
PubMed
PubMed Central
Google Scholar
Rozas, J. et al. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol. Biol. Evol. 34, 3299–3302 (2017).Article
CAS
PubMed
Google Scholar
Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30, 2725–2729 (2013).Article
CAS
PubMed
PubMed Central
Google Scholar
Nei, M. & Gojobori, T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3, 418–426 (1986).CAS
PubMed
Google Scholar
Tajima, F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123, 585–595 (1989).Article
CAS
PubMed
PubMed Central
Google Scholar
Fu, Y. X. & Li, W. H. Statistical tests of neutrality of mutations. Genetics. 133, 693–709 (1993).Article
CAS
PubMed
PubMed Central
Google Scholar
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature. 596, 583–589 (2021).Article
ADS
CAS
PubMed
PubMed Central
Google Scholar
Mirdita, M. et al. ColabFold: making protein folding accessible to all. Nat. Methods. 19, 679–682 (2022).Article
CAS
PubMed
PubMed Central
Google Scholar
Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).Article
CAS
PubMed
Google Scholar
Belfield, E. J. et al. DNA mismatch repair preferentially protects genes from mutation. Genome Res. 28, 66–74 (2018).Article
CAS
PubMed
PubMed Central
Google Scholar
Frigola, J. et al. Reduced mutation rate in exons due to differential mismatch repair. Nat. Genet. 49, 1684–1692 (2017).Article
CAS
PubMed
PubMed Central
Google Scholar
Loo, S. S., Blake, D. P., Mohd-Adnan, A., Mohamed, R. & Wan, K. L. Eimeria tenella glucose-6-phosphate isomerase: molecular characterization and assessment as a target for anti-coccidial control. Parasitology. 137, 1169–1177 (2010).Article
CAS
PubMed
Google Scholar
López-Osorio, S., Chaparro-Gutiérrez, J. J. & Gómez-Osorio, L. M. Overview of poultry Eimeria life cycle and host-parasite interactions. Front. Vet. Sci. 7, 384 (2020).Article
PubMed
PubMed Central
Google Scholar
Bondos, S. E., Dunker, A. K. & Uversky, V. N. intrinsically disordered proteins play diverse roles in cell signaling. Cell. Commun. Signal. 20, 20 (2022).Article
CAS
PubMed
PubMed Central
Google Scholar
Hatsuzawa, K., Tagaya, M. & Mizushima, S. The hydrophobic region of signal peptides is a determinant for SRP recognition and protein translocation across the ER membrane. J. Biochem. 121, 270–277 (1997).Article
CAS
PubMed
Google Scholar
He, X. L., Grigg, M. E., Boothroyd, J. C. & Garcia, K. C. Structure of the immunodominant surface antigen from the Toxoplasma gondii SRS superfamily. Nat. Struct. Biol. 9, 606–611 (2002).CAS
PubMed
Google Scholar
Ramly, N. Z. et al. The structure of a major surface antigen SAG19 from Eimeria tenella unifies the Eimeria SAG family. Commun. Biol. 4, 376 (2021).Article
CAS
PubMed
PubMed Central
Google Scholar