Draft genome resources for Chicken Coccidiosis Causal Agents for developing improved control strategies for Avian Coccidosis

Eimeria maxima is considered one of the most important coccidian species because it affects nutrient uptake and predisposes chickens to necrotic enteritis caused by Clostridium perfringens. Differences in the virulence and immunogenicity of E. maxima strains have been observed by researchers. Our laboratory has developed draft genome sequences for a highly virulent strain, namely E. maxima APU1 and a less virulent strain named E. maxima APU2. The genome sequences of these two strains- E. maxima APU1 and APU2 were obtained by long read Oxford Nanopore Technology (ONT). These high-quality reads passed through quality check parameters and assembled into 54.25 Mb with 7693 genes (E. maxima APU1) and 54.78 Mb with 7813 genes (E. maxima APU2) genomes, using hybrid assembly method. The other related Eimeria species (E. acervulina APU1, E. tenella APU2, and E. maxima APU3) are being sequenced followed by downstream analysis i.e., gene annotation, identification on common and unique genic candidates and comparative genomics analyses to understand the biological significance of these predicted genes and their putative roles. The genome sequence and annotations of these genomes of major Eimeria species, including characterizing genetic markers that allow for the development of markers for species identification that could help understand and unravel the basis for pathogenicity of these protozoa.